Multiplane and fluorescence API design
sucaet at histogenex.com
Tue Jul 10 03:56:12 EDT 2012
For those of you who are interested in this, it may be useful to play
around with some of the software that handles these filetypes (and
fluorescence imaging in itself). One such package that anyone can download
is AxioVision LE, which is available at http://www.zeiss.de/axiovision.
I've submitted four ZVI sample datasets to Benjamin yesterday. That in
combination with the files from Mailly Philippe should help you get
started, to appreciate what common tasks and operations are performed on
Another thought I've had: does the upcoming DICOM 145 format say anything
about this? As this WILL be the standard in the future (if the evolution
in radiology is any guide), it may be desirable for OpenSlide to model any
new functionality after DICOM, if they have any notes on such functions
Just my two cents,
From: Benjamin Gilbert <bgilbert at cs.cmu.edu>
To: openslide-users at lists.andrew.cmu.edu
Date: 09-07-12 20:01
Subject: Multiplane and fluorescence API design
openslide-users-bounces+sucaet=histogenex.com at lists.andrew.cmu.edu
Hamamatsu VMS and Zeiss ZVI both support multiplane images, and MIRAX
and ZVI both support fluorescence imaging. Either or both of these
features would require additions to the OpenSlide API. Consistent with
the rest of OpenSlide, any additional API should be as simple as
possible but not too much simpler.
I am interested in any comments on what an API for these features should
look like. Off the top of my head, the design issues include:
- For fluorescence images, is it reasonable to return only one channel
per API call?
- What principal metadata should be associated with each channel? (Is
it sufficient to provide a short name such as "Cy3"?) With each focal
- Can we assume that every focal plane and fluorescence channel at a
particular pyramid level has the same pixel dimensions?
- Should alpha be treated as just one of the channels, or should it be
returned alongside each channel? MIRAX could conceivably discard
different tiles in different channels. (I'm not sure whether the format
actually supports this, however.)
- Will every channel exist on every focal plane and pyramid level? If
not, is it sufficient to return fully-transparent alpha for the missing
- Is it critical to support more than 8 bits per channel? This would
require (non-trivial) additional support from Cairo and pixman.
- How should existing API behave when confronted with a fluorescence
image? Should openslide_read_region() return the first three
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