Posted by
Eric Scarfone on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Preparing-figures-for-publication-PPI-vs-DPI-tp5232491p5239417.html
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 )
> >
>