New open image format

[David Gutman]

Can you clarify what you mean re: low cost?  Will the code/product for
VIRMIK be released?  Or do you mean buying 3 microscopes is expensive... :-)


dg


On Wed, Jun 26, 2013 at 5:15 PM, Niels Werner Mortensen <nwm at sund.ku.dk>wrote:

>  Dear all,
>
>
> At the University of Copenhagen we are almost finished with a virtual
> microscopy project  named VIRMIK. This project accepts slides from the
> 3DHISTECH Pannoramic MIDI scanner, the Olympus VS120 scanner and (very
> soon) the Zeiss Axio Scan.Z1. This again means support for the MRXS, VSI
> and CZI file formats.
>
> In my experience all slide scanner vendors delivers a web service that
> support their own slide scanner but our VIRMIK solution accepts (or will
> accept) slide scanner formats from most vendors providing users with a
> common platform/service for publishing slides (with annotations) and
> creating Tests for examinations.
>
> But I would hardly call it a low-cost solution J
>
>
> Best regards,
>
> *Niels Werner Mortensen
> *IT Project Manager
>
> *Department of Biomedical Sciences
> *Faculty Of Health Sciences
> University of Copenhagen
> Blegdamsvej 3B,
> DK-2200 Copenhagen N
> Denmark
>
> TEL +45 35327457
> DIR +45 28757520
> MOB +45 28757520
> FAX +45 35327537
> Room 12.3.14
> *nwm at sund.ku.dk
> **bmi.ku.dk
> *
>
> -----Original Message-----
> From: openslide-users-bounces+nwm=sund.ku.dk at lists.andrew.cmu.edu [
> mailto:openslide-users-bounces+nwm=sund.ku.dk at lists.andrew.cmu.edu<openslide-users-bounces+nwm=sund.ku.dk at lists.andrew.cmu.edu>]
> On Behalf Of Dr. M. Weihrauch
> Sent: 26. juni 2013 14:39
> To: openslide-users at lists.andrew.cmu.edu; Alberto Perez-Bouza; M Omar
> Tariq
> Subject: New open image format
>
> Dear openslide-community:
>
> Yesterday I talked to a German microscope-expert, who builds a new
> microscope-scanner system with his company to target the
> "low-budget"-institutions (which cannot easily afford €120.000 for a Leica
> scanner e. g.). His machine will go to 83-100x, which would be especially
> great for me as a hematologist, who needs to do cytology. He is great on
> the technical part and the scanner prototype is almost done.
> He does not know much about the software side and I talked to him that my
> company can handle that for him.
>
> Now I would like to define an image format for his company that would be
> completely open for openslide. I learnt a lot about image processing /
> pyramids and tiles from Benjamin and John, but I dont understand the
> inside-concept of e. g. SVS, SCN, etc completely.
>
> What I believe should be the requirements:
>
> 1. The image format should be open (non-proprietary) 2. One file contains
> the complete image (pyramid) - so not as Zeiss, etc did it in folders 3.
> All zoom-levels should be included to give the user a very fast
> microscopy-experience (not like SVS with every 2nd zoom-level)
>
> My questions:
>
> 1. What is the format of choice? TIF? What is the format inside? JPEG?
> JPEG2000?
> 2. Is it necessary to pretile the 256x256 tiles and how are they accessed
> "from the outside"?
> 3. If there is a complete image pyramid inside - comparable to the
> deepzoom-directory structure, do we need an extra thumbnail?
> 4. Is there already a free, open, well-documented format that we could tap
> into?
>
> I appreciate any suggestions.
>
> Martin
>
>
>
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-- 
David A Gutman, M.D. Ph.D.
Assistant Professor of Biomedical Informatics
Senior Research Scientist, Center for Comprehensive Informatics
Emory University School of Medicine
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