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Resolution vs pixelation whinge

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simon walker (BI)

Resolution vs pixelation whinge

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[whinge] Is it just me, or does anyone else get annoyed when a journal
requests higher resolution images for publication? Typical requests are "FigX is
not at the required 300 dpi. We require a higher resolution version of this
figure" or "Your cover submission is not at the required resolution, you must
supply a higher resolution version?".
Well no, I can't. I've acquired the image with an optimal pixel size to satisfy
Nyquist-Shannon theorem. Just because you want to print the image at a
size where it might look pixelated does not allow me to break the laws of
physics. The result is invariably resubmission of a Photoshop upsampled
version of the image, which yes looks less pixelated, but no, is not at a higher
resolution. Presumably the publishers are just as capable of doing this as I
am. [/whinge]

Bill Miller-3

Re: Resolution vs pixelation whinge

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You might try PhotoZoom Pro2 - it seems to do a better job than
Photoshop when blowing up images --

Although you are right that the pixel/resolution for the Nyquist
limit is the correct theoretical setting to use to be able to
actually "see" the resolution you need to over sampling by a factor
of 5-10 so you have enough pixels

Bill Miller

At 11:49 AM 8/6/2008 -0400, you wrote:

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>[whinge] Is it just me, or does anyone else get annoyed when a journal
>requests higher resolution images for publication? Typical requests
>are "FigX is
>not at the required 300 dpi. We require a higher resolution version of this
>figure" or "Your cover submission is not at the required resolution, you must
>supply a higher resolution version?".
>Well no, I can't. I've acquired the image with an optimal pixel
>size to satisfy
>Nyquist-Shannon theorem. Just because you want to print the image at a
>size where it might look pixelated does not allow me to break the laws of
>physics. The result is invariably resubmission of a Photoshop upsampled
>version of the image, which yes looks less pixelated, but no, is not
>at a higher
>resolution. Presumably the publishers are just as capable of doing this as I
>am. [/whinge]

Chris Tully

Re: Resolution vs pixelation whinge

In reply to this post by simon walker (BI)

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

While this may not be strictly kosher for an image to be handled as data it does work for those "pretty pictures" well like to put on the cover page. Try using a smoothing option when resizing the image to make it larger. Bill's suggestion of PhotoZoom sounds like a good idea, although I have no specific experience with this package.

Keep in mind that the Nyquist sampling requirements simply tell you the minimum samples per unit to resolve a particular sized structure. There is no reason (except lack of storage space) not to sample at a higher rate. You may even be surprised and find a structure that you were not looking for... Of course higher sampling rates take longer, cause more bleaching etc. So that may not be the standard operating mode, but if you suddenly see a really great field while capturing images, why not go ahead and bump up the sampling rate and capture a second image just in case?

Chris Tully

--
Chris Tully
Microscopy and Image Analysis Expert
[hidden email]
240-888-1021
http://www.linkedin.com/in/christully

On Wed, Aug 6, 2008 at 11:49 AM, Simon Walker <[hidden email]> wrote:

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

[whinge] Is it just me, or does anyone else get annoyed when a journal
requests higher resolution images for publication? Typical requests are "FigX is
not at the required 300 dpi. We require a higher resolution version of this
figure" or "Your cover submission is not at the required resolution, you must
supply a higher resolution version?".
Well no, I can't. I've acquired the image with an optimal pixel size to satisfy
Nyquist-Shannon theorem. Just because you want to print the image at a
size where it might look pixelated does not allow me to break the laws of
physics. The result is invariably resubmission of a Photoshop upsampled
version of the image, which yes looks less pixelated, but no, is not at a higher
resolution. Presumably the publishers are just as capable of doing this as I
am. [/whinge]

Carol Heckman

Re: Resolution vs pixelation whinge

In reply to this post by simon walker (BI)

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

In the education business, we say "we have met the enemy and he is us." For every editor out there who is asking us to break the laws of physics, there is a teacher somewhere along the line who failed to teach him/her those laws.
Carol Heckman

Center for Microscopy & Microanalysis
Bowling Green State University
________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Simon Walker [[hidden email]]
Sent: Wednesday, August 06, 2008 11:49 AM
To: [hidden email]
Subject: Resolution vs pixelation whinge

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

[whinge] Is it just me, or does anyone else get annoyed when a journal
requests higher resolution images for publication? Typical requests are "FigX is
not at the required 300 dpi. We require a higher resolution version of this
figure" or "Your cover submission is not at the required resolution, you must
supply a higher resolution version?".
Well no, I can't. I've acquired the image with an optimal pixel size to satisfy
Nyquist-Shannon theorem. Just because you want to print the image at a
size where it might look pixelated does not allow me to break the laws of
physics. The result is invariably resubmission of a Photoshop upsampled
version of the image, which yes looks less pixelated, but no, is not at a higher
resolution. Presumably the publishers are just as capable of doing this as I
am. [/whinge]

Michael Herron

Re: Resolution vs pixelation whinge

In reply to this post by simon walker (BI)

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Modern management: Push the work to someone else.

