Preparing figures for publication --PPI vs DPI

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Jay Vyas Jay Vyas
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Preparing figures for publication --PPI vs DPI

Hi all--

We have a spinning disck confocal microscope that uses Metamorph. We are
in the process of preparing figures for a manuscript. We consulted with the
information for authors for the desired journal and was confused to learn that
the images must be 300 DPI (dots per inch). I understand that images are
measured using PPI (pixels per inch) and DPI is not the same as PPI. When I
consulted with the copy editor of the journal, I did not get useful information.
I will assume that they wish to have images at 300 PPI

How do you take images from Metamorph (raw data) and end up with a TIFF
ready for publication?

I propose to do the following
1. Open raw data image in photoshop. It is 672 pixels by 512 pixels.
2. adjust contrast
3. If I open the image information, it reads 72 pixels/inch
4. Crop image to select cell
5. SAve image as tiff file
6. Open adobe illustrator
7. place file in adobe illustrator
8. scale image to final size (this typically reduces the physical dimensions of
the image by 50%)
9. annotate file with arrows and labels as necessary
10. Set raster effect to 300ppi on the print dialog.

I would love input from the group to see if I have done anything here that
would be considered suboptimal (or wrong...).
cromey cromey
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Re: Preparing figures for publication --PPI vs DPI

Jay,

Changing the image resolution from 72dpi (screen) to 300dpi (print) ought to
be about as easy as converting from inches to centimeters.  The Photoshop
image size dialog box is powerful and a bit of landmine.  Which is why I
wrote this handout for our local users:
http://swehsc.pharmacy.arizona.edu/exppath/resources/pdf/Photoshop_Image_Siz
e_dialog_box.pdf  "Potentially the most dangerous dialog box in Adobe
PhotoshopT"

672x512 pixels is approximately 2.25in by 1.7in at 300dpi.

For the purposes of printing bitmapped images 300dpi is pretty much the same
as 300ppi.

I'm not much of an Adobe Illustrator guy, so I'll leave it to others to
comment on.

At the risk of seeming self-promoting, I'd like to pass on this article that
I wrote, which just became available online last week:

Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and
Manipulation of Scientific Digital Images
http://www.springerlink.com/content/00311qw26613m261/?p=499e7ec2a1174fad863e
7b597298edd4&pi=0

Best regards,
Doug

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Douglas W. Cromey, M.S. - Assistant Scientific Investigator
Dept. of Cell Biology & Anatomy, University of Arizona
1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA

office:  AHSC 4212         email: [hidden email]
voice:  520-626-2824       fax:  520-626-2097

http://swehsc.pharmacy.arizona.edu/exppath/
Home of: "Microscopy and Imaging Resources on the WWW"


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Jay Vyas
Sent: Monday, June 28, 2010 1:23 PM
To: [hidden email]
Subject: Preparing figures for publication --PPI vs DPI

Hi all--

We have a spinning disck confocal microscope that uses Metamorph. We are
in the process of preparing figures for a manuscript. We consulted with the
information for authors for the desired journal and was confused to learn
that
the images must be 300 DPI (dots per inch). I understand that images are
measured using PPI (pixels per inch) and DPI is not the same as PPI. When I
consulted with the copy editor of the journal, I did not get useful
information.
I will assume that they wish to have images at 300 PPI

How do you take images from Metamorph (raw data) and end up with a TIFF
ready for publication?

I propose to do the following
1. Open raw data image in photoshop. It is 672 pixels by 512 pixels.
2. adjust contrast
3. If I open the image information, it reads 72 pixels/inch
4. Crop image to select cell
5. SAve image as tiff file
6. Open adobe illustrator
7. place file in adobe illustrator
8. scale image to final size (this typically reduces the physical dimensions
of
the image by 50%)
9. annotate file with arrows and labels as necessary
10. Set raster effect to 300ppi on the print dialog.

I would love input from the group to see if I have done anything here that
would be considered suboptimal (or wrong...).
Daniel James White Daniel James White
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Re: Preparing figures for publication --PPI vs DPI

In reply to this post by Jay Vyas
Dear Jay and list members,

Jay raises a common source of hassle and confusion here:

I really should write a page in the Fiji Wiki with an instructions list.... (watch this space i suppose...)

DO NOT let the publishing houses push their layout and other jobs onto you.
In any case you can hope to get it right, and they will change it anyway.

Microscope digital images come out of the software that drives the microscope,
hopefully with a spatial calibration (also true for metamorph if you calibrate each magnification setting in that software)
Typically confocal images come with probably correct spatial calibration metadata in the .lsm / .oif /.oib / .lif etc file.

So the spatial resolution is set hard by the microscope hardware.
It makes no sense at all to ask for a microscopic image at 300 DPI or PPI
(a 256 x 256 image would be less than an inch wide!!!)
If you are asked for this by a publisher, you can quote me, and even direct them to me,
telling them the following:

It is their job to resize and layout the original images that you provide them.
The original image data is at the number of pixels and spatial resolution set by the hardware.
You can supply them with a single tiff (greyscale or CYMK / RGB as they like - the colours will be messed up in print anyway!!!)

It is then the publishers job to take that full resolution spatially calibrated image
(already including a scale bar made by you!!!)
and resize it and resample it to their print specifications.
I strongly advise that you refuse to do this part of their job for them.
You have very little chance of getting it exactly how they want it anyway,
and by the time you images appear in print or in a PDF then will be likely much resuved in number of pixels,
and also badly lossy compressed and ugly compared to the original.

This is why we need digital storage of original data/images in supplemental online info,
so reviewers and reader have access to the ORIGINAL image data
(I mean the raw unprocessed file that comoes out of the microscope software  .lsm, .oib, .ids/ics .stk .whatever)

more details below.

On Jun 29, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system wrote:

>
> Date:    Mon, 28 Jun 2010 15:22:49 -0500
> From:    Jay Vyas <[hidden email]>
> Subject: Preparing figures for publication --PPI vs DPI
>
> Hi all--
>
> We have a spinning disck confocal microscope that uses Metamorph. We are=20=
>
> in the process of preparing figures for a manuscript. We consulted with t=
> he=20
> information for authors for the desired journal and was confused to learn=
> that=20
> the images must be 300 DPI (dots per inch). I understand that images are=20=
>
> measured using PPI (pixels per inch) and DPI is not the same as PPI. When=
> I=20
> consulted with the copy editor of the journal, I did not get useful infor=
> mation.=20
> I will assume that they wish to have images at 300 PPI

The editors rarely have much idea about this problem,
and are perhaps more used to dealing with photographic images,
that have no intrinsic spatial calibration (unlike our images)

What they are really asking for is that the images do not look pixelated and ugly...

However, if your confocal or CCD images are at a high "zoom" / small region of interest, with 128x128 pixels,
and still at high resolution, ie at the resolution limit of the light microscope (1.4 NA objective) with pixels at 60 or so nm spacing,
then of course the print image will look pixelated if it is printed at the normal column width size!

This is just how it should be and is NOT a problem.
The image should probably not be interpolated (giving false higher resolution)
but yes, it still needs to be "blown up" to a full column or full page width.

More of a problem is when you send in an image with 2048x2048 pixels,
and they print it in half column width. In this case all the resolution you had
is not visible to the reader, as the pixel spacing is then smaller than the 300ish dpi the printer can do.
(another reason to have full resolution / image size images available as supp. info).
What was the point of taking a large high resolution image, when all the reader sees is a postage stamp size version of it?

>
> How do you take images from Metamorph (raw data) and end up with a TIFF=20=
>
> ready for publication?
>
> I propose to do the following

I propose some different steps to get what you need in this case.


> 1. Open raw data image in photoshop. It is 672 pixels by 512 pixels.

Why use photoshop....? Its for making models look pretty... not really designed from the ground up as
a scientific microscopy image processing software.

Fiji / ImageJ is free, and open source (so is not a black box like photoshop... you CAN know what happens when you click something)
and easily does all the thing you need here.

Use the bio-formats importer to read data and get spatial calibration meta data also
In Fiji
-Plugins-LOCI- bio-foromats importer

> 2. adjust contrast

In ImageJ/Fiji
-Image-Adjust-Brightness and Contrast

Be careful if you use a gamma curve (non linear function)
to make the darker areas bright enough to see compared to the bright areas,
as it can give the reader a false impression of the relative intensities.

I strongly suggest to use a colour look up table (as is done in the harder sciences... they laugh at us for showing images in a black to green or worse blue scale that is impossible to see much contrast in)
I like the Fire LUT/palette.
LUT tool in the imageJ main toolbar.
You can than also have a "calibration bar" which is like a scale bar but for intensity.
-Analyze  -Tools - Calibration bar
Now the reader can see what colour is what intensity and much more easily compare the intensity at different places in the image.


> 3. If I open the image information, it reads 72 pixels/inch

which for sure is wrong, as it s a microscope image!!!

in Fiji / imageJ, the
Edit - Image Properties
will show the spatial calibration meta data, if it was read in by bio-formats or other reader.

If its wrong, or not read, you can set it here!

> 4. Crop image to select cell

Fiji/ImageJ
rectangle selection tool, then
Image-Crop

Now add annotations like the scale bar
-Analyze - tools - scale bar
and calibration bar
-Analyze  -Tools - Calibration bar
and arrows, time stamps or whatever....

> 5. SAve image as tiff file

File - Save As - TIFF
(before this you might need to make a multi channel image or monochrome image with a fire look up table into an RBG image type
- Image - Type
)

> 6. Open adobe illustrator

> 7. place file in adobe illustrator
> 8. scale image to final size (this typically reduces the physical dimensi=
> ons of=20
> the image by 50%)

this is NOT your job.
Send them the TIFF file as you want it to be, already containing the scale and calibration bar and other annotations.


> 9. annotate file with arrows and labels as necessary

already done

> 10. Set raster effect to 300ppi on the print dialog.

not your job.

>
> I would love input from the group to see if I have done anything here tha=
> t=20
> would be considered suboptimal (or wrong...).

I think we must make it clear to the publishers that we want an online place to put our original data,
so others can download and analyze it (this is a scientific publication requirement that is often ignored in our field
and that is very very bad!!!

They also need to know that we are not concerned with the layout and image scaling of images,
which is THEIR job during the page layout process.
They are the layout professionals, and they have to do this job.

There is no point in us taking the time to lay out the images in a layout program like illustrator,
when all that happens next is the images are copy pasted out, resized (destructively)
and laid out again in the final page setup  software for printing/pdf output.  
One should simply supply the full TIFF image containing scale bar and calibration bar,
and tell the publishers that the image should be full width or half full page width or whatever other size.

We supply the tiff images containing all the image data,
and they have to publish it in a reasonable way (perhaps following our suggestions)
I wish they would not use lossy compression in the PDF versions, but its a matter of file size....
so the full image should be downloadable separately as supp. info.

The print resolution (DPI / PPI) has nothing to do with us,  it's only their business.

BUT readers should have electronic access to original images and their meta data.

I am happy to continue this discussion online, especially with the publishers!

cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )
JOEL B. SHEFFIELD JOEL B. SHEFFIELD
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Re: Preparing figures for publication --PPI vs DPI

Dan, Doug, Jay, and the rest of the community.

This is an excellent discussion, and Dan's comments are right on.  I would just stress the difference between our data and the printer's needs.  The pixel density in our original data is selected by us as a compromise between the resolution that we need, the storage capacity of our system, and the sensitivity of our capture system.  i.e., if we need to do serious binning to capture a weak signal, we will lose resolution; if we select a pixel density to match the resolution of our lenses, each image may very well have a different density.  The printer's job is to get these different images into a format that can match the constraints of the (antiquated) print medium.  That is 300dpi >>600 pixels for a 2 inch column.  If the width of your original image, in pixels, is greater or less than that number, and if the system takes the images literally, the image will not fit into the two column width. And so, as Dan suggests, the printer has to make adjustments in the image to get it to fit.  There are several ways to make these adjustments, and we need to be aware of them.  In most software, when you rescale an image (that is change the number of pixels), some kind of interpolation is imposed.  Often, when you increase the number, the interpolation smooths the edges of the original pixels.  This is wonderful, if the picture is of your family, but not so good with data, since it actually adds artificial values to the image.  If you are aware of this, you can scale an image without interpolation, at least in some software, but as Dan says, it will make each pixel larger, and the image will be "pixelated". (You will, however, get into an integer problem.  How do you scale from 256 to 300?)   If you give the images to the printer, you can't be sure what procedure they will use. 

The problems with letting the publisher do the work is that we often have a particular layout in mind, and we submit complete "plates" rather than individual images.  This is one way to avoid the kinds of printer errors that we are all familiar with.  In order to comply with the printer's constraints, and get the results that we want, it is probably safest to create our own 300 dpi image that falls within the plate size of the publication.

As one more thought, increasing numbers of journals actually do a very poor job of producing images in print, with the idea that the printed image is a marker for a high resolution version that is online.  I would just ask that the publishers make the the original images available, and not just the pdf conversions of the print versions.



On Tue, Jun 29, 2010 at 8:47 AM, Daniel James White <[hidden email]> wrote:
Dear Jay and list members,

Jay raises a common source of hassle and confusion here:

I really should write a page in the Fiji Wiki with an instructions list.... (watch this space i suppose...)

DO NOT let the publishing houses push their layout and other jobs onto you.
In any case you can hope to get it right, and they will change it anyway.

Microscope digital images come out of the software that drives the microscope,
hopefully with a spatial calibration (also true for metamorph if you calibrate each magnification setting in that software)
Typically confocal images come with probably correct spatial calibration metadata in the .lsm / .oif /.oib / .lif etc file.

So the spatial resolution is set hard by the microscope hardware.
It makes no sense at all to ask for a microscopic image at 300 DPI or PPI
(a 256 x 256 image would be less than an inch wide!!!)
If you are asked for this by a publisher, you can quote me, and even direct them to me,
telling them the following:

It is their job to resize and layout the original images that you provide them.
The original image data is at the number of pixels and spatial resolution set by the hardware.
You can supply them with a single tiff (greyscale or CYMK / RGB as they like - the colours will be messed up in print anyway!!!)

It is then the publishers job to take that full resolution spatially calibrated image
(already including a scale bar made by you!!!)
and resize it and resample it to their print specifications.
I strongly advise that you refuse to do this part of their job for them.
You have very little chance of getting it exactly how they want it anyway,
and by the time you images appear in print or in a PDF then will be likely much resuved in number of pixels,
and also badly lossy compressed and ugly compared to the original.

This is why we need digital storage of original data/images in supplemental online info,
so reviewers and reader have access to the ORIGINAL image data
(I mean the raw unprocessed file that comoes out of the microscope software  .lsm, .oib, .ids/ics .stk .whatever)

more details below.

On Jun 29, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system wrote:

>
> Date:    Mon, 28 Jun 2010 15:22:49 -0500
> From:    Jay Vyas <[hidden email]>
> Subject: Preparing figures for publication --PPI vs DPI
>
> Hi all--
>
> We have a spinning disck confocal microscope that uses Metamorph. We are=20=
>
> in the process of preparing figures for a manuscript. We consulted with t=
> he=20
> information for authors for the desired journal and was confused to learn=
> that=20
> the images must be 300 DPI (dots per inch). I understand that images are=20=
>
> measured using PPI (pixels per inch) and DPI is not the same as PPI. When=
> I=20
> consulted with the copy editor of the journal, I did not get useful infor=
> mation.=20
> I will assume that they wish to have images at 300 PPI

The editors rarely have much idea about this problem,
and are perhaps more used to dealing with photographic images,
that have no intrinsic spatial calibration (unlike our images)

What they are really asking for is that the images do not look pixelated and ugly...

However, if your confocal or CCD images are at a high "zoom" / small region of interest, with 128x128 pixels,
and still at high resolution, ie at the resolution limit of the light microscope (1.4 NA objective) with pixels at 60 or so nm spacing,
then of course the print image will look pixelated if it is printed at the normal column width size!

This is just how it should be and is NOT a problem.
The image should probably not be interpolated (giving false higher resolution)
but yes, it still needs to be "blown up" to a full column or full page width.

More of a problem is when you send in an image with 2048x2048 pixels,
and they print it in half column width. In this case all the resolution you had
is not visible to the reader, as the pixel spacing is then smaller than the 300ish dpi the printer can do.
(another reason to have full resolution / image size images available as supp. info).
What was the point of taking a large high resolution image, when all the reader sees is a postage stamp size version of it?

