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

[Melissa Linkert]

Hi Dmitry,

On Fri, Jul 06, 2012 at 12:26:25AM -0700, Dmitry Fedorov wrote:
> 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, I've put in a fix which seems to work for the files that you have
sent already, so once the 4.4 release is out those files should just work.

> > 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.

Double-checking 3-25-11.sld in the free Slidebook viewer [0], I definitely
see 3 channels.  Can you please verify that that is actually correct?

> > 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.

OK, this is fixed on a new branch and will be in the 4.4 release at the
end of the week.

> 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!

Instructions for building from source are here:

http://loci.wisc.edu/bio-formats/source-code

Regards,
-Melissa

[0] https://www.slidebook.com/reader.php; note that one can export
OME-TIFFs from this software, so you might consider that as another
alternative.

> -dmitry