On Aug 6, 2008, at 10:49 AM, Simon Walker wrote:

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

[whinge] Is it just me, or does anyone else get annoyed when a journal
requests higher resolution images for publication? Typical requests are "FigX is
not at the required 300 dpi. We require a higher resolution version of this
figure" or "Your cover submission is not at the required resolution, you must
supply a higher resolution version?".
Well no, I can't. I've acquired the image with an optimal pixel size to satisfy
Nyquist-Shannon theorem. Just because you want to print the image at a
size where it might look pixelated does not allow me to break the laws of
physics. The result is invariably resubmission of a Photoshop upsampled
version of the image, which yes looks less pixelated, but no, is not at a higher
resolution. Presumably the publishers are just as capable of doing this as I
am. [/whinge]

Michael J. Herron, U of MN, Dept. of Entomology

[hidden email]

612-624-3688 (office) 612-625-5299 (FAX)

Steffen Dietzel

Re: Resolution vs pixelation whinge

In reply to this post by simon walker (BI)

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

been there, done that.

Hi Simon,

nope, it's not just you. I that situation I first
try to get away with upscaling with the nearest
neighbor algorithm with a power of two or four in
Photoshop. Looks just as pixelated as the
original but has a higher dpi (I also use this
sometimes to show blow-ups of details in the same
figure as the rest of the image). Once a journal,
actually a so called "top journal", wouldn't let
me get away with that, so I had to interpolate
(i.e: make up) the missing pixels.

Looks like the figure art department guys don't have physics education.

I am not sure this eases your pain though....

Steffen

At 17:49 06.08.2008, you wrote:

>Search the CONFOCAL archive at
>http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
>Is it just me, or does anyone else get annoyed when a journal
>requests higher resolution images for
>publication? Typical requests are "FigX is
>not at the required 300 dpi. We require a higher resolution version of this
>figure" or "Your cover submission is not at the required resolution, you must
>supply a higher resolution version?".
>Well no, I can't. I've acquired the image with
>an optimal pixel size to satisfy
>Nyquist-Shannon theorem. Just because you want to print the image at a
>size where it might look pixelated does not allow me to break the laws of
>physics. The result is invariably resubmission of a Photoshop upsampled
>version of the image, which yes looks less
>pixelated, but no, is not at a higher
>resolution. Presumably the publishers are just as capable of doing this as I
>am. [/whinge]

--
---------------------------------------------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
Head of light microscopy

Mail room (for letters etc.):
Marchioninistr. 15, D-81377 München

Building location and address for courier, parcel services etc:
Marchioninistr. 27, D-81377 München (Großhadern)

Phone: +49/89/2180-76509
Fax-to-email: +49/89/2180-9976509
skype: steffendietzel
e-mail: [hidden email]

Phillips, Thomas E.

Re: Resolution vs pixelation whinge

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

Even worse in my opinion, a major journal that I publish in requires Tiff formatted RGB images for review but once the paper is accepted, they want the final submitted images in CMYK. The conversion changes the images from what the reviewers approved but they never see them again. Crazy.

Thomas E. Phillips, Ph.D
Professor of Biological Sciences
Chair, MU Faculty Council
Director, Molecular Cytology Core
2 Tucker Hall
University of Missouri
Columbia, MO 65211-7400
573-882-4712 (office)
573-882-0123 (fax)
[hidden email]

http://www.biology.missouri.edu/faculty/phillips.html
http://www.biotech.missouri.edu/mcc/

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Steffen Dietzel
Sent: Wednesday, August 06, 2008 11:55 AM
To: [hidden email]
Subject: Re: Resolution vs pixelation whinge

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

been there, done that.

Hi Simon,

nope, it's not just you. I that situation I first
try to get away with upscaling with the nearest
neighbor algorithm with a power of two or four in
Photoshop. Looks just as pixelated as the
original but has a higher dpi (I also use this
sometimes to show blow-ups of details in the same
figure as the rest of the image). Once a journal,
actually a so called "top journal", wouldn't let
me get away with that, so I had to interpolate
(i.e: make up) the missing pixels.

