Multiplane and fluorescence API design

Benjamin Gilbert bgilbert at
Mon Jul 9 14:01:00 EDT 2012

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 

- 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 
fluorescence channels?

--Benjamin Gilbert

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