Preparing figures for publication --PPI vs DPI

[Stanislav Vitha]

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I think it absolutely fine to resample the images for presentation.
After all, when you give a PowerPoint presentation, quite often you are
resampling your pictures as well, depending on the particular LCD projector
that is used.

In order for the image to look reasonably well when printed on paper, you need
about 300 pixels per inch. If you have some annotation with hard edges, like
letters, arrows, these may still look a little jagged at this resolution  (it
probably has something to do with the compression that the print facility may
use), so a lot of journals will want such figures at 600 pixels per inch.

So depending how large you want the printed figures, you may need to make-
up for the imperfections of the printing process by adding pixels (resampling).
A second consideration is whether a stamp-size figure on the paper is
comfortable to look at, even if the resolution is there - as I get older, I prefer
the smallest detail in the printed image to be represented by more than just
one speck of ink.
 
I agree with Guy and others - resample the grayscale images, or resample RGB
images (after all, they are just three grayscale channels). I like to do the
resampling while I still have the grayscale image as 16 or 32 bits per pixel - I
use ImageJ for that, picking the higher quality resampling options (cubic, or
quintic, IIRC).


Stan

Dr. Stanislav Vitha      
Microscopy and Imaging Center
Texas A&M University
BSBW 119
College Station, TX 77843-2257
http://microscopy.tamu.edu



On Thu, 8 Sep 2011 10:31:39 -0700, Armstrong, Brian
<[hidden email]> wrote:
>
>Is the request to upload an image that has increased Dpi?
>For this I would open the image in Photoshop, open image size dialogue box,
type in resolution 300dpi, UNCHECK Resample image, and choose OK.
>It seems to me that resampling a scientific image using an algorithm such as
bicubic is interpolating pixels and therefore creating new data where it did not
exist before.
>Am I missing something?
>
>Brian Armstrong PhD

[Tim Feinstein-2]

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This issue is one reason why I lean towards quantitative analysis of the raw data, e.g. Pearson's colocalization, ratio, object detection etc., to accompany an image whenever the point is not obvious when you step back and squint.  One reason is the arbitrary filtering that happens at any publisher, which creates more artifacts (IMO at least) than a resampling that uses reasonable best practices.

In addition, this helps resolve the question of how well one or two small images can represent a phenomenon, or how impartial a person is when choosing a representative image.  

Just my 2c.  

cheers,


TF

Timothy Feinstein, PhD
Postdoctoral Fellow
Laboratory for GPCR Biology
Dept. of Pharmacology & Chemical Biology
University of Pittsburgh, School of Medicine
BST W1301, 200 Lothrop St.
Pittsburgh, PA  15261

On Sep 9, 2011, at 11:34 AM, Stanislav Vitha wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I think it absolutely fine to resample the images for presentation.
> After all, when you give a PowerPoint presentation, quite often you are
> resampling your pictures as well, depending on the particular LCD projector
> that is used.
>
> In order for the image to look reasonably well when printed on paper, you need
> about 300 pixels per inch. If you have some annotation with hard edges, like
> letters, arrows, these may still look a little jagged at this resolution  (it
> probably has something to do with the compression that the print facility may
> use), so a lot of journals will want such figures at 600 pixels per inch.
>
> So depending how large you want the printed figures, you may need to make-
> up for the imperfections of the printing process by adding pixels (resampling).
> A second consideration is whether a stamp-size figure on the paper is
> comfortable to look at, even if the resolution is there - as I get older, I prefer
> the smallest detail in the printed image to be represented by more than just
> one speck of ink.
>
> I agree with Guy and others - resample the grayscale images, or resample RGB
> images (after all, they are just three grayscale channels). I like to do the
> resampling while I still have the grayscale image as 16 or 32 bits per pixel - I
> use ImageJ for that, picking the higher quality resampling options (cubic, or
> quintic, IIRC).
>
>
> Stan
>
> Dr. Stanislav Vitha      
> Microscopy and Imaging Center
> Texas A&M University
> BSBW 119
> College Station, TX 77843-2257
> http://microscopy.tamu.edu
>
>
>
> On Thu, 8 Sep 2011 10:31:39 -0700, Armstrong, Brian
> <[hidden email]> wrote:
>>
>> Is the request to upload an image that has increased Dpi?
>> For this I would open the image in Photoshop, open image size dialogue box,
> type in resolution 300dpi, UNCHECK Resample image, and choose OK.
>> It seems to me that resampling a scientific image using an algorithm such as
> bicubic is interpolating pixels and therefore creating new data where it did not
> exist before.
>> Am I missing something?
>>
>> Brian Armstrong PhD

[Dmitry Sokolov-2]

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Sorry, I've overlooked the notes from Brian Armstrong below.

Thanks Brian, the data processed are new data as they depend on the
processing protocol. There is no much of science left when an image gets
filtered at resampling (controlled) and printing (unpredictable). What we
see in most of publications nowadays is not the visual representation of
primary (=scientific) datasets. Those become just illustrations to what a
researcher has seen on his screen at looking at the initial images. Those
data were then processed and analysed by researcher to come to his
conclusions and described in the paper in words, equations, plots and
tables.

Thank you,
Dmitry

On Sat, September 10, 2011 3:34 am, Stanislav Vitha wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> I think it absolutely fine to resample the images for presentation.
> After all, when you give a PowerPoint presentation, quite often you are
> resampling your pictures as well, depending on the particular LCD
> projector
> that is used.
>
> In order for the image to look reasonably well when printed on paper, you
> need
> about 300 pixels per inch. If you have some annotation with hard edges,
> like
> letters, arrows, these may still look a little jagged at this resolution
> (it
> probably has something to do with the compression that the print facility
> may
> use), so a lot of journals will want such figures at 600 pixels per inch.
>
> So depending how large you want the printed figures, you may need to make-
> up for the imperfections of the printing process by adding pixels
> (resampling).
> A second consideration is whether a stamp-size figure on the paper is
> comfortable to look at, even if the resolution is there - as I get older,
> I prefer
> the smallest detail in the printed image to be represented by more than
> just
> one speck of ink.
>
> I agree with Guy and others - resample the grayscale images, or resample
> RGB
> images (after all, they are just three grayscale channels). I like to do
> the
> resampling while I still have the grayscale image as 16 or 32 bits per
> pixel - I
> use ImageJ for that, picking the higher quality resampling options (cubic,
> or
> quintic, IIRC).
>
>
> Stan
>
> Dr. Stanislav Vitha
> Microscopy and Imaging Center
> Texas A&M University
> BSBW 119
> College Station, TX 77843-2257
> http://microscopy.tamu.edu
>
>
>
> On Thu, 8 Sep 2011 10:31:39 -0700, Armstrong, Brian
> <[hidden email]> wrote:
>>
>>Is the request to upload an image that has increased Dpi?
>>For this I would open the image in Photoshop, open image size dialogue
>> box,
> type in resolution 300dpi, UNCHECK Resample image, and choose OK.
>>It seems to me that resampling a scientific image using an algorithm such
>> as
> bicubic is interpolating pixels and therefore creating new data where it
> did not
> exist before.
>>Am I missing something?
>>
>>Brian Armstrong PhD
>

--
Dr. Dmitry Sokolov
Institute of Fundamental Sciences
Massey University, Palmerston North
New Zealand

[Monique Vasseur]

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Dear All,

We have to fit a new microscope somewhere and I don't like the idea "to squeeze in" much. So I would like your input on what most of you use as average space dedicated to one livecell microscopy station (Microscope, accessory devices, microscopist chair and free space to move) and what would you consider as a confortable space for the user (microscopist) if different.  Thanks a lot!

Monique Vasseur
Microscopie et imagerie
Département de biochimie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal QC    H3C 3J7   Canada

[Sripad Ram]

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Hello Monique,
In my experience, the microscope room size is largely determined by the size
of the table on which you are going to put the microscope setup.

Typically you need ~ 2 - 3 feet of space around the "accessible regions" of
the table.

If you have a big table, then you might require access to all sides of the
table in order to adjust/install the equipment.

However, if you have a small table, then you could put it against a wall or
against two adjacent walls (i.e. at the corner of the room) and this could
save you space.

Also, you need to find out if there are any specific requirements (from your
university) to accommodate wheelchair access.

Hope this helps.

Regards,
Sripad


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On
Behalf Of Vasseur Monique
Sent: Monday, September 12, 2011 11:50 AM
To: [hidden email]
Subject: Average livecell microscope room size

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Dear All,

We have to fit a new microscope somewhere and I don't like the idea "to
squeeze in" much. So I would like your input on what most of you use as
average space dedicated to one livecell microscopy station (Microscope,
accessory devices, microscopist chair and free space to move) and what would
you consider as a confortable space for the user (microscopist) if
different.  Thanks a lot!

Monique Vasseur
Microscopie et imagerie
Département de biochimie
Université de Montréal
C.P. 6128, succursale Centre-ville
Montréal QC    H3C 3J7   Canada

[Craig Brideau]

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Also consider the heat load of the room.  A smaller space, if enclosed, will
require very good ventilation to deal with the heat from any lamps, etc on
the microscope.  We are cramming a 2-photon system into a ~10'x12' room.  It
is on a 6'x4' optical table.  Conversely, our basic confocal system only
required a 4'x3' table.  You can get away with a smaller table as long as
you can put some of the equipment on overhead racks above the table.  This
has been a great space saver for us.

Craig

On Mon, Sep 12, 2011 at 11:08 AM, Sripad Ram
<[hidden email]>wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hello Monique,
> In my experience, the microscope room size is largely determined by the
> size
> of the table on which you are going to put the microscope setup.
>
> Typically you need ~ 2 - 3 feet of space around the "accessible regions" of
> the table.
>
> If you have a big table, then you might require access to all sides of the
> table in order to adjust/install the equipment.
>
> However, if you have a small table, then you could put it against a wall or
> against two adjacent walls (i.e. at the corner of the room) and this could
> save you space.
>
> Also, you need to find out if there are any specific requirements (from
> your
> university) to accommodate wheelchair access.
>
> Hope this helps.
>
> Regards,
> Sripad
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On
> Behalf Of Vasseur Monique
> Sent: Monday, September 12, 2011 11:50 AM
> To: [hidden email]
> Subject: Average livecell microscope room size
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear All,
>
> We have to fit a new microscope somewhere and I don't like the idea "to
> squeeze in" much. So I would like your input on what most of you use as
> average space dedicated to one livecell microscopy station (Microscope,
> accessory devices, microscopist chair and free space to move) and what
> would
> you consider as a confortable space for the user (microscopist) if
> different.  Thanks a lot!
>
> Monique Vasseur
> Microscopie et imagerie
> Département de biochimie
> Université de Montréal
> C.P. 6128, succursale Centre-ville
> Montréal QC    H3C 3J7   Canada
>

[Zac Arrac Atelaz]

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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
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Monique:
 
You might have to consider manufacturer specific measurements, but this is to give you a general idea, the average antivibration table will have 1.2mx1.2m, one desk, 1.5mx1m, and basically everything you purchase can be on top or below of both tables, so the minimal room used for this will be about 2.5mx2.5m this will be tight I know but it can work.
 
Something more, if you add things, like incubator, sink or something else, then you have to consider growing the available space. Also consider the growing possibilities for your device, for instance TIRFM, DSU, Confocal, MPE will be demanding you more room availability, the most important part is the isolation table, one a little bit bigger doesnt add too much in price to the first purchase, it will get some space ocuppied in the mean time, but on the long run you are going to save your self some money, and wont end up with two tables.
 
Hope this helps
 
Gabriel OH
 
 

 

> Date: Mon, 12 Sep 2011 12:49:40 -0400
> From: [hidden email]
> Subject: Average livecell microscope room size
> To: [hidden email]
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear All,
>
> We have to fit a new microscope somewhere and I don't like the idea "to squeeze in" much. So I would like your input on what most of you use as average space dedicated to one livecell microscopy station (Microscope, accessory devices, microscopist chair and free space to move) and what would you consider as a confortable space for the user (microscopist) if different. Thanks a lot!
>
> Monique Vasseur
> Microscopie et imagerie
> Département de biochimie
> Université de Montréal
> C.P. 6128, succursale Centre-ville
> Montréal QC H3C 3J7 Canada