>
> How do you take images from Metamorph (raw data) and end up with a TIFF=20=
>
> ready for publication?
>
> I propose to do the following

I propose some different steps to get what you need in this case.


> 1. Open raw data image in photoshop. It is 672 pixels by 512 pixels.

Why use photoshop....? Its for making models look pretty... not really designed from the ground up as
a scientific microscopy image processing software.

Fiji / ImageJ is free, and open source (so is not a black box like photoshop... you CAN know what happens when you click something)
and easily does all the thing you need here.

Use the bio-formats importer to read data and get spatial calibration meta data also
In Fiji
-Plugins-LOCI- bio-foromats importer

> 2. adjust contrast

In ImageJ/Fiji
-Image-Adjust-Brightness and Contrast

Be careful if you use a gamma curve (non linear function)
to make the darker areas bright enough to see compared to the bright areas,
as it can give the reader a false impression of the relative intensities.

I strongly suggest to use a colour look up table (as is done in the harder sciences... they laugh at us for showing images in a black to green or worse blue scale that is impossible to see much contrast in)
I like the Fire LUT/palette.
LUT tool in the imageJ main toolbar.
You can than also have a "calibration bar" which is like a scale bar but for intensity.
-Analyze  -Tools - Calibration bar
Now the reader can see what colour is what intensity and much more easily compare the intensity at different places in the image.


> 3. If I open the image information, it reads 72 pixels/inch

which for sure is wrong, as it s a microscope image!!!

in Fiji / imageJ, the
Edit - Image Properties
will show the spatial calibration meta data, if it was read in by bio-formats or other reader.

If its wrong, or not read, you can set it here!

> 4. Crop image to select cell

Fiji/ImageJ
rectangle selection tool, then
Image-Crop

Now add annotations like the scale bar
-Analyze - tools - scale bar
and calibration bar
-Analyze  -Tools - Calibration bar
and arrows, time stamps or whatever....

> 5. SAve image as tiff file

File - Save As - TIFF
(before this you might need to make a multi channel image or monochrome image with a fire look up table into an RBG image type
- Image - Type
)

> 6. Open adobe illustrator

> 7. place file in adobe illustrator
> 8. scale image to final size (this typically reduces the physical dimensi=
> ons of=20
> the image by 50%)

this is NOT your job.
Send them the TIFF file as you want it to be, already containing the scale and calibration bar and other annotations.


> 9. annotate file with arrows and labels as necessary

already done

> 10. Set raster effect to 300ppi on the print dialog.

not your job.

>
> I would love input from the group to see if I have done anything here tha=
> t=20
> would be considered suboptimal (or wrong...).

I think we must make it clear to the publishers that we want an online place to put our original data,
so others can download and analyze it (this is a scientific publication requirement that is often ignored in our field
and that is very very bad!!!

They also need to know that we are not concerned with the layout and image scaling of images,
which is THEIR job during the page layout process.
They are the layout professionals, and they have to do this job.

There is no point in us taking the time to lay out the images in a layout program like illustrator,
when all that happens next is the images are copy pasted out, resized (destructively)
and laid out again in the final page setup  software for printing/pdf output.
One should simply supply the full TIFF image containing scale bar and calibration bar,
and tell the publishers that the image should be full width or half full page width or whatever other size.

We supply the tiff images containing all the image data,
and they have to publish it in a reasonable way (perhaps following our suggestions)
I wish they would not use lossy compression in the PDF versions, but its a matter of file size....
so the full image should be downloadable separately as supp. info.

The print resolution (DPI / PPI) has nothing to do with us,  it's only their business.

BUT readers should have electronic access to original images and their meta data.

I am happy to continue this discussion online, especially with the publishers!

cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net       BioImageXD
http://pacific.mpi-cbg.de               Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk               Dan's Homepages
https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )



--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

Boswell, Carl A - (cboswell) Boswell, Carl A - (cboswell)
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Re: Preparing figures for publication --PPI vs DPI

My view is that the fewer options the publisher (in reality, the printer) have to modify your image, the better.  Given that, I would think that making all the necessary adjustments, using the tips already mentioned, would give you the best chance of having your work appear as planned in your publication.  If it is left up to someone who knows printing but not cell biology, you could be in for a very special surprise. 
 
At the least, insist on a galley proof with the actual pictures that are going into the paper.  That way you can at least be prepared for what will show up in the journal, and maybe you can have them fix the more glaring errors.  Problems with hue and contrast may be irritating but not terminal.  However, if your images have been repeatedly resaved as jpg's, or resampled incorrectly, and the mitochondria look like they are made from Lego's, then something needs to be said.
 
c
 
 
Carl A. Boswell, Ph.D.
Molecular and Cellular Biology
University of Arizona
520-954-7053
FAX 520-621-3709
----- Original Message -----
Sent: Tuesday, June 29, 2010 7:46 AM
Subject: Re: Preparing figures for publication --PPI vs DPI

Dan, Doug, Jay, and the rest of the community.

This is an excellent discussion, and Dan's comments are right on.  I would just stress the difference between our data and the printer's needs.  The pixel density in our original data is selected by us as a compromise between the resolution that we need, the storage capacity of our system, and the sensitivity of our capture system.  i.e., if we need to do serious binning to capture a weak signal, we will lose resolution; if we select a pixel density to match the resolution of our lenses, each image may very well have a different density.  The printer's job is to get these different images into a format that can match the constraints of the (antiquated) print medium.  That is 300dpi >>600 pixels for a 2 inch column.  If the width of your original image, in pixels, is greater or less than that number, and if the system takes the images literally, the image will not fit into the two column width. And so, as Dan suggests, the printer has to make adjustments in the image to get it to fit.  There are several ways to make these adjustments, and we need to be aware of them.  In most software, when you rescale an image (that is change the number of pixels), some kind of interpolation is imposed.  Often, when you increase the number, the interpolation smooths the edges of the original pixels.  This is wonderful, if the picture is of your family, but not so good with data, since it actually adds artificial values to the image.  If you are aware of this, you can scale an image without interpolation, at least in some software, but as Dan says, it will make each pixel larger, and the image will be "pixelated". (You will, however, get into an integer problem.  How do you scale from 256 to 300?)   If you give the images to the printer, you can't be sure what procedure they will use. 

The problems with letting the publisher do the work is that we often have a particular layout in mind, and we submit complete "plates" rather than individual images.  This is one way to avoid the kinds of printer errors that we are all familiar with.  In order to comply with the printer's constraints, and get the results that we want, it is probably safest to create our own 300 dpi image that falls within the plate size of the publication.

As one more thought, increasing numbers of journals actually do a very poor job of producing images in print, with the idea that the printed image is a marker for a high resolution version that is online.  I would just ask that the publishers make the the original images available, and not just the pdf conversions of the print versions.



On Tue, Jun 29, 2010 at 8:47 AM, Daniel James White <[hidden email]> wrote:
Dear Jay and list members,

Jay raises a common source of hassle and confusion here:

I really should write a page in the Fiji Wiki with an instructions list.... (watch this space i suppose...)

DO NOT let the publishing houses push their layout and other jobs onto you.
In any case you can hope to get it right, and they will change it anyway.

Microscope digital images come out of the software that drives the microscope,
hopefully with a spatial calibration (also true for metamorph if you calibrate each magnification setting in that software)
Typically confocal images come with probably correct spatial calibration metadata in the .lsm / .oif /.oib / .lif etc file.

So the spatial resolution is set hard by the microscope hardware.
It makes no sense at all to ask for a microscopic image at 300 DPI or PPI
(a 256 x 256 image would be less than an inch wide!!!)
If you are asked for this by a publisher, you can quote me, and even direct them to me,
telling them the following:

It is their job to resize and layout the original images that you provide them.
The original image data is at the number of pixels and spatial resolution set by the hardware.
You can supply them with a single tiff (greyscale or CYMK / RGB as they like - the colours will be messed up in print anyway!!!)

It is then the publishers job to take that full resolution spatially calibrated image
(already including a scale bar made by you!!!)
and resize it and resample it to their print specifications.
I strongly advise that you refuse to do this part of their job for them.
You have very little chance of getting it exactly how they want it anyway,
and by the time you images appear in print or in a PDF then will be likely much resuved in number of pixels,
and also badly lossy compressed and ugly compared to the original.

This is why we need digital storage of original data/images in supplemental online info,
so reviewers and reader have access to the ORIGINAL image data
(I mean the raw unprocessed file that comoes out of the microscope software  .lsm, .oib, .ids/ics .stk .whatever)

more details below.

On Jun 29, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system wrote:

>
> Date:    Mon, 28 Jun 2010 15:22:49 -0500
> From:    Jay Vyas <[hidden email]>
> Subject: Preparing figures for publication --PPI vs DPI
>
> Hi all--
>
> We have a spinning disck confocal microscope that uses Metamorph. We are=20=
>
> in the process of preparing figures for a manuscript. We consulted with t=
> he=20
> information for authors for the desired journal and was confused to learn=
> that=20
> the images must be 300 DPI (dots per inch). I understand that images are=20=
>
> measured using PPI (pixels per inch) and DPI is not the same as PPI. When=
> I=20
> consulted with the copy editor of the journal, I did not get useful infor=
> mation.=20
> I will assume that they wish to have images at 300 PPI

The editors rarely have much idea about this problem,
and are perhaps more used to dealing with photographic images,
that have no intrinsic spatial calibration (unlike our images)

What they are really asking for is that the images do not look pixelated and ugly...

However, if your confocal or CCD images are at a high "zoom" / small region of interest, with 128x128 pixels,
and still at high resolution, ie at the resolution limit of the light microscope (1.4 NA objective) with pixels at 60 or so nm spacing,
then of course the print image will look pixelated if it is printed at the normal column width size!

This is just how it should be and is NOT a problem.
The image should probably not be interpolated (giving false higher resolution)
but yes, it still needs to be "blown up" to a full column or full page width.

More of a problem is when you send in an image with 2048x2048 pixels,
and they print it in half column width. In this case all the resolution you had
is not visible to the reader, as the pixel spacing is then smaller than the 300ish dpi the printer can do.
(another reason to have full resolution / image size images available as supp. info).
What was the point of taking a large high resolution image, when all the reader sees is a postage stamp size version of it?

>
> How do you take images from Metamorph (raw data) and end up with a TIFF=20=
>
> ready for publication?
>
> I propose to do the following

I propose some different steps to get what you need in this case.


> 1. Open raw data image in photoshop. It is 672 pixels by 512 pixels.

Why use photoshop....? Its for making models look pretty... not really designed from the ground up as
a scientific microscopy image processing software.

Fiji / ImageJ is free, and open source (so is not a black box like photoshop... you CAN know what happens when you click something)
and easily does all the thing you need here.

Use the bio-formats importer to read data and get spatial calibration meta data also
In Fiji
-Plugins-LOCI- bio-foromats importer

> 2. adjust contrast

In ImageJ/Fiji
-Image-Adjust-Brightness and Contrast

Be careful if you use a gamma curve (non linear function)
to make the darker areas bright enough to see compared to the bright areas,
as it can give the reader a false impression of the relative intensities.

I strongly suggest to use a colour look up table (as is done in the harder sciences... they laugh at us for showing images in a black to green or worse blue scale that is impossible to see much contrast in)
I like the Fire LUT/palette.
LUT tool in the imageJ main toolbar.
You can than also have a "calibration bar" which is like a scale bar but for intensity.
-Analyze  -Tools - Calibration bar
Now the reader can see what colour is what intensity and much more easily compare the intensity at different places in the image.


> 3. If I open the image information, it reads 72 pixels/inch

which for sure is wrong, as it s a microscope image!!!

in Fiji / imageJ, the
Edit - Image Properties
will show the spatial calibration meta data, if it was read in by bio-formats or other reader.

If its wrong, or not read, you can set it here!

> 4. Crop image to select cell

Fiji/ImageJ
rectangle selection tool, then
Image-Crop

Now add annotations like the scale bar
-Analyze - tools - scale bar
and calibration bar
-Analyze  -Tools - Calibration bar
and arrows, time stamps or whatever....

> 5. SAve image as tiff file

File - Save As - TIFF
(before this you might need to make a multi channel image or monochrome image with a fire look up table into an RBG image type
- Image - Type
)

> 6. Open adobe illustrator

> 7. place file in adobe illustrator
> 8. scale image to final size (this typically reduces the physical dimensi=
> ons of=20
> the image by 50%)

this is NOT your job.
Send them the TIFF file as you want it to be, already containing the scale and calibration bar and other annotations.


> 9. annotate file with arrows and labels as necessary

already done

> 10. Set raster effect to 300ppi on the print dialog.

not your job.

>
> I would love input from the group to see if I have done anything here tha=
> t=20
> would be considered suboptimal (or wrong...).

I think we must make it clear to the publishers that we want an online place to put our original data,
so others can download and analyze it (this is a scientific publication requirement that is often ignored in our field
and that is very very bad!!!

They also need to know that we are not concerned with the layout and image scaling of images,
which is THEIR job during the page layout process.
They are the layout professionals, and they have to do this job.

There is no point in us taking the time to lay out the images in a layout program like illustrator,
when all that happens next is the images are copy pasted out, resized (destructively)
and laid out again in the final page setup  software for printing/pdf output.
One should simply supply the full TIFF image containing scale bar and calibration bar,
and tell the publishers that the image should be full width or half full page width or whatever other size.

We supply the tiff images containing all the image data,
and they have to publish it in a reasonable way (perhaps following our suggestions)
I wish they would not use lossy compression in the PDF versions, but its a matter of file size....
so the full image should be downloadable separately as supp. info.

The print resolution (DPI / PPI) has nothing to do with us,  it's only their business.

BUT readers should have electronic access to original images and their meta data.

I am happy to continue this discussion online, especially with the publishers!

cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net       BioImageXD
http://pacific.mpi-cbg.de               Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk               Dan's Homepages
https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )



--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

cromey cromey
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Re: Preparing figures for publication --PPI vs DPI

Carl and others,

 

Don’t count on the journals to know what to do.  The typesetting from the paper I cited in my earlier post was outsourced to a far away country, the publishing was being done in an EU country, and the Editor was in the USA.  The first two galleys I saw had major JPEG artifacts in my carefully prepared figures (PDF includes JPEG for the figures).  Fortunately the Editor pushed for the publisher to be less aggressive with my paper (5 large figures) and instead of final PDF of less than 1MB, the paper came out at 4.7MB with no appreciable artifacts.

 

The “art” department at most publishers seems to mostly consist of people who are accustomed to graphic design, not science.  I’m afraid that Daniel’s complaints about being forced to do the publisher’s work are unrealistic, unfortunately we often need to be smarter than the publisher, even if that should not have to be our job.

 

Doug

 

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Douglas W. Cromey, M.S. - Assistant Scientific Investigator

Dept. of Cell Biology & Anatomy, University of Arizona

1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA

 

office:  AHSC 4212         email: [hidden email]

voice:  520-626-2824       fax:  520-626-2097

 

http://swehsc.pharmacy.arizona.edu/exppath/

Home of: "Microscopy and Imaging Resources on the WWW"

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carl Boswell
Sent: Tuesday, June 29, 2010 11:19 AM
To: [hidden email]
Subject: Re: Preparing figures for publication --PPI vs DPI

 

My view is that the fewer options the publisher (in reality, the printer) have to modify your image, the better.  Given that, I would think that making all the necessary adjustments, using the tips already mentioned, would give you the best chance of having your work appear as planned in your publication.  If it is left up to someone who knows printing but not cell biology, you could be in for a very special surprise. 

 

At the least, insist on a galley proof with the actual pictures that are going into the paper.  That way you can at least be prepared for what will show up in the journal, and maybe you can have them fix the more glaring errors.  Problems with hue and contrast may be irritating but not terminal.  However, if your images have been repeatedly resaved as jpg's, or resampled incorrectly, and the mitochondria look like they are made from Lego's, then something needs to be said.

 

c

 

 

Carl A. Boswell, Ph.D.
Molecular and Cellular Biology
University of Arizona
520-954-7053
FAX 520-621-3709

----- Original Message -----

Sent: Tuesday, June 29, 2010 7:46 AM

Subject: Re: Preparing figures for publication --PPI vs DPI

 

Dan, Doug, Jay, and the rest of the community.

