Re: Axiovision: Panorama and Multidimensional acquisition

[Viereck, Friedhelm]

- Commercial interest -
Hi Eric,

I'm working as a product manager for AxioVision...

I'm sorry but there is no way to bring a multichannel image into a "Panorama
generated" image, because the "Snap F2" button performs a snap of a single
channel only.

Sorry for the inconvenience,
Friedhelm

On Wed, 30 Jun 2010 13:46:26 +0200, Eric Scarfone <[hidden email]> 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: [phone],
>Cell: [phone]
>Fax: [phone]
>
>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: [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 )
>> >
>>
>