Multiplane and fluorescence API design

[Yves Sucaet]

Hi list,

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 
these data.

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 
yet.

Just my two cents,

Yves



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
Sent by:        
openslide-users-bounces+sucaet=histogenex.com at lists.andrew.cmu.edu



Hello list,

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 
plane?

- 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 
channels?

- 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 
fluorescence channels?

--Benjamin Gilbert
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