This is an excellent discussion, and Dan's comments are right on.  I would just stress the difference between our data and the printer's needs.  The pixel density in our original data is selected by us as a compromise between the resolution that we need, the storage capacity of our system, and the sensitivity of our capture system.  i.e., if we need to do serious binning to capture a weak signal, we will lose resolution; if we select a pixel density to match the resolution of our lenses, each image may very well have a different density.  The printer's job is to get these different images into a format that can match the constraints of the (antiquated) print medium.  That is 300dpi >>600 pixels for a 2 inch column.  If the width of your original image, in pixels, is greater or less than that number, and if the system takes the images literally, the image will not fit into the two column width. And so, as Dan suggests, the printer has to make adjustments in the image to get it to fit.  There are several ways to make these adjustments, and we need to be aware of them.  In most software, when you rescale an image (that is change the number of pixels), some kind of interpolation is imposed.  Often, when you increase the number, the interpolation smooths the edges of the original pixels.  This is wonderful, if the picture is of your family, but not so good with data, since it actually adds artificial values to the image.  If you are aware of this, you can scale an image without interpolation, at least in some software, but as Dan says, it will make each pixel larger, and the image will be "pixelated". (You will, however, get into an integer problem.  How do you scale from 256 to 300?)   If you give the images to the printer, you can't be sure what procedure they will use. 

The problems with letting the publisher do the work is that we often have a particular layout in mind, and we submit complete "plates" rather than individual images.  This is one way to avoid the kinds of printer errors that we are all familiar with.  In order to comply with the printer's constraints, and get the results that we want, it is probably safest to create our own 300 dpi image that falls within the plate size of the publication.

As one more thought, increasing numbers of journals actually do a very poor job of producing images in print, with the idea that the printed image is a marker for a high resolution version that is online.  I would just ask that the publishers make the the original images available, and not just the pdf conversions of the print versions.


On Tue, Jun 29, 2010 at 8:47 AM, Daniel James White <[hidden email]> wrote:

Dear Jay and list members,

Jay raises a common source of hassle and confusion here:

I really should write a page in the Fiji Wiki with an instructions list.... (watch this space i suppose...)

DO NOT let the publishing houses push their layout and other jobs onto you.
In any case you can hope to get it right, and they will change it anyway.

Microscope digital images come out of the software that drives the microscope,
hopefully with a spatial calibration (also true for metamorph if you calibrate each magnification setting in that software)
Typically confocal images come with probably correct spatial calibration metadata in the .lsm / .oif /.oib / .lif etc file.

So the spatial resolution is set hard by the microscope hardware.
It makes no sense at all to ask for a microscopic image at 300 DPI or PPI
(a 256 x 256 image would be less than an inch wide!!!)
If you are asked for this by a publisher, you can quote me, and even direct them to me,
telling them the following:

It is their job to resize and layout the original images that you provide them.
The original image data is at the number of pixels and spatial resolution set by the hardware.
You can supply them with a single tiff (greyscale or CYMK / RGB as they like - the colours will be messed up in print anyway!!!)

It is then the publishers job to take that full resolution spatially calibrated image
(already including a scale bar made by you!!!)
and resize it and resample it to their print specifications.
I strongly advise that you refuse to do this part of their job for them.
You have very little chance of getting it exactly how they want it anyway,
and by the time you images appear in print or in a PDF then will be likely much resuved in number of pixels,
and also badly lossy compressed and ugly compared to the original.

This is why we need digital storage of original data/images in supplemental online info,
so reviewers and reader have access to the ORIGINAL image data
(I mean the raw unprocessed file that comoes out of the microscope software  .lsm, .oib, .ids/ics .stk .whatever)

more details below.

On Jun 29, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system wrote:

>
> Date:    Mon, 28 Jun 2010 15:22:49 -0500
> From:    Jay Vyas <[hidden email]>

> Subject: Preparing figures for publication --PPI vs DPI
>
> Hi all--
>

> We have a spinning disck confocal microscope that uses Metamorph. We are=20=
>
> in the process of preparing figures for a manuscript. We consulted with t=
> he=20

> information for authors for the desired journal and was confused to learn=

> that=20
> the images must be 300 DPI (dots per inch). I understand that images are=20=

>
> measured using PPI (pixels per inch) and DPI is not the same as PPI. When=

> I=20
> consulted with the copy editor of the journal, I did not get useful infor=
> mation.=20

> I will assume that they wish to have images at 300 PPI

The editors rarely have much idea about this problem,
and are perhaps more used to dealing with photographic images,
that have no intrinsic spatial calibration (unlike our images)

What they are really asking for is that the images do not look pixelated and ugly...

However, if your confocal or CCD images are at a high "zoom" / small region of interest, with 128x128 pixels,
and still at high resolution, ie at the resolution limit of the light microscope (1.4 NA objective) with pixels at 60 or so nm spacing,
then of course the print image will look pixelated if it is printed at the normal column width size!

This is just how it should be and is NOT a problem.
The image should probably not be interpolated (giving false higher resolution)
but yes, it still needs to be "blown up" to a full column or full page width.

More of a problem is when you send in an image with 2048x2048 pixels,
and they print it in half column width. In this case all the resolution you had
is not visible to the reader, as the pixel spacing is then smaller than the 300ish dpi the printer can do.
(another reason to have full resolution / image size images available as supp. info).
What was the point of taking a large high resolution image, when all the reader sees is a postage stamp size version of it?

>
> How do you take images from Metamorph (raw data) and end up with a TIFF=20=

>
> ready for publication?
>
> I propose to do the following

I propose some different steps to get what you need in this case.



> 1. Open raw data image in photoshop. It is 672 pixels by 512 pixels.

Why use photoshop....? Its for making models look pretty... not really designed from the ground up as
a scientific microscopy image processing software.

Fiji / ImageJ is free, and open source (so is not a black box like photoshop... you CAN know what happens when you click something)
and easily does all the thing you need here.

Use the bio-formats importer to read data and get spatial calibration meta data also
In Fiji
-Plugins-LOCI- bio-foromats importer

> 2. adjust contrast

In ImageJ/Fiji
-Image-Adjust-Brightness and Contrast

Be careful if you use a gamma curve (non linear function)
to make the darker areas bright enough to see compared to the bright areas,
as it can give the reader a false impression of the relative intensities.

I strongly suggest to use a colour look up table (as is done in the harder sciences... they laugh at us for showing images in a black to green or worse blue scale that is impossible to see much contrast in)
I like the Fire LUT/palette.
LUT tool in the imageJ main toolbar.
You can than also have a "calibration bar" which is like a scale bar but for intensity.
-Analyze  -Tools - Calibration bar
Now the reader can see what colour is what intensity and much more easily compare the intensity at different places in the image.



> 3. If I open the image information, it reads 72 pixels/inch

which for sure is wrong, as it s a microscope image!!!

in Fiji / imageJ, the
Edit - Image Properties
will show the spatial calibration meta data, if it was read in by bio-formats or other reader.

If its wrong, or not read, you can set it here!


> 4. Crop image to select cell

Fiji/ImageJ
rectangle selection tool, then
Image-Crop

Now add annotations like the scale bar
-Analyze - tools - scale bar
and calibration bar
-Analyze  -Tools - Calibration bar
and arrows, time stamps or whatever....


> 5. SAve image as tiff file

File - Save As - TIFF
(before this you might need to make a multi channel image or monochrome image with a fire look up table into an RBG image type
- Image - Type

)

> 6. Open adobe illustrator

> 7. place file in adobe illustrator

> 8. scale image to final size (this typically reduces the physical dimensi=
> ons of=20
> the image by 50%)

this is NOT your job.
Send them the TIFF file as you want it to be, already containing the scale and calibration bar and other annotations.



> 9. annotate file with arrows and labels as necessary

already done


> 10. Set raster effect to 300ppi on the print dialog.

not your job.

>
> I would love input from the group to see if I have done anything here tha=
> t=20

> would be considered suboptimal (or wrong...).

I think we must make it clear to the publishers that we want an online place to put our original data,
so others can download and analyze it (this is a scientific publication requirement that is often ignored in our field
and that is very very bad!!!

They also need to know that we are not concerned with the layout and image scaling of images,
which is THEIR job during the page layout process.
They are the layout professionals, and they have to do this job.

There is no point in us taking the time to lay out the images in a layout program like illustrator,
when all that happens next is the images are copy pasted out, resized (destructively)
and laid out again in the final page setup  software for printing/pdf output.
One should simply supply the full TIFF image containing scale bar and calibration bar,
and tell the publishers that the image should be full width or half full page width or whatever other size.

We supply the tiff images containing all the image data,
and they have to publish it in a reasonable way (perhaps following our suggestions)
I wish they would not use lossy compression in the PDF versions, but its a matter of file size....
so the full image should be downloadable separately as supp. info.

The print resolution (DPI / PPI) has nothing to do with us,  it's only their business.

BUT readers should have electronic access to original images and their meta data.

I am happy to continue this discussion online, especially with the publishers!

cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net       BioImageXD
http://pacific.mpi-cbg.de               Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk               Dan's Homepages
https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )




--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs

Lee, Mariko Lee, Mariko
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Re: Preparing figures for publication --PPI vs DPI

In reply to this post by Boswell, Carl A - (cboswell)

We’ll decide after I talk to Dad.

 

Best Wishes, 

Mariko Lee
Assistant Manager
Light Microscopy & Imaging Facility
City of Hope
1500 E. Duarte Rd.
Duarte, CA  91010
626-256-4673 x62874
mlee @coh.org
http://www.cityofhope.org/research/support/Light-Microscopy-Digital-Imaging/

 


From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carl Boswell
Sent: Tuesday, June 29, 2010 11:19 AM
To: [hidden email]
Subject: Re: Preparing figures for publication --PPI vs DPI

 

My view is that the fewer options the publisher (in reality, the printer) have to modify your image, the better.  Given that, I would think that making all the necessary adjustments, using the tips already mentioned, would give you the best chance of having your work appear as planned in your publication.  If it is left up to someone who knows printing but not cell biology, you could be in for a very special surprise. 

 

At the least, insist on a galley proof with the actual pictures that are going into the paper.  That way you can at least be prepared for what will show up in the journal, and maybe you can have them fix the more glaring errors.  Problems with hue and contrast may be irritating but not terminal.  However, if your images have been repeatedly resaved as jpg's, or resampled incorrectly, and the mitochondria look like they are made from Lego's, then something needs to be said.

 

c

 

 

Carl A. Boswell, Ph.D.
Molecular and Cellular Biology
University of Arizona
520-954-7053
FAX 520-621-3709

----- Original Message -----

Sent: Tuesday, June 29, 2010 7:46 AM

Subject: Re: Preparing figures for publication --PPI vs DPI

 

Dan, Doug, Jay, and the rest of the community.

This is an excellent discussion, and Dan's comments are right on.  I would just stress the difference between our data and the printer's needs.  The pixel density in our original data is selected by us as a compromise between the resolution that we need, the storage capacity of our system, and the sensitivity of our capture system.  i.e., if we need to do serious binning to capture a weak signal, we will lose resolution; if we select a pixel density to match the resolution of our lenses, each image may very well have a different density.  The printer's job is to get these different images into a format that can match the constraints of the (antiquated) print medium.  That is 300dpi >>600 pixels for a 2 inch column.  If the width of your original image, in pixels, is greater or less than that number, and if the system takes the images literally, the image will not fit into the two column width. And so, as Dan suggests, the printer has to make adjustments in the image to get it to fit.  There are several ways to make these adjustments, and we need to be aware of them.  In most software, when you rescale an image (that is change the number of pixels), some kind of interpolation is imposed.  Often, when you increase the number, the interpolation smooths the edges of the original pixels.  This is wonderful, if the picture is of your family, but not so good with data, since it actually adds artificial values to the image.  If you are aware of this, you can scale an image without interpolation, at least in some software, but as Dan says, it will make each pixel larger, and the image will be "pixelated". (You will, however, get into an integer problem.  How do you scale from 256 to 300?)   If you give the images to the printer, you can't be sure what procedure they will use. 

The problems with letting the publisher do the work is that we often have a particular layout in mind, and we submit complete "plates" rather than individual images.  This is one way to avoid the kinds of printer errors that we are all familiar with.  In order to comply with the printer's constraints, and get the results that we want, it is probably safest to create our own 300 dpi image that falls within the plate size of the publication.

As one more thought, increasing numbers of journals actually do a very poor job of producing images in print, with the idea that the printed image is a marker for a high resolution version that is online.  I would just ask that the publishers make the the original images available, and not just the pdf conversions of the print versions.


On Tue, Jun 29, 2010 at 8:47 AM, Daniel James White <[hidden email]> wrote:

Dear Jay and list members,

Jay raises a common source of hassle and confusion here:

I really should write a page in the Fiji Wiki with an instructions list.... (watch this space i suppose...)

DO NOT let the publishing houses push their layout and other jobs onto you.
In any case you can hope to get it right, and they will change it anyway.

Microscope digital images come out of the software that drives the microscope,
hopefully with a spatial calibration (also true for metamorph if you calibrate each magnification setting in that software)
Typically confocal images come with probably correct spatial calibration metadata in the .lsm / .oif /.oib / .lif etc file.

So the spatial resolution is set hard by the microscope hardware.
It makes no sense at all to ask for a microscopic image at 300 DPI or PPI
(a 256 x 256 image would be less than an inch wide!!!)
If you are asked for this by a publisher, you can quote me, and even direct them to me,
telling them the following:

It is their job to resize and layout the original images that you provide them.
The original image data is at the number of pixels and spatial resolution set by the hardware.
You can supply them with a single tiff (greyscale or CYMK / RGB as they like - the colours will be messed up in print anyway!!!)

It is then the publishers job to take that full resolution spatially calibrated image
(already including a scale bar made by you!!!)
and resize it and resample it to their print specifications.
I strongly advise that you refuse to do this part of their job for them.
You have very little chance of getting it exactly how they want it anyway,
and by the time you images appear in print or in a PDF then will be likely much resuved in number of pixels,
and also badly lossy compressed and ugly compared to the original.

This is why we need digital storage of original data/images in supplemental online info,
so reviewers and reader have access to the ORIGINAL image data
(I mean the raw unprocessed file that comoes out of the microscope software  .lsm, .oib, .ids/ics .stk .whatever)

more details below.

On Jun 29, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system wrote:

>
> Date:    Mon, 28 Jun 2010 15:22:49 -0500
> From:    Jay Vyas <[hidden email]>

> Subject: Preparing figures for publication --PPI vs DPI
>
> Hi all--
>

> We have a spinning disck confocal microscope that uses Metamorph. We are=20=
>
> in the process of preparing figures for a manuscript. We consulted with t=
> he=20

> information for authors for the desired journal and was confused to learn=

> that=20
> the images must be 300 DPI (dots per inch). I understand that images are=20=

>
> measured using PPI (pixels per inch) and DPI is not the same as PPI. When=

> I=20
> consulted with the copy editor of the journal, I did not get useful infor=
> mation.=20

> I will assume that they wish to have images at 300 PPI

The editors rarely have much idea about this problem,
and are perhaps more used to dealing with photographic images,
that have no intrinsic spatial calibration (unlike our images)

What they are really asking for is that the images do not look pixelated and ugly...

However, if your confocal or CCD images are at a high "zoom" / small region of interest, with 128x128 pixels,
and still at high resolution, ie at the resolution limit of the light microscope (1.4 NA objective) with pixels at 60 or so nm spacing,
then of course the print image will look pixelated if it is printed at the normal column width size!

This is just how it should be and is NOT a problem.
The image should probably not be interpolated (giving false higher resolution)
but yes, it still needs to be "blown up" to a full column or full page width.

More of a problem is when you send in an image with 2048x2048 pixels,
and they print it in half column width. In this case all the resolution you had
is not visible to the reader, as the pixel spacing is then smaller than the 300ish dpi the printer can do.
(another reason to have full resolution / image size images available as supp. info).
What was the point of taking a large high resolution image, when all the reader sees is a postage stamp size version of it?

>
> How do you take images from Metamorph (raw data) and end up with a TIFF=20=

>
> ready for publication?
>
> I propose to do the following

I propose some different steps to get what you need in this case.



> 1. Open raw data image in photoshop. It is 672 pixels by 512 pixels.

Why use photoshop....? Its for making models look pretty... not really designed from the ground up as
a scientific microscopy image processing software.