Looks like the figure art department guys don't have physics education.

I am not sure this eases your pain though....

Steffen

At 17:49 06.08.2008, you wrote:

Grant MacGregor

Re: Resolution vs pixelation whinge

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I agree with the concerns and frustration. One potential solution is
for a few independent folks to band together, write a brief 'report'
with data that will help to educate the publishing houses, then to
find an editor at a suitable journal, who has a sympathetic ear and
ask that this be reviewed and published. Then, when this next
happens, you can forward the 'minimum dpi request issue' to the editor
of which ever journal you're dealing with, along with the citation or
reprint of your report. This is the sort of thing that is required to
educate and make a change in the publishing field.

Grant MacGregor D. Phil.,

Associate Director,
Optical Biology Core, Developmental Biology Center

Associate Professor,
Department of Developmental and Cell Biology,
Center for Molecular & Mitochondrial Medicine & Genetics,
Developmental Biology Center,

University of California, Irvine
2042 Hewitt Hall
Irvine, CA 92697-3940
e-mail [hidden email]

On Aug 6, 2008, at 10:08 AM, Phillips, Thomas E. wrote:

> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Even worse in my opinion, a major journal that I publish in requires
> Tiff formatted RGB images for review but once the paper is accepted,
> they want the final submitted images in CMYK. The conversion changes
> the images from what the reviewers approved but they never see them
> again. Crazy.
>
> Thomas E. Phillips, Ph.D
> Professor of Biological Sciences
> Chair, MU Faculty Council
> Director, Molecular Cytology Core
> 2 Tucker Hall
> University of Missouri
> Columbia, MO 65211-7400
> 573-882-4712 (office)
> 573-882-0123 (fax)
> [hidden email]
>
> http://www.biology.missouri.edu/faculty/phillips.html
> http://www.biotech.missouri.edu/mcc/
>
>
> -----Original Message-----
> From: Confocal Microscopy List
> [mailto:[hidden email]] On Behalf Of Steffen Dietzel
> Sent: Wednesday, August 06, 2008 11:55 AM
> To: [hidden email]
> Subject: Re: Resolution vs pixelation whinge
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> been there, done that.
>
> Hi Simon,
>
> nope, it's not just you. I that situation I first
> try to get away with upscaling with the nearest
> neighbor algorithm with a power of two or four in
> Photoshop. Looks just as pixelated as the
> original but has a higher dpi (I also use this
> sometimes to show blow-ups of details in the same
> figure as the rest of the image). Once a journal,
> actually a so called "top journal", wouldn't let
> me get away with that, so I had to interpolate
> (i.e: make up) the missing pixels.
>
> Looks like the figure art department guys don't have physics
> education.
>
> I am not sure this eases your pain though....
>
> Steffen
>
> At 17:49 06.08.2008, you wrote:
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>> Is it just me, or does anyone else get annoyed when a journal
>> requests higher resolution images for
>> publication? Typical requests are "FigX is
>> not at the required 300 dpi. We require a higher resolution
>> version of this
>> figure" or "Your cover submission is not at the required
>> resolution, you must
>> supply a higher resolution version?".
>> Well no, I can't. I've acquired the image with
>> an optimal pixel size to satisfy
>> Nyquist-Shannon theorem. Just because you want to print the image
>> at a
>> size where it might look pixelated does not allow me to break the
>> laws of
>> physics. The result is invariably resubmission of a Photoshop
>> upsampled
>> version of the image, which yes looks less
>> pixelated, but no, is not at a higher
>> resolution. Presumably the publishers are just as capable of doing
>> this as I
>> am. [/whinge]
>
> --
> ---------------------------------------------------------------------------------------------------
> Steffen Dietzel, PD Dr. rer. nat
> Ludwig-Maximilians-Universität München
> Walter-Brendel-Zentrum für experimentelle Medizin (WBex)
> Head of light microscopy
>
> Mail room (for letters etc.):
> Marchioninistr. 15, D-81377 München
>
> Building location and address for courier, parcel services etc:
> Marchioninistr. 27, D-81377 München (Großhadern)
>
> Phone: +49/89/2180-76509
> Fax-to-email: +49/89/2180-9976509
> skype: steffendietzel
> e-mail: [hidden email]
>

Julio Vazquez

Re: Resolution vs pixelation whinge

In reply to this post by Michael Herron

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal -

I agree with most points. However, I can also see reasons why journals would do this. For instance, It's not far-fetched to think that without some standards about image size and resolution, some Scientists would send sub-par images that would not be suitable for printing (printers do need at least 300 dpi for good quality, and a standard 512x512 image would then print at less than 2 inches). Also, I'd rather resample my image myself, so I may have some control over the final quality. I can also imagine people sending images in unusual formats, and we can't expect Journals to support every possible format out there (such as a DeltaVision of Odyssey scanner file, that I can imagine someone sending...).

