New open image format

[Niels Werner Mortensen]

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 ☺


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

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-----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] 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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