Fiji / ImageJ is free, and open source (so is not a black box like photoshop... you CAN know what happens when you click something)
and easily does all the thing you need here.

Use the bio-formats importer to read data and get spatial calibration meta data also
In Fiji
-Plugins-LOCI- bio-foromats importer

> 2. adjust contrast

In ImageJ/Fiji
-Image-Adjust-Brightness and Contrast

Be careful if you use a gamma curve (non linear function)
to make the darker areas bright enough to see compared to the bright areas,
as it can give the reader a false impression of the relative intensities.

I strongly suggest to use a colour look up table (as is done in the harder sciences... they laugh at us for showing images in a black to green or worse blue scale that is impossible to see much contrast in)
I like the Fire LUT/palette.
LUT tool in the imageJ main toolbar.
You can than also have a "calibration bar" which is like a scale bar but for intensity.
-Analyze  -Tools - Calibration bar
Now the reader can see what colour is what intensity and much more easily compare the intensity at different places in the image.



> 3. If I open the image information, it reads 72 pixels/inch

which for sure is wrong, as it s a microscope image!!!

in Fiji / imageJ, the
Edit - Image Properties
will show the spatial calibration meta data, if it was read in by bio-formats or other reader.

If its wrong, or not read, you can set it here!


> 4. Crop image to select cell

Fiji/ImageJ
rectangle selection tool, then
Image-Crop

Now add annotations like the scale bar
-Analyze - tools - scale bar
and calibration bar
-Analyze  -Tools - Calibration bar
and arrows, time stamps or whatever....


> 5. SAve image as tiff file

File - Save As - TIFF
(before this you might need to make a multi channel image or monochrome image with a fire look up table into an RBG image type
- Image - Type

)

> 6. Open adobe illustrator

> 7. place file in adobe illustrator

> 8. scale image to final size (this typically reduces the physical dimensi=
> ons of=20
> the image by 50%)

this is NOT your job.
Send them the TIFF file as you want it to be, already containing the scale and calibration bar and other annotations.



> 9. annotate file with arrows and labels as necessary

already done


> 10. Set raster effect to 300ppi on the print dialog.

not your job.

>
> I would love input from the group to see if I have done anything here tha=
> t=20

> would be considered suboptimal (or wrong...).

I think we must make it clear to the publishers that we want an online place to put our original data,
so others can download and analyze it (this is a scientific publication requirement that is often ignored in our field
and that is very very bad!!!

They also need to know that we are not concerned with the layout and image scaling of images,
which is THEIR job during the page layout process.
They are the layout professionals, and they have to do this job.

There is no point in us taking the time to lay out the images in a layout program like illustrator,
when all that happens next is the images are copy pasted out, resized (destructively)
and laid out again in the final page setup  software for printing/pdf output.
One should simply supply the full TIFF image containing scale bar and calibration bar,
and tell the publishers that the image should be full width or half full page width or whatever other size.

We supply the tiff images containing all the image data,
and they have to publish it in a reasonable way (perhaps following our suggestions)
I wish they would not use lossy compression in the PDF versions, but its a matter of file size....
so the full image should be downloadable separately as supp. info.

The print resolution (DPI / PPI) has nothing to do with us,  it's only their business.

BUT readers should have electronic access to original images and their meta data.

I am happy to continue this discussion online, especially with the publishers!

cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net       BioImageXD
http://pacific.mpi-cbg.de               Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk               Dan's Homepages
https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )




--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs


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Lee, Mariko Lee, Mariko
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|

Re: Preparing figures for publication --PPI vs DPI

Sorry about this everyone.  I clicked the wrong email.

 

Best Wishes, 

Mariko Lee
Assistant Manager
Light Microscopy & Imaging Facility
City of Hope
1500 E. Duarte Rd.
Duarte, CA  91010
626-256-4673 x62874
mlee @coh.org
http://www.cityofhope.org/research/support/Light-Microscopy-Digital-Imaging/

 


From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Lee, Mariko
Sent: Tuesday, June 29, 2010 2:49 PM
To: [hidden email]
Subject: Re: Preparing figures for publication --PPI vs DPI

 

We’ll decide after I talk to Dad.

 

Best Wishes, 

Mariko Lee
Assistant Manager
Light Microscopy & Imaging Facility
City of Hope
1500 E. Duarte Rd.
Duarte, CA  91010
626-256-4673 x62874
mlee @coh.org
http://www.cityofhope.org/research/support/Light-Microscopy-Digital-Imaging/

 


From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Carl Boswell
Sent: Tuesday, June 29, 2010 11:19 AM
To: [hidden email]
Subject: Re: Preparing figures for publication --PPI vs DPI

 

My view is that the fewer options the publisher (in reality, the printer) have to modify your image, the better.  Given that, I would think that making all the necessary adjustments, using the tips already mentioned, would give you the best chance of having your work appear as planned in your publication.  If it is left up to someone who knows printing but not cell biology, you could be in for a very special surprise. 

 

At the least, insist on a galley proof with the actual pictures that are going into the paper.  That way you can at least be prepared for what will show up in the journal, and maybe you can have them fix the more glaring errors.  Problems with hue and contrast may be irritating but not terminal.  However, if your images have been repeatedly resaved as jpg's, or resampled incorrectly, and the mitochondria look like they are made from Lego's, then something needs to be said.

 

c

 

 

Carl A. Boswell, Ph.D.
Molecular and Cellular Biology
University of Arizona
520-954-7053
FAX 520-621-3709

----- Original Message -----

Sent: Tuesday, June 29, 2010 7:46 AM

Subject: Re: Preparing figures for publication --PPI vs DPI

 

Dan, Doug, Jay, and the rest of the community.

This is an excellent discussion, and Dan's comments are right on.  I would just stress the difference between our data and the printer's needs.  The pixel density in our original data is selected by us as a compromise between the resolution that we need, the storage capacity of our system, and the sensitivity of our capture system.  i.e., if we need to do serious binning to capture a weak signal, we will lose resolution; if we select a pixel density to match the resolution of our lenses, each image may very well have a different density.  The printer's job is to get these different images into a format that can match the constraints of the (antiquated) print medium.  That is 300dpi >>600 pixels for a 2 inch column.  If the width of your original image, in pixels, is greater or less than that number, and if the system takes the images literally, the image will not fit into the two column width. And so, as Dan suggests, the printer has to make adjustments in the image to get it to fit.  There are several ways to make these adjustments, and we need to be aware of them.  In most software, when you rescale an image (that is change the number of pixels), some kind of interpolation is imposed.  Often, when you increase the number, the interpolation smooths the edges of the original pixels.  This is wonderful, if the picture is of your family, but not so good with data, since it actually adds artificial values to the image.  If you are aware of this, you can scale an image without interpolation, at least in some software, but as Dan says, it will make each pixel larger, and the image will be "pixelated". (You will, however, get into an integer problem.  How do you scale from 256 to 300?)   If you give the images to the printer, you can't be sure what procedure they will use. 

The problems with letting the publisher do the work is that we often have a particular layout in mind, and we submit complete "plates" rather than individual images.  This is one way to avoid the kinds of printer errors that we are all familiar with.  In order to comply with the printer's constraints, and get the results that we want, it is probably safest to create our own 300 dpi image that falls within the plate size of the publication.

As one more thought, increasing numbers of journals actually do a very poor job of producing images in print, with the idea that the printed image is a marker for a high resolution version that is online.  I would just ask that the publishers make the the original images available, and not just the pdf conversions of the print versions.

On Tue, Jun 29, 2010 at 8:47 AM, Daniel James White <[hidden email]> wrote:

Dear Jay and list members,

Jay raises a common source of hassle and confusion here:

I really should write a page in the Fiji Wiki with an instructions list.... (watch this space i suppose...)

DO NOT let the publishing houses push their layout and other jobs onto you.
In any case you can hope to get it right, and they will change it anyway.

Microscope digital images come out of the software that drives the microscope,
hopefully with a spatial calibration (also true for metamorph if you calibrate each magnification setting in that software)
Typically confocal images come with probably correct spatial calibration metadata in the .lsm / .oif /.oib / .lif etc file.

So the spatial resolution is set hard by the microscope hardware.
It makes no sense at all to ask for a microscopic image at 300 DPI or PPI
(a 256 x 256 image would be less than an inch wide!!!)
If you are asked for this by a publisher, you can quote me, and even direct them to me,
telling them the following:

It is their job to resize and layout the original images that you provide them.
The original image data is at the number of pixels and spatial resolution set by the hardware.
You can supply them with a single tiff (greyscale or CYMK / RGB as they like - the colours will be messed up in print anyway!!!)

It is then the publishers job to take that full resolution spatially calibrated image
(already including a scale bar made by you!!!)
and resize it and resample it to their print specifications.
I strongly advise that you refuse to do this part of their job for them.
You have very little chance of getting it exactly how they want it anyway,
and by the time you images appear in print or in a PDF then will be likely much resuved in number of pixels,
and also badly lossy compressed and ugly compared to the original.

This is why we need digital storage of original data/images in supplemental online info,
so reviewers and reader have access to the ORIGINAL image data
(I mean the raw unprocessed file that comoes out of the microscope software  .lsm, .oib, .ids/ics .stk .whatever)

more details below.

On Jun 29, 2010, at 7:01 AM, CONFOCALMICROSCOPY automatic digest system wrote:

>
> Date:    Mon, 28 Jun 2010 15:22:49 -0500
> From:    Jay Vyas <[hidden email]>

> Subject: Preparing figures for publication --PPI vs DPI
>
> Hi all--
>

> We have a spinning disck confocal microscope that uses Metamorph. We are=20=
>
> in the process of preparing figures for a manuscript. We consulted with t=
> he=20

> information for authors for the desired journal and was confused to learn=

> that=20
> the images must be 300 DPI (dots per inch). I understand that images are=20=

>
> measured using PPI (pixels per inch) and DPI is not the same as PPI. When=

> I=20
> consulted with the copy editor of the journal, I did not get useful infor=
> mation.=20

> I will assume that they wish to have images at 300 PPI

The editors rarely have much idea about this problem,
and are perhaps more used to dealing with photographic images,
that have no intrinsic spatial calibration (unlike our images)

What they are really asking for is that the images do not look pixelated and ugly...

However, if your confocal or CCD images are at a high "zoom" / small region of interest, with 128x128 pixels,
and still at high resolution, ie at the resolution limit of the light microscope (1.4 NA objective) with pixels at 60 or so nm spacing,
then of course the print image will look pixelated if it is printed at the normal column width size!

This is just how it should be and is NOT a problem.
The image should probably not be interpolated (giving false higher resolution)
but yes, it still needs to be "blown up" to a full column or full page width.

More of a problem is when you send in an image with 2048x2048 pixels,
and they print it in half column width. In this case all the resolution you had
is not visible to the reader, as the pixel spacing is then smaller than the 300ish dpi the printer can do.
(another reason to have full resolution / image size images available as supp. info).
What was the point of taking a large high resolution image, when all the reader sees is a postage stamp size version of it?

>
> How do you take images from Metamorph (raw data) and end up with a TIFF=20=

>
> ready for publication?
>
> I propose to do the following

I propose some different steps to get what you need in this case.



> 1. Open raw data image in photoshop. It is 672 pixels by 512 pixels.

Why use photoshop....? Its for making models look pretty... not really designed from the ground up as
a scientific microscopy image processing software.

Fiji / ImageJ is free, and open source (so is not a black box like photoshop... you CAN know what happens when you click something)
and easily does all the thing you need here.

Use the bio-formats importer to read data and get spatial calibration meta data also
In Fiji
-Plugins-LOCI- bio-foromats importer

> 2. adjust contrast

In ImageJ/Fiji
-Image-Adjust-Brightness and Contrast

Be careful if you use a gamma curve (non linear function)
to make the darker areas bright enough to see compared to the bright areas,
as it can give the reader a false impression of the relative intensities.

I strongly suggest to use a colour look up table (as is done in the harder sciences... they laugh at us for showing images in a black to green or worse blue scale that is impossible to see much contrast in)
I like the Fire LUT/palette.
LUT tool in the imageJ main toolbar.
You can than also have a "calibration bar" which is like a scale bar but for intensity.
-Analyze  -Tools - Calibration bar
Now the reader can see what colour is what intensity and much more easily compare the intensity at different places in the image.



> 3. If I open the image information, it reads 72 pixels/inch

which for sure is wrong, as it s a microscope image!!!

in Fiji / imageJ, the
Edit - Image Properties
will show the spatial calibration meta data, if it was read in by bio-formats or other reader.

If its wrong, or not read, you can set it here!


> 4. Crop image to select cell

Fiji/ImageJ
rectangle selection tool, then
Image-Crop

Now add annotations like the scale bar
-Analyze - tools - scale bar
and calibration bar
-Analyze  -Tools - Calibration bar
and arrows, time stamps or whatever....


> 5. SAve image as tiff file

File - Save As - TIFF
(before this you might need to make a multi channel image or monochrome image with a fire look up table into an RBG image type
- Image - Type

)

> 6. Open adobe illustrator

> 7. place file in adobe illustrator

> 8. scale image to final size (this typically reduces the physical dimensi=
> ons of=20
> the image by 50%)

this is NOT your job.
Send them the TIFF file as you want it to be, already containing the scale and calibration bar and other annotations.



> 9. annotate file with arrows and labels as necessary

already done


> 10. Set raster effect to 300ppi on the print dialog.

not your job.

>
> I would love input from the group to see if I have done anything here tha=
> t=20

> would be considered suboptimal (or wrong...).

I think we must make it clear to the publishers that we want an online place to put our original data,
so others can download and analyze it (this is a scientific publication requirement that is often ignored in our field
and that is very very bad!!!

They also need to know that we are not concerned with the layout and image scaling of images,
which is THEIR job during the page layout process.
They are the layout professionals, and they have to do this job.

There is no point in us taking the time to lay out the images in a layout program like illustrator,
when all that happens next is the images are copy pasted out, resized (destructively)
and laid out again in the final page setup  software for printing/pdf output.
One should simply supply the full TIFF image containing scale bar and calibration bar,
and tell the publishers that the image should be full width or half full page width or whatever other size.

We supply the tiff images containing all the image data,
and they have to publish it in a reasonable way (perhaps following our suggestions)
I wish they would not use lossy compression in the PDF versions, but its a matter of file size....
so the full image should be downloadable separately as supp. info.

The print resolution (DPI / PPI) has nothing to do with us,  it's only their business.

BUT readers should have electronic access to original images and their meta data.

I am happy to continue this discussion online, especially with the publishers!

cheers

Dan

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net       BioImageXD
http://pacific.mpi-cbg.de               Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk               Dan's Homepages
https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )




--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs


---------------------------------------------------------------------
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Daniel James White Daniel James White
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Re: Preparing figures for publication --PPI vs DPI

In reply to this post by Jay Vyas
Dear All,

On Jun 30, 2010, at 7:02 AM, CONFOCALMICROSCOPY automatic digest system wrote:

>
> Date:    Tue, 29 Jun 2010 10:46:53 -0400
> From:    "JOEL B. SHEFFIELD" <[hidden email]>
> Subject: Re: Preparing figures for publication --PPI vs DPI
>
>
> The problems with letting the publisher do the work is that we often have a
> particular layout in mind, and we submit complete "plates" rather than
> individual images.  This is one way to avoid the kinds of printer errors
> that we are all familiar with.  In order to comply with the printer's
> constraints, and get the results that we want, it is probably safest to
> create our own 300 dpi image that falls within the plate size of the
> publication.

In principle I agree Joel,
but the problem really lies not really in the print versions,
which are always going to be poor representation of a digital image...

rather in the PDF version, which contain a mashed, lossy compressed,
resampled and generally destroyed version of the image data.

Let us not forget, out microscpes are fanct spectrometers that collect numerical data.
A digital image is not analogue artwork, its just a table of numbers!!!

we would never allow a text table of numbers to have its information destroyed like this
on the way to it being read by a reader/reviewer, so why do we accept it as normal for images?

We meed to change the way publication works, and make sure editors understand that images
are tables of numbers and should be treated as such.
The original non destroyed image data should always be made available over the web.

Chemists and physicists thing cell biology etc are very very soft fluffy disciplines,
and trust very little they read of out work,
exactly for reasons like this.

>
> As one more thought, increasing numbers of journals actually do a very poor
> job of producing images in print, with the idea that the printed image is a
> marker for a high resolution version that is online.  I would just ask that
> the publishers make the the original images available, and not just the pdf
> conversions of the print versions.

Hear Hear!!!


> On Behalf Of Carl Boswell
> Sent: Tuesday, June 29, 2010 11:19 AM
> To: [hidden email]
> Subject: Re: Preparing figures for publication --PPI vs DPI
>
> =20
>
> My view is that the fewer options the publisher (in reality, the
> printer) have to modify your image, the better.  Given that, I would
> think that making all the necessary adjustments, using the tips already
> mentioned, would give you the best chance of having your work appear as
> planned in your publication.  If it is left up to someone who knows
> printing but not cell biology, you could be in for a very special
> surprise. =20

sure, it sounds like a good plan, but in the end the image is always destroyed at the final stage - the printer,
which imposes its very limited capabilities on any image.
We can try to make sureimages look nice, but this really is only art.

What a reader really needs is access to the full resolution original image to open in ImageJ/Fiji etc.

>
> =20
>
> At the least, insist on a galley proof with the actual pictures that are
> going into the paper.  That way you can at least be prepared for what
> will show up in the journal, and maybe you can have them fix the more
> glaring errors.  Problems with hue and contrast may be irritating but
> not terminal.  However, if your images have been repeatedly resaved as
> jpg's, or resampled incorrectly, and the mitochondria look like they are
> made from Lego's, then something needs to be said.

I agree ver strongly. We must to accept badly destroyed images , even in print.
Lobby your editor until you get what is right.


>

> Date:    Tue, 29 Jun 2010 14:45:58 -0700
> From:    Doug Cromey <[hidden email]>
> Subject: Re: Preparing figures for publication --PPI vs DPI
>
> Carl and others,
>
> Don't count on the journals to know what to do.  The typesetting from the
> paper I cited in my earlier post was outsourced to a far away country, the
> publishing was being done in an EU country, and the Editor was in the USA.
> The first two galleys I saw had major JPEG artifacts in my carefully
> prepared figures (PDF includes JPEG for the figures).  Fortunately the
> Editor pushed for the publisher to be less aggressive with my paper (5 large
> figures) and instead of final PDF of less than 1MB, the paper came out at
> 4.7MB with no appreciable artifacts.

but the images are still not really good enough for someone to take and re do your image analysis,
or make their own new measurements from .

this is a basic requirement of scientific publication,
and is harly ever me in our discipline,
and this is very wrong.
Physicists laugh at us... and biochemists.

there is no technical reason that raw data can not be made available on line
even big screens,
its just missing infrastructure that needs to be put in place.

Where is our biological image equivalent of the  PDB database, the GENBANK database,
all the other databases other disciplines have.
Where is ours? We need to get that funded and organised through eg Euro-Bioimaging project.
http://www.eurobioimaging.eu/
and an USA / asia pacific equivlaent
>
>
>
> The "art" department at most publishers seems to mostly consist of people
> who are accustomed to graphic design, not science.  I'm afraid that Daniel's
> complaints about being forced to do the publisher's work are unrealistic,
> unfortunately we often need to be smarter than the publisher, even if that
> should not have to be our job.

Or we need to force our publishers to get smart about the kind of images we give them.
and how to treat them.

I would suggest we be proactive here, rather than defeatist.
No matter how hard we try to make a well formatted plate for the publisher,
it will most likely still be mashed by the time the pdf arrived on a readers screen.

We need to educate the publishing system of our needs.
I suggest using the argument that our images are 2D/3xD tables of spectroscopic measurement NUMBERS,
and should be treated as such, not as photos - which they are NOT.


cheers

Dan

>
>
>
> Doug
>
>
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>
> Douglas W. Cromey, M.S. - Assistant Scientific Investigator
>
> Dept. of Cell Biology & Anatomy, University of Arizona
>
> 1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA
>
>
>
> office:  AHSC 4212         email: [hidden email]
>
> voice:  520-626-2824       fax:  520-626-2097
>
>
>
> http://swehsc.pharmacy.arizona.edu/exppath/
>
> Home of: "Microscopy and Imaging Resources on the WWW"


Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49 (0)351 210 2627 (Work phone at MPI-CBG)
+49 (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )
Eric Scarfone Eric Scarfone
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Re: Preparing figures for publication --PPI vs DPI

Hej List!
I fully endorse Daniel's points in this thread. The imaging community must work towards an "ImageBank" where the original data from all published scientific image would be accessible.


It happens more than once that published images are so degraded that it becomes impossible to assess the author’s claims. Maybe the referees have had access to the data supporting the claims but the readers often do not. We are not anymore at the analog time when only referees could aces the original prints made by authors (which by the way was not that perfect-a-time since the original data, -the negatives- were not at all accessible!). Indeed the advent of the digital age makes it possible to look with the same ccd eye into someone else’s microscope.

This is important for the respect of the reproducibility requirement.
This is also fundamental for the tracing of image modifications made by authors. Here this thread joins another discussion that was vivid sometimes on the list about what is allowed and not to improve images.

A problem remains though; it is that original data really must be “original” (meaning “un-tampered with”!)

Cheers
Eric



Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,
Cell: +46 (0)70 888 2352
Fax: +46 (0)8-301876

email: [hidden email]
http://www.ki.se/cfh/


----- Original Message -----
From: Daniel James White <[hidden email]>
Date: Wednesday, June 30, 2010 10:34 am
Subject: Re: Preparing figures for publication --PPI vs DPI
To: [hidden email]

> Dear All,
>
> On Jun 30, 2010, at 7:02 AM, CONFOCALMICROSCOPY automatic digest
> system wrote:
>
> >
> > Date: Tue, 29 Jun 2010 10:46:53 -0400
> > From: "JOEL B. SHEFFIELD" <[hidden email]>

> > Subject: Re: Preparing figures for publication --PPI vs DPI
> >
> >
> > The problems with letting the publisher do the work is that we
> often have a
> > particular layout in mind, and we submit complete "plates"
> rather than
> > individual images. This is one way to avoid the kinds of
> printer errors
> > that we are all familiar with. In order to comply with the
> printer's> constraints, and get the results that we want, it is
> probably safest to
> > create our own 300 dpi image that falls within the plate size of the
> > publication.
>
> In principle I agree Joel,
> but the problem really lies not really in the print versions,
> which are always going to be poor representation of a digital image...
>
> rather in the PDF version, which contain a mashed, lossy

> compressed,
> resampled and generally destroyed version of the image data.
>
> Let us not forget, out microscpes are fanct spectrometers that
> collect numerical data.
> A digital image is not analogue artwork, its just a table of
> numbers!!!
> we would never allow a text table of numbers to have its
> information destroyed like this
> on the way to it being read by a reader/reviewer, so why do we
> accept it as normal for images?
>
> We meed to change the way publication works, and make sure editors
> understand that images
> are tables of numbers and should be treated as such.
> The original non destroyed image data should always be made
> available over the web.
>
> Chemists and physicists thing cell biology etc are very very soft
> fluffy disciplines,
> and trust very little they read of out work,

> exactly for reasons like this.
>
> >
> > As one more thought, increasing numbers of journals actually do
> a very poor
> > job of producing images in print, with the idea that the printed
> image is a
> > marker for a high resolution version that is online. I would
> just ask that
> > the publishers make the the original images available, and not
> just the pdf
> > conversions of the print versions.
>
> Hear Hear!!!
>
>
> > On Behalf Of Carl Boswell
> > Sent: Tuesday, June 29, 2010 11:19 AM
> > To: [hidden email]
> > Subject: Re: Preparing figures for publication --PPI vs DPI
> >
> > =20
> >
> > My view is that the fewer options the publisher (in reality, the
> > printer) have to modify your image, the better. Given that, I would

> > think that making all the necessary adjustments, using the tips
> already> mentioned, would give you the best chance of having your
> work appear as
> > planned in your publication. If it is left up to someone who knows
> > printing but not cell biology, you could be in for a very special
> > surprise. =20
>
> sure, it sounds like a good plan, but in the end the image is
> always destroyed at the final stage - the printer,
> which imposes its very limited capabilities on any image.
> We can try to make sureimages look nice, but this really is only art.
>
> What a reader really needs is access to the full resolution
> original image to open in ImageJ/Fiji etc.
>
> >
> > =20
> >
> > At the least, insist on a galley proof with the actual pictures

> that are
> > going into the paper. That way you can at least be prepared for
> what> will show up in the journal, and maybe you can have them fix
> the more
> > glaring errors. Problems with hue and contrast may be
> irritating but
> > not terminal. However, if your images have been repeatedly
> resaved as
> > jpg's, or resampled incorrectly, and the mitochondria look like
> they are
> > made from Lego's, then something needs to be said.
>
> I agree ver strongly. We must to accept badly destroyed images ,
> even in print.
> Lobby your editor until you get what is right.
>
>
> >
>
> > Date: Tue, 29 Jun 2010 14:45:58 -0700
> > From: Doug Cromey <[hidden email]>
> > Subject: Re: Preparing figures for publication --PPI vs DPI

> >
> > Carl and others,
> >
> > Don't count on the journals to know what to do. The typesetting
> from the
> > paper I cited in my earlier post was outsourced to a far away
> country, the
> > publishing was being done in an EU country, and the Editor was
> in the USA.
> > The first two galleys I saw had major JPEG artifacts in my carefully
> > prepared figures (PDF includes JPEG for the figures).
> Fortunately the
> > Editor pushed for the publisher to be less aggressive with my
> paper (5 large
> > figures) and instead of final PDF of less than 1MB, the paper
> came out at
> > 4.7MB with no appreciable artifacts.
>
> but the images are still not really good enough for someone to
> take and re do your image analysis,
> or make their own new measurements from .

>
> this is a basic requirement of scientific publication,
> and is harly ever me in our discipline,
> and this is very wrong.
> Physicists laugh at us... and biochemists.
>
> there is no technical reason that raw data can not be made
> available on line
> even big screens,
> its just missing infrastructure that needs to be put in place.
>
> Where is our biological image equivalent of the PDB database, the
> GENBANK database,
> all the other databases other disciplines have.
> Where is ours? We need to get that funded and organised through eg
> Euro-Bioimaging project.
> http://www.eurobioimaging.eu/
> and an USA / asia pacific equivlaent
> >
> >
> >
> > The "art" department at most publishers seems to mostly consist
> of people
> > who are accustomed to graphic design, not science. I'm afraid

> that Daniel's
> > complaints about being forced to do the publisher's work are
> unrealistic,> unfortunately we often need to be smarter than the
> publisher, even if that
> > should not have to be our job.
>
> Or we need to force our publishers to get smart about the kind of
> images we give them.
> and how to treat them.
>
> I would suggest we be proactive here, rather than defeatist.
> No matter how hard we try to make a well formatted plate for the
> publisher,
> it will most likely still be mashed by the time the pdf arrived on
> a readers screen.
>
> We need to educate the publishing system of our needs.
> I suggest using the argument that our images are 2D/3xD tables of
> spectroscopic measurement NUMBERS,
> and should be treated as such, not as photos - which they are NOT.

>
>
> cheers
>
> Dan
>
> >
> >
> >
> > Doug
> >
> >
> >
> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> >
> > Douglas W. Cromey, M.S. - Assistant Scientific Investigator
> >
> > Dept. of Cell Biology & Anatomy, University of Arizona
> >
> > 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA
> >
> >
> >
> > office: AHSC 4212 email: [hidden email]
> >
> > voice: 520-626-2824 fax: 520-626-2097
> >
> >
> >
> > http://swehsc.pharmacy.arizona.edu/exppath/
> >
> > Home of: "Microscopy and Imaging Resources on the WWW"
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis

> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> +49 (0)15114966933 (German Mobile)
> +49 (0)351 210 2627 (Work phone at MPI-CBG)
> +49 (0)351 210 1078 (Fax MPI-CBG LMF)
>
> http://www.bioimagexd.net BioImageXD
> http://pacific.mpi-cbg.de Fiji - is just ImageJ
> (Batteries Included)
> http://www.chalkie.org.uk Dan's Homepages
> https://ifn.mpi-cbg.de Dresden Imaging Facility
> Networkdan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
>
Eric Scarfone Eric Scarfone
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|

Axiovision: Panorama and Multidimensional acquisition

Hi List.
This is not a confocal question but I do not know where to find a better goup of imaging experts!
We are trying to make mosaic images using the "Panorama" feature of Zeiss Axiovision software (our mic does not have a motorized stage so this is manual). It works well, but I would like each frame of the mosaic to be a multidimensional image (ie multiple fluorescence).
And I could not find a way to do that!
Any ideas?
Cheers

Eric


Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,
Cell: +46 (0)70 888 2352
Fax: +46 (0)8-301876

email: [hidden email]
http://www.ki.se/cfh/


----- Original Message -----
From: Eric Scarfone <[hidden email]>
Date: Wednesday, June 30, 2010 1:24 pm
Subject: Re: Preparing figures for publication --PPI vs DPI
To: [hidden email]

> Hej List!
> I fully endorse Daniel's points in this thread. The imaging
> community must work towards an "ImageBank" where the original data
> from all published scientific image would be accessible.
>
> It happens more than once that published images are so degraded
> that it becomes impossible to assess the author’s claims. Maybe


> the referees have had access to the data supporting the claims but
> the readers often do not. We are not anymore at the analog time
> when only referees could aces the original prints made by authors
> (which by the way was not that perfect-a-time since the original
> data, -the negatives- were not at all accessible!). Indeed the
> advent of the digital age makes it possible to look with the same
> ccd eye into someone else’s microscope.
> This is important for the respect of the reproducibility
> requirement.
> This is also fundamental for the tracing of image modifications
> made by authors. Here this thread joins another discussion that
> was vivid sometimes on the list about what is allowed and not to
> improve images.
> A problem remains though; it is that original data really must be
> “original” (meaning “un-tampered with”!)

> Cheers
> Eric
>
>
> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet
>
> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden
>
> Work: +46 (0)8-517 79343,
> Cell: +46 (0)70 888 2352
> Fax: +46 (0)8-301876
>
> email: [hidden email]
> http://www.ki.se/cfh/
>
>
> ----- Original Message -----
> From: Daniel James White <[hidden email]>
> Date: Wednesday, June 30, 2010 10:34 am
> Subject: Re: Preparing figures for publication --PPI vs DPI
> To: [hidden email]
>
> > Dear All,
> >
> > On Jun 30, 2010, at 7:02 AM, CONFOCALMICROSCOPY automatic digest
> > system wrote:

> >
> > >
> > > Date: Tue, 29 Jun 2010 10:46:53 -0400
> > > From: "JOEL B. SHEFFIELD" <[hidden email]>
> > > Subject: Re: Preparing figures for publication --PPI vs DPI
> > >
> > >
> > > The problems with letting the publisher do the work is that we
> > often have a
> > > particular layout in mind, and we submit complete "plates"
> > rather than
> > > individual images. This is one way to avoid the kinds of
> > printer errors
> > > that we are all familiar with. In order to comply with the
> > printer's> constraints, and get the results that we want, it is
> > probably safest to
> > > create our own 300 dpi image that falls within the plate size
> of the
> > > publication.
> >
> > In principle I agree Joel,

> > but the problem really lies not really in the print versions,
> > which are always going to be poor representation of a digital
> image...
> >
> > rather in the PDF version, which contain a mashed, lossy
> > compressed,
> > resampled and generally destroyed version of the image data.
> >
> > Let us not forget, out microscpes are fanct spectrometers that
> > collect numerical data.
> > A digital image is not analogue artwork, its just a table of
> > numbers!!!
> > we would never allow a text table of numbers to have its
> > information destroyed like this
> > on the way to it being read by a reader/reviewer, so why do we
> > accept it as normal for images?
> >
> > We meed to change the way publication works, and make sure
> editors
> > understand that images

> > are tables of numbers and should be treated as such.
> > The original non destroyed image data should always be made
> > available over the web.
> >
> > Chemists and physicists thing cell biology etc are very very
> soft
> > fluffy disciplines,
> > and trust very little they read of out work,
> > exactly for reasons like this.
> >
> > >
> > > As one more thought, increasing numbers of journals actually
> do
> > a very poor
> > > job of producing images in print, with the idea that the
> printed
> > image is a
> > > marker for a high resolution version that is online. I would
> > just ask that
> > > the publishers make the the original images available, and not
> > just the pdf
> > > conversions of the print versions.

> >
> > Hear Hear!!!
> >
> >
> > > On Behalf Of Carl Boswell
> > > Sent: Tuesday, June 29, 2010 11:19 AM
> > > To: [hidden email]
> > > Subject: Re: Preparing figures for publication --PPI vs DPI
> > >
> > > =20
> > >
> > > My view is that the fewer options the publisher (in reality,
> the
> > > printer) have to modify your image, the better. Given that, I
> would
> > > think that making all the necessary adjustments, using the
> tips
> > already> mentioned, would give you the best chance of having
> your
> > work appear as
> > > planned in your publication. If it is left up to someone who
> knows
> > > printing but not cell biology, you could be in for a very

> special
> > > surprise. =20
> >
> > sure, it sounds like a good plan, but in the end the image is
> > always destroyed at the final stage - the printer,
> > which imposes its very limited capabilities on any image.
> > We can try to make sureimages look nice, but this really is only
> art.
> >
> > What a reader really needs is access to the full resolution
> > original image to open in ImageJ/Fiji etc.
> >
> > >
> > > =20
> > >
> > > At the least, insist on a galley proof with the actual
> pictures
> > that are
> > > going into the paper. That way you can at least be prepared
> for
> > what> will show up in the journal, and maybe you can have them
> fix
> > the more
> > > glaring errors. Problems with hue and contrast may be

> > irritating but
> > > not terminal. However, if your images have been repeatedly
> > resaved as
> > > jpg's, or resampled incorrectly, and the mitochondria look
> like
> > they are
> > > made from Lego's, then something needs to be said.
> >
> > I agree ver strongly. We must to accept badly destroyed images ,
> > even in print.
> > Lobby your editor until you get what is right.
> >
> >
> > >
> >
> > > Date: Tue, 29 Jun 2010 14:45:58 -0700
> > > From: Doug Cromey <[hidden email]>
> > > Subject: Re: Preparing figures for publication --PPI vs DPI
> > >
> > > Carl and others,
> > >
> > > Don't count on the journals to know what to do. The
> typesetting

> > from the
> > > paper I cited in my earlier post was outsourced to a far away
> > country, the
> > > publishing was being done in an EU country, and the Editor was
> > in the USA.
> > > The first two galleys I saw had major JPEG artifacts in my
> carefully
> > > prepared figures (PDF includes JPEG for the figures).
> > Fortunately the
> > > Editor pushed for the publisher to be less aggressive with my
> > paper (5 large
> > > figures) and instead of final PDF of less than 1MB, the paper
> > came out at
> > > 4.7MB with no appreciable artifacts.
> >
> > but the images are still not really good enough for someone to
> > take and re do your image analysis,
> > or make their own new measurements from .
> >
> > this is a basic requirement of scientific publication,

> > and is harly ever me in our discipline,
> > and this is very wrong.
> > Physicists laugh at us... and biochemists.
> >
> > there is no technical reason that raw data can not be made
> > available on line
> > even big screens,
> > its just missing infrastructure that needs to be put in place.
> >
> > Where is our biological image equivalent of the PDB database,
> the
> > GENBANK database,
> > all the other databases other disciplines have.
> > Where is ours? We need to get that funded and organised through
> eg
> > Euro-Bioimaging project.
> > http://www.eurobioimaging.eu/
> > and an USA / asia pacific equivlaent
> > >
> > >
> > >
> > > The "art" department at most publishers seems to mostly

> consist
> > of people
> > > who are accustomed to graphic design, not science. I'm afraid
> > that Daniel's
> > > complaints about being forced to do the publisher's work are
> > unrealistic,> unfortunately we often need to be smarter than the
> > publisher, even if that
> > > should not have to be our job.
> >
> > Or we need to force our publishers to get smart about the kind
> of
> > images we give them.
> > and how to treat them.
> >
> > I would suggest we be proactive here, rather than defeatist.
> > No matter how hard we try to make a well formatted plate for the
> > publisher,
> > it will most likely still be mashed by the time the pdf arrived
> on
> > a readers screen.
> >
> > We need to educate the publishing system of our needs.

> > I suggest using the argument that our images are 2D/3xD tables
> of
> > spectroscopic measurement NUMBERS,
> > and should be treated as such, not as photos - which they are
> NOT.
> >
> >
> > cheers
> >
> > Dan
> >
> > >
> > >
> > >
> > > Doug
> > >
> > >
> > >
> > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> > >
> > > Douglas W. Cromey, M.S. - Assistant Scientific Investigator
> > >
> > > Dept. of Cell Biology & Anatomy, University of Arizona
> > >
> > > 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA
> > >
> > >
> > >
> > > office: AHSC 4212 email: [hidden email]

> > >
> > > voice: 520-626-2824 fax: 520-626-2097
> > >
> > >
> > >
> > > http://swehsc.pharmacy.arizona.edu/exppath/
> > >
> > > Home of: "Microscopy and Imaging Resources on the WWW"
> >
> >
> > Dr. Daniel James White BSc. (Hons.) PhD
> > Senior Microscopist / Image Visualisation, Processing and
> Analysis
> > Light Microscopy and Image Processing Facilities
> > Max Planck Institute of Molecular Cell Biology and Genetics
> > Pfotenhauerstrasse 108
> > 01307 DRESDEN
> > Germany
> >
> > +49 (0)15114966933 (German Mobile)
> > +49 (0)351 210 2627 (Work phone at MPI-CBG)
> > +49 (0)351 210 1078 (Fax MPI-CBG LMF)
> >
> > http://www.bioimagexd.net BioImageXD
> > http://pacific.mpi-cbg.de Fiji - is just ImageJ
> > (Batteries Included)
> > http://www.chalkie.org.uk Dan's Homepages
> > https://ifn.mpi-cbg.de Dresden Imaging Facility
> > Networkdan (at) chalkie.org.uk
> > ( white (at) mpi-cbg.de )
> >
>

Christoph Ruediger Bauer Christoph Ruediger Bauer
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|

Re: Axiovision: Panorama and Multidimensional acquisition

Hi Eric,

you might try out ImageJ as there are multiple Plugins for stitching
(2D, 3D, stitching from dirctory etc).
Chris

On 30-Jun-10 13:46, Eric Scarfone wrote:

>
> Hi List.
> This is not a confocal question but I do not know where to find a
> better goup of imaging experts!
> We are trying to make mosaic images using the "Panorama" feature
> of Zeiss Axiovision software (our mic does not have a motorized stage
> so this is manual). It works well, but I would like each frame of the
> mosaic to be a multidimensional image (ie multiple fluorescence).
> And I could not find a way to do that!
> Any ideas?
> Cheers
>
> Eric
>
>
> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet
>
> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden
>
> Work: +46 (0)8-517 79343,
> Cell: +46 (0)70 888 2352
> Fax: +46 (0)8-301876
>
> email: [hidden email]
> http://www.ki.se/cfh/
>
>
> -----
>

--
BIOIMAGING PLATFORM
University of Geneva - Science II
Room 245
30, Quai Ernest Ansermet
CH – 1211 Genève 4

Dr. Christoph Bauer
Tel.: + 41 22 3796743
Fax: + 41 22 3796868
email: [hidden email]
website: http://bioimaging.frontiers-in-genetics.org
Guy Cox-2 Guy Cox-2
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|

Re: Preparing figures for publication --PPI vs DPI

In reply to this post by Eric Scarfone

There are a whole lot of points here.  In the days of silver bromide prints there was really no possibility of access to any meaningful ‘original data’.  Even if you got hold of the negatives there was no way of telling the exposure and development conditions, and hence the final gamma.   The digital world gives us much more control, but also much more traceablility.

 

Sadly (and I speak as a journal editor) publishers (with absolutely NO exceptions) do not understand the world of scientific digital imaging.  Images in a journal are typically printed with a 133 dpi screen (150 or better if it is a high-class image-focussed journal).  Now Nyquist applies here as everywhere and that means that they should give 2.3 dots to every pixel of your original image.  So a 512x512 confocal image should appear ~9 inches wide.   This will not happen.  They want 300 dpi to give them a margin of error.  Therefore the only way to get a satisfactory reproduction of your digital image is to resample to that resolution.  The algorithm you use for resampling is important (see my chapter in the legendary Pawley Handbook of Confocal Microscopy) but most high-end image software will do the right thing.  There is absolutely nothing wrong in doing this – it is no different to choosing the magnification on an enlarger – but in an ideal world it should not be necessary.

 

However, I really do advise against importing your images into vector graphics programs such as Adobe Illustrator or Corel Draw unless they are going to be part of a really complex final graphic.  Once your image is in that sort of software you have lost control of it.  Bitmap software such as Photoshop or Paintshop Pro is quite capable of doing routine annotations – in vector or bitmap form – without modifying your base image.

 

                                                                                                    Guy

 

Optical Imaging Techniques in Cell Biology

by Guy Cox    CRC Press / Taylor & Francis

     http://www.guycox.com/optical.htm

______________________________________________

Associate Professor Guy Cox, MA, DPhil(Oxon)

Australian Centre for Microscopy & Microanalysis,

Madsen Building F09, University of Sydney, NSW 2006

 

Phone +61 2 9351 3176     Fax +61 2 9351 7682

             Mobile 0413 281 861

______________________________________________

      http://www.guycox.net

 

 

From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Eric Scarfone
Sent: Wednesday, 30 June 2010 9:24 PM
To: [hidden email]
Subject: Re: Preparing figures for publication --PPI vs DPI

 

Hej List!
I fully endorse Daniel's points in this thread. The imaging community must work towards an "ImageBank" where the original data from all published scientific image would be accessible.


It happens more than once that published images are so degraded that it becomes impossible to assess the author’s claims. Maybe the referees have had access to the data supporting the claims but the readers often do not. We are not anymore at the analog time when only referees could aces the original prints made by authors (which by the way was not that perfect-a-time since the original data, -the negatives- were not at all accessible!). Indeed the advent of the digital age makes it possible to look with the same ccd eye into someone else’s microscope.

This is important for the respect of the reproducibility requirement.
This is also fundamental for the tracing of image modifications made by authors. Here this thread joins another discussion that was vivid sometimes on the list about what is allowed and not to improve images.

A problem remains though; it is that original data really must be “original” (meaning “un-tampered with”!)

Cheers
Eric



Eric Scarfone, PhD, CNRS,
Center for Hearing and communication Research
Department of Clinical Neuroscience
Karolinska Institutet

Postal Address:
CFH, M1:02
Karolinska Hospital,
SE-171 76 Stockholm, Sweden

Work: +46 (0)8-517 79343,
Cell: +46 (0)70 888 2352
Fax: +46 (0)8-301876

email: [hidden email]
http://www.ki.se/cfh/


----- Original Message -----
From: Daniel James White <[hidden email]>
Date: Wednesday, June 30, 2010 10:34 am
Subject: Re: Preparing figures for publication --PPI vs DPI
To: [hidden email]

> Dear All,
>
> On Jun 30, 2010, at 7:02 AM, CONFOCALMICROSCOPY automatic digest
> system wrote:
>
> >
> > Date: Tue, 29 Jun 2010 10:46:53 -0400
> > From: "JOEL B. SHEFFIELD" <[hidden email]>
> > Subject: Re: Preparing figures for publication --PPI vs DPI
> >
> >
> > The problems with letting the publisher do the work is that we
> often have a
> > particular layout in mind, and we submit complete "plates"
> rather than
> > individual images. This is one way to avoid the kinds of
> printer errors
> > that we are all familiar with. In order to comply with the
> printer's> constraints, and get the results that we want, it is
> probably safest to
> > create our own 300 dpi image that falls within the plate size of the
> > publication.
>
> In principle I agree Joel,
> but the problem really lies not really in the print versions,
> which are always going to be poor representation of a digital image...
>
> rather in the PDF version, which contain a mashed, lossy
> compressed,
> resampled and generally destroyed version of the image data.
>
> Let us not forget, out microscpes are fanct spectrometers that
> collect numerical data.
> A digital image is not analogue artwork, its just a table of
> numbers!!!
> we would never allow a text table of numbers to have its
> information destroyed like this
> on the way to it being read by a reader/reviewer, so why do we
> accept it as normal for images?
>
> We meed to change the way publication works, and make sure editors
> understand that images
> are tables of numbers and should be treated as such.
> The original non destroyed image data should always be made
> available over the web.
>
> Chemists and physicists thing cell biology etc are very very soft
> fluffy disciplines,
> and trust very little they read of out work,
> exactly for reasons like this.
>
> >
> > As one more thought, increasing numbers of journals actually do
> a very poor
> > job of producing images in print, with the idea that the printed
> image is a
> > marker for a high resolution version that is online. I would
> just ask that
> > the publishers make the the original images available, and not
> just the pdf
> > conversions of the print versions.
>
> Hear Hear!!!
>
>
> > On Behalf Of Carl Boswell
> > Sent: Tuesday, June 29, 2010 11:19 AM
> > To: [hidden email]
> > Subject: Re: Preparing figures for publication --PPI vs DPI
> >
> > =20
> >
> > My view is that the fewer options the publisher (in reality, the
> > printer) have to modify your image, the better. Given that, I would
> > think that making all the necessary adjustments, using the tips
> already> mentioned, would give you the best chance of having your
> work appear as
> > planned in your publication. If it is left up to someone who knows
> > printing but not cell biology, you could be in for a very special
> > surprise. =20
>
> sure, it sounds like a good plan, but in the end the image is
> always destroyed at the final stage - the printer,
> which imposes its very limited capabilities on any image.
> We can try to make sureimages look nice, but this really is only art.
>
> What a reader really needs is access to the full resolution
> original image to open in ImageJ/Fiji etc.
>
> >
> > =20
> >
> > At the least, insist on a galley proof with the actual pictures
> that are
> > going into the paper. That way you can at least be prepared for
> what> will show up in the journal, and maybe you can have them fix
> the more
> > glaring errors. Problems with hue and contrast may be
> irritating but
> > not terminal. However, if your images have been repeatedly
> resaved as
> > jpg's, or resampled incorrectly, and the mitochondria look like
> they are
> > made from Lego's, then something needs to be said.
>
> I agree ver strongly. We must to accept badly destroyed images ,
> even in print.
> Lobby your editor until you get what is right.
>
>
> >
>
> > Date: Tue, 29 Jun 2010 14:45:58 -0700
> > From: Doug Cromey <[hidden email]>
> > Subject: Re: Preparing figures for publication --PPI vs DPI
> >
> > Carl and others,
> >
> > Don't count on the journals to know what to do. The typesetting
> from the
> > paper I cited in my earlier post was outsourced to a far away
> country, the
> > publishing was being done in an EU country, and the Editor was
> in the USA.
> > The first two galleys I saw had major JPEG artifacts in my carefully
> > prepared figures (PDF includes JPEG for the figures).
> Fortunately the
> > Editor pushed for the publisher to be less aggressive with my
> paper (5 large
> > figures) and instead of final PDF of less than 1MB, the paper
> came out at
> > 4.7MB with no appreciable artifacts.
>
> but the images are still not really good enough for someone to
> take and re do your image analysis,
> or make their own new measurements from .
>
> this is a basic requirement of scientific publication,
> and is harly ever me in our discipline,
> and this is very wrong.
> Physicists laugh at us... and biochemists.
>
> there is no technical reason that raw data can not be made
> available on line
> even big screens,
> its just missing infrastructure that needs to be put in place.
>
> Where is our biological image equivalent of the PDB database, the
> GENBANK database,
> all the other databases other disciplines have.
> Where is ours? We need to get that funded and organised through eg
> Euro-Bioimaging project.
> http://www.eurobioimaging.eu/
> and an USA / asia pacific equivlaent
> >
> >
> >
> > The "art" department at most publishers seems to mostly consist
> of people
> > who are accustomed to graphic design, not science. I'm afraid
> that Daniel's
> > complaints about being forced to do the publisher's work are
> unrealistic,> unfortunately we often need to be smarter than the
> publisher, even if that
> > should not have to be our job.
>
> Or we need to force our publishers to get smart about the kind of
> images we give them.
> and how to treat them.
>
> I would suggest we be proactive here, rather than defeatist.
> No matter how hard we try to make a well formatted plate for the
> publisher,
> it will most likely still be mashed by the time the pdf arrived on
> a readers screen.
>
> We need to educate the publishing system of our needs.
> I suggest using the argument that our images are 2D/3xD tables of
> spectroscopic measurement NUMBERS,
> and should be treated as such, not as photos - which they are NOT.
>
>
> cheers
>
> Dan
>
> >
> >
> >
> > Doug
> >
> >
> >
> > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> >
> > Douglas W. Cromey, M.S. - Assistant Scientific Investigator
> >
> > Dept. of Cell Biology & Anatomy, University of Arizona
> >
> > 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA
> >
> >
> >
> > office: AHSC 4212 email: [hidden email]
> >
> > voice: 520-626-2824 fax: 520-626-2097
> >
> >
> >
> > http://swehsc.pharmacy.arizona.edu/exppath/
> >
> > Home of: "Microscopy and Imaging Resources on the WWW"
>
>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> +49 (0)15114966933 (German Mobile)
> +49 (0)351 210 2627 (Work phone at MPI-CBG)
> +49 (0)351 210 1078 (Fax MPI-CBG LMF)
>
> http://www.bioimagexd.net BioImageXD
> http://pacific.mpi-cbg.de Fiji - is just ImageJ
> (Batteries Included)
> http://www.chalkie.org.uk Dan's Homepages
> https://ifn.mpi-cbg.de Dresden Imaging Facility
> Networkdan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
>

No virus found in this incoming message.
Checked by AVG - www.avg.com
Version: 9.0.830 / Virus Database: 271.1.1/2914 - Release Date: 06/30/10 04:35:00

RICHARD BURRY RICHARD BURRY
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Re: Preparing figures for publication --PPI vs DPI

In reply to this post by Eric Scarfone

One problem I find most frustrating is that many high impact journals are publishing smaller and smaller micrographs.  The result is that even if the data was originally there it is impossible to see it in the online enlarged image.  In the review process, the Editors need to evaluate the micrographs included in manuscripts to insure that they are at sufficient size to show the data described in the text.   

 

Dick Burry


----- Original Message -----
From: Eric Scarfone <[hidden email]>
Date: Wednesday, June 30, 2010 7:31 am
Subject: Re: Preparing figures for publication --PPI vs DPI
To: [hidden email]

> Hej List!
> I fully endorse Daniel's points in this thread. The imaging community must work towards an "ImageBank" where the original data from all published scientific image would be accessible.


> It happens more than once that published images are so degraded that it becomes impossible to assess the author’s claims. Maybe the referees have had access to the data supporting the claims but the readers often do not. We are not anymore at the analog time when only referees could aces the original prints made by authors (which by the way was not that perfect-a-time since the original data, -the negatives- were not at all accessible!). Indeed the advent of the digital age makes it possible to look with the same ccd eye into someone else’s microscope.

This is important for the respect of the reproducibility requirement.
> This is also fundamental for the tracing of image modifications made by authors. Here this thread joins another discussion that was vivid sometimes on the list about what is allowed and not to improve images.

A problem remains though; it is that original data really must be “original” (meaning “un-tampered with”!)

Cheers
> Eric



> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet

> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden

> Work: +46 (0)8-517 79343,
> Cell: +46 (0)70 888 2352
> Fax: +46 (0)8-301876

> email: [hidden email]
> http://www.ki.se/cfh/


> ----- Original Message -----
> From: Daniel James White <[hidden email]>
> Date: Wednesday, June 30, 2010 10:34 am
> Subject: Re: Preparing figures for publication --PPI vs DPI
> To: [hidden email]

> > Dear All,
> >
> > On Jun 30, 2010, at 7:02 AM, CONFOCALMICROSCOPY automatic digest
> > system wrote:
> >
> > >
> > > Date: Tue, 29 Jun 2010 10:46:53 -0400
> > > From: "JOEL B. SHEFFIELD" <[hidden email]>
> > > Subject: Re: Preparing figures for publication --PPI vs DPI
> > >
> > >
> > > The problems with letting the publisher do the work is that we
> > often have a
> > > particular layout in mind, and we submit complete "plates"
> > rather than
> > > individual images. This is one way to avoid the kinds of
> > printer errors
> > > that we are all familiar with. In order to comply with the
> > printer's> constraints, and get the results that we want, it is
> > probably safest to
> > > create our own 300 dpi image that falls within the plate size of the
> > > publication.
> >
> > In principle I agree Joel,
> > but the problem really lies not really in the print versions,
> > which are always going to be poor representation of a digital image...
> >
> > rather in the PDF version, which contain a mashed, lossy
> > compressed,
> > resampled and generally destroyed version of the image data.
> >
> > Let us not forget, out microscpes are fanct spectrometers that
> > collect numerical data.
> > A digital image is not analogue artwork, its just a table of
> > numbers!!!
> > we would never allow a text table of numbers to have its
> > information destroyed like this
> > on the way to it being read by a reader/reviewer, so why do we
> > accept it as normal for images?
> >
> > We meed to change the way publication works, and make sure editors
> > understand that images
> > are tables of numbers and should be treated as such.
> > The original non destroyed image data should always be made
> > available over the web.
> >
> > Chemists and physicists thing cell biology etc are very very soft
> > fluffy disciplines,
> > and trust very little they read of out work,
> > exactly for reasons like this.
> >
> > >
> > > As one more thought, increasing numbers of journals actually do
> > a very poor
> > > job of producing images in print, with the idea that the printed
> > image is a
> > > marker for a high resolution version that is online. I would
> > just ask that
> > > the publishers make the the original images available, and not
> > just the pdf
> > > conversions of the print versions.
> >
> > Hear Hear!!!
> >
> >
> > > On Behalf Of Carl Boswell
> > > Sent: Tuesday, June 29, 2010 11:19 AM
> > > To: [hidden email]
> > > Subject: Re: Preparing figures for publication --PPI vs DPI
> > >
> > > =20
> > >
> > > My view is that the fewer options the publisher (in reality, the
> > > printer) have to modify your image, the better. Given that, I would
> > > think that making all the necessary adjustments, using the tips
> > already> mentioned, would give you the best chance of having your
> > work appear as
> > > planned in your publication. If it is left up to someone who knows
> > > printing but not cell biology, you could be in for a very special
> > > surprise. =20
> >
> > sure, it sounds like a good plan, but in the end the image is
> > always destroyed at the final stage - the printer,
> > which imposes its very limited capabilities on any image.
> > We can try to make sureimages look nice, but this really is only art.
> >
> > What a reader really needs is access to the full resolution
> > original image to open in ImageJ/Fiji etc.
> >
> > >
> > > =20
> > >
> > > At the least, insist on a galley proof with the actual pictures
> > that are
> > > going into the paper. That way you can at least be prepared for
> > what> will show up in the journal, and maybe you can have them fix
> > the more
> > > glaring errors. Problems with hue and contrast may be
> > irritating but
> > > not terminal. However, if your images have been repeatedly
> > resaved as
> > > jpg's, or resampled incorrectly, and the mitochondria look like
> > they are
> > > made from Lego's, then something needs to be said.
> >
> > I agree ver strongly. We must to accept badly destroyed images ,
> > even in print.
> > Lobby your editor until you get what is right.
> >
> >
> > >
> >
> > > Date: Tue, 29 Jun 2010 14:45:58 -0700
> > > From: Doug Cromey <[hidden email]>
> > > Subject: Re: Preparing figures for publication --PPI vs DPI
> > >
> > > Carl and others,
> > >
> > > Don't count on the journals to know what to do. The typesetting
> > from the
> > > paper I cited in my earlier post was outsourced to a far away
> > country, the
> > > publishing was being done in an EU country, and the Editor was
> > in the USA.
> > > The first two galleys I saw had major JPEG artifacts in my carefully
> > > prepared figures (PDF includes JPEG for the figures).
> > Fortunately the
> > > Editor pushed for the publisher to be less aggressive with my
> > paper (5 large
> > > figures) and instead of final PDF of less than 1MB, the paper
> > came out at
> > > 4.7MB with no appreciable artifacts.
> >
> > but the images are still not really good enough for someone to
> > take and re do your image analysis,
> > or make their own new measurements from .
> >
> > this is a basic requirement of scientific publication,
> > and is harly ever me in our discipline,
> > and this is very wrong.
> > Physicists laugh at us... and biochemists.
> >
> > there is no technical reason that raw data can not be made
> > available on line
> > even big screens,
> > its just missing infrastructure that needs to be put in place.
> >
> > Where is our biological image equivalent of the PDB database, the
> > GENBANK database,
> > all the other databases other disciplines have.
> > Where is ours? We need to get that funded and organised through eg
> > Euro-Bioimaging project.
> > http://www.eurobioimaging.eu/
> > and an USA / asia pacific equivlaent
> > >
> > >
> > >
> > > The "art" department at most publishers seems to mostly consist
> > of people
> > > who are accustomed to graphic design, not science. I'm afraid
> > that Daniel's
> > > complaints about being forced to do the publisher's work are
> > unrealistic,> unfortunately we often need to be smarter than the
> > publisher, even if that
> > > should not have to be our job.
> >
> > Or we need to force our publishers to get smart about the kind of
> > images we give them.
> > and how to treat them.
> >
> > I would suggest we be proactive here, rather than defeatist.
> > No matter how hard we try to make a well formatted plate for the
> > publisher,
> > it will most likely still be mashed by the time the pdf arrived on
> > a readers screen.
> >
> > We need to educate the publishing system of our needs.
> > I suggest using the argument that our images are 2D/3xD tables of
> > spectroscopic measurement NUMBERS,
> > and should be treated as such, not as photos - which they are NOT.
> >
> >
> > cheers
> >
> > Dan
> >
> > >
> > >
> > >
> > > Doug
> > >
> > >
> > >
> > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> > >
> > > Douglas W. Cromey, M.S. - Assistant Scientific Investigator
> > >
> > > Dept. of Cell Biology & Anatomy, University of Arizona
> > >
> > > 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA
> > >
> > >
> > >
> > > office: AHSC 4212 email: [hidden email]
> > >
> > > voice: 520-626-2824 fax: 520-626-2097
> > >
> > >
> > >
> > > http://swehsc.pharmacy.arizona.edu/exppath/
> > >
> > > Home of: "Microscopy and Imaging Resources on the WWW"
> >
> >
> > Dr. Daniel James White BSc. (Hons.) PhD
> > Senior Microscopist / Image Visualisation, Processing and Analysis
> > Light Microscopy and Image Processing Facilities
> > Max Planck Institute of Molecular Cell Biology and Genetics
> > Pfotenhauerstrasse 108
> > 01307 DRESDEN
> > Germany
> >
> > +49 (0)15114966933 (German Mobile)
> > +49 (0)351 210 2627 (Work phone at MPI-CBG)
> > +49 (0)351 210 1078 (Fax MPI-CBG LMF)
> >
> > http://www.bioimagexd.net BioImageXD
> > http://pacific.mpi-cbg.de Fiji - is just ImageJ
> > (Batteries Included)
> > http://www.chalkie.org.uk Dan's Homepages
> > https://ifn.mpi-cbg.de Dresden Imaging Facility
> > Networkdan (at) chalkie.org.uk
> > ( white (at) mpi-cbg.de )
> >

> Spam
> Not spam
> Forget previous vote



Richard W. Burry, Ph.D.
Department of Neuroscience, College of Medicine
Campus Microscopy and Imaging Facility, Director
The Ohio State University
Associate Editor, Journal of Histochemistry and Cytochemistry
277 Biomedical Research Tower
460 West Twelfth Avenue
Columbus, Ohio 43210
Voice 614.292.2814  Cell 614.638.3345  Fax 614.247.8849

Michael Weber-4 Michael Weber-4
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Re: Axiovision: Panorama and Multidimensional acquisition

In reply to this post by Eric Scarfone
Eric,

the "Stitching 2D/3D" plugin in Fiji should be able to do the job:

http://pacific.mpi-cbg.de/wiki/index.php/Stitching_2D/3D

Michael


> Hi List.
> This is not a confocal question but I do not know where to find a better
> goup of imaging experts!
> We are trying to make mosaic images using the "Panorama" feature of Zeiss
> Axiovision software (our mic does not have a motorized stage so this is
> manual). It works well, but I would like each frame of the mosaic to be a
> multidimensional image (ie multiple fluorescence).
> And I could not find a way to do that!
> Any ideas?
> Cheers
> Eric
>
>
> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet
>
> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden
>
> Work: +46 (0)8-517 79343,
> Cell: +46 (0)70 888 2352
> Fax: +46 (0)8-301876
>
> email: [hidden email]
> http://www.ki.se/cfh/
>
>
> ----- Original Message -----
> From: Eric Scarfone <[hidden email]>
> Date: Wednesday, June 30, 2010 1:24 pm
> Subject: Re: Preparing figures for publication --PPI vs DPI
> To: [hidden email]
>
>> Hej List!
>> I fully endorse Daniel's points in this thread. The imaging
>> community must work towards an "ImageBank" where the original data
>> from all published scientific image would be accessible.
>>
>> It happens more than once that published images are so degraded
>> that it becomes impossible to assess the author’s claims. Maybe
>> the referees have had access to the data supporting the claims but
>> the readers often do not. We are not anymore at the analog time
>> when only referees could aces the original prints made by authors
>> (which by the way was not that perfect-a-time since the original
>> data, -the negatives- were not at all accessible!). Indeed the
>> advent of the digital age makes it possible to look with the same
>> ccd eye into someone else’s microscope.
>> This is important for the respect of the reproducibility
>> requirement.
>> This is also fundamental for the tracing of image modifications
>> made by authors. Here this thread joins another discussion that
>> was vivid sometimes on the list about what is allowed and not to
>> improve images.
>> A problem remains though; it is that original data really must be
>> “original” (meaning “un-tampered with”!)
>> Cheers
>> Eric
>>
>>
>> Eric Scarfone, PhD, CNRS,
>> Center for Hearing and communication Research
>> Department of Clinical Neuroscience
>> Karolinska Institutet
>>
>> Postal Address:
>> CFH, M1:02
>> Karolinska Hospital,
>> SE-171 76 Stockholm, Sweden
>>
>> Work: +46 (0)8-517 79343,
>> Cell: +46 (0)70 888 2352
>> Fax: +46 (0)8-301876
>>
>> email: [hidden email]
>> http://www.ki.se/cfh/
>>
>>
>> ----- Original Message -----
>> From: Daniel James White <[hidden email]>
>> Date: Wednesday, June 30, 2010 10:34 am
>> Subject: Re: Preparing figures for publication --PPI vs DPI
>> To: [hidden email]
>>
>> > Dear All,
>> >
>> > On Jun 30, 2010, at 7:02 AM, CONFOCALMICROSCOPY automatic digest
>> > system wrote:
>> >
>> > >
>> > > Date: Tue, 29 Jun 2010 10:46:53 -0400
>> > > From: "JOEL B. SHEFFIELD" <[hidden email]>
>> > > Subject: Re: Preparing figures for publication --PPI vs DPI
>> > >
>> > >
>> > > The problems with letting the publisher do the work is that we
>> > often have a
>> > > particular layout in mind, and we submit complete "plates"
>> > rather than
>> > > individual images. This is one way to avoid the kinds of
>> > printer errors
>> > > that we are all familiar with. In order to comply with the
>> > printer's> constraints, and get the results that we want, it is
>> > probably safest to
>> > > create our own 300 dpi image that falls within the plate size
>> of the
>> > > publication.
>> >
>> > In principle I agree Joel,
>> > but the problem really lies not really in the print versions,
>> > which are always going to be poor representation of a digital
>> image...
>> >
>> > rather in the PDF version, which contain a mashed, lossy
>> > compressed,
>> > resampled and generally destroyed version of the image data.
>> >
>> > Let us not forget, out microscpes are fanct spectrometers that
>> > collect numerical data.
>> > A digital image is not analogue artwork, its just a table of
>> > numbers!!!
>> > we would never allow a text table of numbers to have its
>> > information destroyed like this
>> > on the way to it being read by a reader/reviewer, so why do we
>> > accept it as normal for images?
>> >
>> > We meed to change the way publication works, and make sure
>> editors
>> > understand that images
>> > are tables of numbers and should be treated as such.
>> > The original non destroyed image data should always be made
>> > available over the web.
>> >
>> > Chemists and physicists thing cell biology etc are very very
>> soft
>> > fluffy disciplines,
>> > and trust very little they read of out work,
>> > exactly for reasons like this.
>> >
>> > >
>> > > As one more thought, increasing numbers of journals actually
>> do
>> > a very poor
>> > > job of producing images in print, with the idea that the
>> printed
>> > image is a
>> > > marker for a high resolution version that is online. I would
>> > just ask that
>> > > the publishers make the the original images available, and not
>> > just the pdf
>> > > conversions of the print versions.
>> >
>> > Hear Hear!!!
>> >
>> >
>> > > On Behalf Of Carl Boswell
>> > > Sent: Tuesday, June 29, 2010 11:19 AM
>> > > To: [hidden email]
>> > > Subject: Re: Preparing figures for publication --PPI vs DPI
>> > >
>> > > =20
>> > >
>> > > My view is that the fewer options the publisher (in reality,
>> the
>> > > printer) have to modify your image, the better. Given that, I
>> would
>> > > think that making all the necessary adjustments, using the
>> tips
>> > already> mentioned, would give you the best chance of having
>> your
>> > work appear as
>> > > planned in your publication. If it is left up to someone who
>> knows
>> > > printing but not cell biology, you could be in for a very
>> special
>> > > surprise. =20
>> >
>> > sure, it sounds like a good plan, but in the end the image is
>> > always destroyed at the final stage - the printer,
>> > which imposes its very limited capabilities on any image.
>> > We can try to make sureimages look nice, but this really is only
>> art.
>> >
>> > What a reader really needs is access to the full resolution
>> > original image to open in ImageJ/Fiji etc.
>> >
>> > >
>> > > =20
>> > >
>> > > At the least, insist on a galley proof with the actual
>> pictures
>> > that are
>> > > going into the paper. That way you can at least be prepared
>> for
>> > what> will show up in the journal, and maybe you can have them
>> fix
>> > the more
>> > > glaring errors. Problems with hue and contrast may be
>> > irritating but
>> > > not terminal. However, if your images have been repeatedly
>> > resaved as
>> > > jpg's, or resampled incorrectly, and the mitochondria look
>> like
>> > they are
>> > > made from Lego's, then something needs to be said.
>> >
>> > I agree ver strongly. We must to accept badly destroyed images ,
>> > even in print.
>> > Lobby your editor until you get what is right.
>> >
>> >
>> > >
>> >
>> > > Date: Tue, 29 Jun 2010 14:45:58 -0700
>> > > From: Doug Cromey <[hidden email]>
>> > > Subject: Re: Preparing figures for publication --PPI vs DPI
>> > >
>> > > Carl and others,
>> > >
>> > > Don't count on the journals to know what to do. The
>> typesetting
>> > from the
>> > > paper I cited in my earlier post was outsourced to a far away
>> > country, the
>> > > publishing was being done in an EU country, and the Editor was
>> > in the USA.
>> > > The first two galleys I saw had major JPEG artifacts in my
>> carefully
>> > > prepared figures (PDF includes JPEG for the figures).
>> > Fortunately the
>> > > Editor pushed for the publisher to be less aggressive with my
>> > paper (5 large
>> > > figures) and instead of final PDF of less than 1MB, the paper
>> > came out at
>> > > 4.7MB with no appreciable artifacts.
>> >
>> > but the images are still not really good enough for someone to
>> > take and re do your image analysis,
>> > or make their own new measurements from .
>> >
>> > this is a basic requirement of scientific publication,
>> > and is harly ever me in our discipline,
>> > and this is very wrong.
>> > Physicists laugh at us... and biochemists.
>> >
>> > there is no technical reason that raw data can not be made
>> > available on line
>> > even big screens,
>> > its just missing infrastructure that needs to be put in place.
>> >
>> > Where is our biological image equivalent of the PDB database,
>> the
>> > GENBANK database,
>> > all the other databases other disciplines have.
>> > Where is ours? We need to get that funded and organised through
>> eg
>> > Euro-Bioimaging project.
>> > http://www.eurobioimaging.eu/
>> > and an USA / asia pacific equivlaent
>> > >
>> > >
>> > >
>> > > The "art" department at most publishers seems to mostly
>> consist
>> > of people
>> > > who are accustomed to graphic design, not science. I'm afraid
>> > that Daniel's
>> > > complaints about being forced to do the publisher's work are
>> > unrealistic,> unfortunately we often need to be smarter than the
>> > publisher, even if that
>> > > should not have to be our job.
>> >
>> > Or we need to force our publishers to get smart about the kind
>> of
>> > images we give them.
>> > and how to treat them.
>> >
>> > I would suggest we be proactive here, rather than defeatist.
>> > No matter how hard we try to make a well formatted plate for the
>> > publisher,
>> > it will most likely still be mashed by the time the pdf arrived
>> on
>> > a readers screen.
>> >
>> > We need to educate the publishing system of our needs.
>> > I suggest using the argument that our images are 2D/3xD tables
>> of
>> > spectroscopic measurement NUMBERS,
>> > and should be treated as such, not as photos - which they are
>> NOT.
>> >
>> >
>> > cheers
>> >
>> > Dan
>> >
>> > >
>> > >
>> > >
>> > > Doug
>> > >
>> > >
>> > >
>> > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>> > >
>> > > Douglas W. Cromey, M.S. - Assistant Scientific Investigator
>> > >
>> > > Dept. of Cell Biology & Anatomy, University of Arizona
>> > >
>> > > 1501 N. Campbell Ave, Tucson, AZ 85724-5044 USA
>> > >
>> > >
>> > >
>> > > office: AHSC 4212 email: [hidden email]
>> > >
>> > > voice: 520-626-2824 fax: 520-626-2097
>> > >
>> > >
>> > >
>> > > http://swehsc.pharmacy.arizona.edu/exppath/
>> > >
>> > > Home of: "Microscopy and Imaging Resources on the WWW"
>> >
>> >
>> > Dr. Daniel James White BSc. (Hons.) PhD
>> > Senior Microscopist / Image Visualisation, Processing and
>> Analysis
>> > Light Microscopy and Image Processing Facilities
>> > Max Planck Institute of Molecular Cell Biology and Genetics
>> > Pfotenhauerstrasse 108
>> > 01307 DRESDEN
>> > Germany
>> >
>> > +49 (0)15114966933 (German Mobile)
>> > +49 (0)351 210 2627 (Work phone at MPI-CBG)
>> > +49 (0)351 210 1078 (Fax MPI-CBG LMF)
>> >
>> > http://www.bioimagexd.net BioImageXD
>> > http://pacific.mpi-cbg.de Fiji - is just ImageJ
>> > (Batteries Included)
>> > http://www.chalkie.org.uk Dan's Homepages
>> > https://ifn.mpi-cbg.de Dresden Imaging Facility
>> > Networkdan (at) chalkie.org.uk
>> > ( white (at) mpi-cbg.de )
rjpalmer rjpalmer
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Re: Preparing figures for publication --PPI vs DPI

In reply to this post by Guy Cox-2
I'll just throw a few other comments out for this image-preparation discussion.
1) does anyone actually read paper journals?  One can lament or
applaud the trend towards "electronic only" but it is unstoppable and
makes some of this discussion irrelevant.  Paper is to give to your
relatives at family reunions - they'll never know the difference
between great images and passable images especially from the
scientific side.
2) many (but not all) journals require you to submit CMYK images that
are then used not only for the print version but also to make the
the PDFs that get put on-line.  Fortunately this is changing also -
there are journals that print in RGB.  I send RGBs and CMYKs and tell
the journal what to do with them.  That is no guarantee it will be
done right.  I just want everything to go electronic/RGB ASAP.
3) journals do what they want and you have no control.  At least in
my field, highly-read journals no longer send you plate proofs you
can hold in your hand - this is expensive and takes time away from a
process we all want to be rapid.  I second the concept that you the
author must do the best you can within the constraints of the journal
or you will see your images come out even worse than without your
limited control.  You need to make your own figures/e-plates.
Rob Palmer
--
Robert J. Palmer Jr., Ph.D.
Natl Inst Dental Craniofacial Res - Natl Insts Health
Oral Infection and Immunity Branch
Bldg 30, Room 310
30 Convent Drive
Bethesda MD 20892
ph 301-594-0025
fax 301-402-0396
Craig Brideau Craig Brideau
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Re: Preparing figures for publication --PPI vs DPI

In reply to this post by Guy Cox-2
On Wed, Jun 30, 2010 at 8:29 AM, Robert J. Palmer Jr.
<[hidden email]> wrote:
> 1) does anyone actually read paper journals?  One can lament or applaud the
> trend towards "electronic only" but it is unstoppable and makes some of this
> discussion irrelevant.

I have to say that 99.9% of the papers I read are PDFs I view on my
monitor.  Occasionally I will print one out if I want to show it to
somebody else, but I usually just forward it via email.  That said, it
is odd that I am viewing an image downsampled in a PDF.  I think it is
worthwhile to have a downsampled 'thumbnail' or 'preview' image in an
electronic paper to keep the file size easily emailed/portable.
However, I think critical images should be hotlinked to the original
data.  That way I could click on the placeholder/thumbnail image and
get the raw data to make my own assessment against the author's
claims.  The tricky part would be to have a static location to store
the raw data so that the links in the PDF stay good.  Also, the reader
would have to have an appropriate application to open the data, so
something free and common, like Fiji/ImageJ would be required.

Craig
Johannes-P. Koch Johannes-P. Koch
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Re: Preparing figures for publication --PPI vs DPI

Just to get it right:

Say, I have a CLSM image with 1024x1024px, which was acquired at exc/em
488/520nm using a 63x NA1.4 objective. The zoom factor was adjusted for
Nyquist sampling, let's say such that I have 50nm pixel size.

I have to use these settings, since I want a whole human cell on my
image and I need the resolution as well.

If I consider now the second part of the Nyquist theorem, I would have
to use at least 2 pixels on the print for one pixel in my image - this
would be some 6.8 inches for a 300dpi printer!


This is obviously not feasible anyway! I assume, that only something
like 256x256 px are acceptable for todays image sizes in journals. This
would imply that either I am not "allowed" to use high NA objectives
(because then my field of view is rather limited if I stick to Nyquist)
or I have to crop excessively such that the whole context in a cell is
lost (see settings above). I suppose, you all agree that neither is a
solution. Then, the question remains for me: How can I properly transmit
such an image to a journal. The answer according to all of you is
simply, that it is not possible!

Am I right? This is disastrous.



Johannes

Am 30.06.2010 21:57, schrieb Craig Brideau:

> On Wed, Jun 30, 2010 at 8:29 AM, Robert J. Palmer Jr.
> <[hidden email]>  wrote:
>    
>> 1) does anyone actually read paper journals?  One can lament or applaud the
>> trend towards "electronic only" but it is unstoppable and makes some of this
>> discussion irrelevant.
>>      
> I have to say that 99.9% of the papers I read are PDFs I view on my
> monitor.  Occasionally I will print one out if I want to show it to
> somebody else, but I usually just forward it via email.  That said, it
> is odd that I am viewing an image downsampled in a PDF.  I think it is
> worthwhile to have a downsampled 'thumbnail' or 'preview' image in an
> electronic paper to keep the file size easily emailed/portable.
> However, I think critical images should be hotlinked to the original
> data.  That way I could click on the placeholder/thumbnail image and
> get the raw data to make my own assessment against the author's
> claims.  The tricky part would be to have a static location to store
> the raw data so that the links in the PDF stay good.  Also, the reader
> would have to have an appropriate application to open the data, so
> something free and common, like Fiji/ImageJ would be required.
>
> Craig
>
>    

--
Mag. Johannes-P. KOCH
Department of Biochemistry and Cell Biology
MFPL, University of Vienna
Dr. Bohrgasse 9/5
A-1030 Vienna
Austria

phone: 0043 1 4277 52809
fax: 0043 1 4277 9528

mail to: [hidden email]
Guy Cox-2 Guy Cox-2
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Re: Preparing figures for publication --PPI vs DPI

A 1024 x 1024 image at 300 dpi will be reproduced at 3.4 inches wide.
This may not show your fine detail.  If you want to make it a full page
width image you should resample to 2048 x 2048.  This will then be 6.8
inches wide.  If it's a high-quality journal using 150 dpi printing you
will then have 1 half-tone dot per (original) pixel.  In practice, this
will look pretty good, in spite of my theoretical discussions.  Since
you won't actually be able to see the dots in the printed image, you can
check if this is adequate by printing the image at that size.  If
important information doesn't show, you'll have to enlarge part of the
image.  

                                Guy

Optical Imaging Techniques in Cell Biology
by Guy Cox    CRC Press / Taylor & Francis
     http://www.guycox.com/optical.htm
______________________________________________
Associate Professor Guy Cox, MA, DPhil(Oxon)
Australian Centre for Microscopy & Microanalysis,
Madsen Building F09, University of Sydney, NSW 2006

Phone +61 2 9351 3176     Fax +61 2 9351 7682
             Mobile 0413 281 861
______________________________________________
      http://www.guycox.net
 


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]]
On Behalf Of Johannes-P. Koch
Sent: Thursday, 1 July 2010 5:54 PM
To: [hidden email]
Subject: Re: Preparing figures for publication --PPI vs DPI

Just to get it right:

Say, I have a CLSM image with 1024x1024px, which was acquired at exc/em
488/520nm using a 63x NA1.4 objective. The zoom factor was adjusted for
Nyquist sampling, let's say such that I have 50nm pixel size.

I have to use these settings, since I want a whole human cell on my
image and I need the resolution as well.

If I consider now the second part of the Nyquist theorem, I would have
to use at least 2 pixels on the print for one pixel in my image - this
would be some 6.8 inches for a 300dpi printer!


This is obviously not feasible anyway! I assume, that only something
like 256x256 px are acceptable for todays image sizes in journals. This
would imply that either I am not "allowed" to use high NA objectives
(because then my field of view is rather limited if I stick to Nyquist)
or I have to crop excessively such that the whole context in a cell is
lost (see settings above). I suppose, you all agree that neither is a
solution. Then, the question remains for me: How can I properly transmit

such an image to a journal. The answer according to all of you is
simply, that it is not possible!

Am I right? This is disastrous.



Johannes

Am 30.06.2010 21:57, schrieb Craig Brideau:
> On Wed, Jun 30, 2010 at 8:29 AM, Robert J. Palmer Jr.
> <[hidden email]>  wrote:
>    
>> 1) does anyone actually read paper journals?  One can lament or
applaud the
>> trend towards "electronic only" but it is unstoppable and makes some
of this

>> discussion irrelevant.
>>      
> I have to say that 99.9% of the papers I read are PDFs I view on my
> monitor.  Occasionally I will print one out if I want to show it to
> somebody else, but I usually just forward it via email.  That said, it
> is odd that I am viewing an image downsampled in a PDF.  I think it is
> worthwhile to have a downsampled 'thumbnail' or 'preview' image in an
> electronic paper to keep the file size easily emailed/portable.
> However, I think critical images should be hotlinked to the original
> data.  That way I could click on the placeholder/thumbnail image and
> get the raw data to make my own assessment against the author's
> claims.  The tricky part would be to have a static location to store
> the raw data so that the links in the PDF stay good.  Also, the reader
> would have to have an appropriate application to open the data, so
> something free and common, like Fiji/ImageJ would be required.
>
> Craig
>
>    

--
Mag. Johannes-P. KOCH
Department of Biochemistry and Cell Biology
MFPL, University of Vienna
Dr. Bohrgasse 9/5
A-1030 Vienna
Austria

phone: 0043 1 4277 52809
fax: 0043 1 4277 9528

mail to: [hidden email]

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04:38:00
Jeremy Adler-3 Jeremy Adler-3
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Re: Preparing figures for publication --PPI vs DPI

In reply to this post by Johannes-P. Koch
It would be simpler if journals would specify the exact width(s) of  
images that they can accommodate in pixels - you can treat dpi as a  
number of pixels.

Making small adjustments to the size of images creates a difference  
between the image you submit and the image as published since the need  
to increase or decrease the number of pixels involves fabricating new  
pixels from the old.

Ideally there should be an integer relationship between the size of  
the original images in pixels as it comes off the microscope and the  
number of pixels in the submitted image. When magnifying an image by  
increasing the number of pixels you should only magnify by an integer  
and specify (Photoshop) that interpolation is by using the nearest  
neighbour. Then one of your original pixels will  still appear to be a  
single pixel when printed.
If necessary pad the final image out with a border but don't give the  
journal an excuse for fiddling with the number of pixels.

Jeremy Adler
Uppsala U
Sweden
1234