Re: Preparing figures for publication --PPI vs DPI

Posted by Eric Scarfone on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Preparing-figures-for-publication-PPI-vs-DPI-tp5232491p5239353.html

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: [phone],
Cell: [phone]
Fax: [phone]

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: [phone]
> >
> >
> >
> > 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
>
> [phone] (German Mobile)
> [phone] (Work phone at MPI-CBG)
> [phone] (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 )
>