Finally, while it is true that people tend to push work to someone else, it sometimes makes sense. It only takes a few seconds for our users to log in their microscope time and budget number, often while they're idling while their stacks are being collected, while it would be quite an investment in time for us to have to do all that record keeping for them and such... It takes only a couple of minutes to resample the six or so Figures needed for a paper (that maybe took one year or more to complete), while it would take quite a few man-hours for the journal to process the hundreds of images in any given issue. Someone obviously would have to pay for that too...

Following Picasso's example, it is sometimes useful to look at things from both sides...

Julio Vazquez

Fred Hutchinson Cancer Research Center

Seattle, WA 98109-1024

http://www.fhcrc.org/

===

On Aug 6, 2008, at 9:39 AM, Michael Herron wrote:

Search the CONFOCAL archive at http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal Modern management: Push the work to someone else.

On Aug 6, 2008, at 10:49 AM, Simon Walker wrote:

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

[whinge] Is it just me, or does anyone else get annoyed when a journal
requests higher resolution images for publication? Typical requests are "FigX is
not at the required 300 dpi. We require a higher resolution version of this
figure" or "Your cover submission is not at the required resolution, you must
supply a higher resolution version?".
Well no, I can't. I've acquired the image with an optimal pixel size to satisfy
Nyquist-Shannon theorem. Just because you want to print the image at a
size where it might look pixelated does not allow me to break the laws of
physics. The result is invariably resubmission of a Photoshop upsampled
version of the image, which yes looks less pixelated, but no, is not at a higher
resolution. Presumably the publishers are just as capable of doing this as I
am. [/whinge]

Michael J. Herron,  U of MN, Dept. of Entomology
  [hidden email]
     612-624-3688 (office) 612-625-5299 (FAX)

Stephen Cody

Re: Resolution vs pixelation whinge

In reply to this post by Grant MacGregor

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I couldn't agree more. Journal of Cell Biology (JCB) for these reasons has switched to the online version of their journal being the prime publishing format. If you triple stain, you probably use red, green and blue dyes. The image capture is usually with RGB filter sets. Your data is saved as RGB images. With JCB at least, you submit RGB, and they publish on line in RGB. The paper version is seen as of secondary importance, and it's up to the printer to work with the image to get it to print correctly. Presumably publishing online avoids much of the need for "upsizing" as well. Editorials on this matter have already been published in JCB.

They also have quite strict rules on what you can and can't do to an image. I don't want to open old debates, but I think declaring what was done, and having to submit raw images, as well as the final images to the reviewers and editors for inspection should be the preferred solution.

See editorial in JCB by Mike Rossner http://www.jcb.org/cgi/reprint/166/1/11 <http://www.jcb.org/cgi/reprint/166/1/11>

No commercial interest in JCB

Steve
Stephen H. Cody
Microscopy Manager
Central Resource for Advanced Microscopy
Ludwig Institute for Cancer Research
PO Box 2008 Royal Melbourne Hospital
Parkville, Victoria, 3050
Australia
Tel: 61 3 9341 3155 Fax: 61 3 9341 3104
email: [hidden email]
www.ludwig.edu.au/labs/confocal.html
www.ludwig.edu.au/confocal

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________________________________

From: Confocal Microscopy List on behalf of Grant MacGregor
Sent: Thu 07/08/2008 4:36 AM
To: [hidden email]
Subject: Re: Resolution vs pixelation whinge

Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I agree with the concerns and frustration. One potential solution is
for a few independent folks to band together, write a brief 'report'
with data that will help to educate the publishing houses, then to
find an editor at a suitable journal, who has a sympathetic ear and
ask that this be reviewed and published. Then, when this next
happens, you can forward the 'minimum dpi request issue' to the editor
of which ever journal you're dealing with, along with the citation or
reprint of your report. This is the sort of thing that is required to
educate and make a change in the publishing field.

Grant MacGregor D. Phil.,

Associate Director,
Optical Biology Core, Developmental Biology Center

Associate Professor,
Department of Developmental and Cell Biology,
Center for Molecular & Mitochondrial Medicine & Genetics,
Developmental Biology Center,

University of California, Irvine
2042 Hewitt Hall
Irvine, CA 92697-3940
e-mail [hidden email]

On Aug 6, 2008, at 10:08 AM, Phillips, Thomas E. wrote: