[ome-users] Problem decoding Slidebook files in bioformats 4.4

[Dmitry Fedorov]

Hi Melissa,

Thank you for the quick response!

>> 1) The problem happening now is that in many images each individual
>> plane of each multi-dimensional series is decoded as a separate series
>> and so in a file with for example 2 time series with 30 frames I get
>> instead 60 2D series. So the number of series decoded now is exactly
>> the cumulative number of individual planes available in all series.
>
> That is not unexpected.  The idea is that now you can at least see all
> of the images.

Hm, so no way to group them into multi-dimensional series anymore?
This format seems like a pain in a butt. I looked into the code and
saw there was a lot of heuristics. How would you guess those series
before? This would be, in some sense, a show stopper for me since
microscopists produce these slidebook files with tens of series in
them and each series may have 20-30 time points, very hard to group
that by hand.

> OK, that should be fixed for 4.4 then.  I only see this problem with
> 3-25-11.sld; does that sound right?

That's right. I do have many more images that I can share if needed or
I can simply do more testing here and report results.

> Again, something that we'll fix for 4.4 - not sure how that
> slipped by in testing.  As far as I can tell, it's just cxs-11-2.sld
> that exhibits that problem, right, and not any of the other files that
> you have sent?

Right, only this image in the uploaded set had actual problem in plane
geometry. Again, I can share more images with full geometry info,
would take me a day or so to prep a document and package files. Could
shoot for Monday.

Melissa, could you also give me some pointers to how should I build
the new source? Are you using ant to build? If I fetch the code off of
your github repos would it be buildable? I could try to also look at
this stupid Slidebook format and try to help you get this hammered out
if you could direct me a tiny bit on building the stuff. Thank you!

-dmitry