Multiplane and fluorescence API design

Tue Jul 10 11:06:27 EDT 2012

Greetings!

Benjamin, further investigations are needed, namely I require a
large sample to answer most of your questions, because for all 6 samples
I saw, there is only
one resolution picture (1388x1040 pixels), and yes, all focal planes and
fluorescent channels
grayscale images are same resolution. There seems to be no combined
color image inside the
file. But this is only conclusions based on 6 similar type of samples,
so I'll be checking that.

- For fluorescence images, is it reasonable to return only one channel
per API call?

This is absolutely certain at this point, since, what can be seen
clearly from examples, the
different fluorescence images can be absolutely different, nothing in
common. And same
applies to the focus layers. The distance between layers in um is also
stored in the file.

- Is it critical to support more than 8 bits per channel?  This would
require (non-trivial) additional support from Cairo and pixman.

This seems to be true, but this conclusion is only based on the fact
that the Zeiss native software
exports these images into 24-bit color jpegs, which is equivalent to
8-bits of data per pixel. However,
the file format itself does not seem to limit the data to 8-bits per
grayscale image.

- How should existing API behave when confronted with a fluorescence
image?  Should openslide_read_region() return the first three
fluorescence channels?

I think this behaviour is reasonable and simplest to implement. However,
I'm pretty sure that the
color of every layer is stored in the file format, so it's equally
possible to return all channels in the
exact same form as it was intended by the person who saved this file.

- You will probably want to take a look at libgsf.

I will take a look, thanks.

BTW, is there a GUI frontend I can use to test the OpenSlide API? I
can't seem to find any.

Yves: I will install AxioVision tomorrow the first thing in the morning...

Best regards,

-Alexandre Kharlamov

On 07/10/12 13:56, Yves Sucaet wrote:
> 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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