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Ticket Resolution Summary Owner Reporter
#1 fixed Leica Reader openBytes() Exception somebody callan

Reported by callan, 13 years ago.


The Leica reader currently throws and exception when the openBytes(String id, int no, byte[] buf) method is called.

#2 fixed Bio-Formats Importer plugin loses some channels when merging melissa curtis

Reported by curtis, 13 years ago.


When using "Merge to RGB" with the Bio-Formats Importer plugin, datasets with more than three channels have some of their channels dropped. For example:

  • data/ics/nico/rotifer488spectral.ics: 32-channel dataset. Produces three RGB images (nine channels of information) when merging is enabled, with 23 channels missing.
  • data/leica-lif/fabrice/test 1.lif: 4-channel dataset. Produces an RGB image, dropping the fourth channel.

Proper behavior in these cases is up for debate, but I would suggest opening each "triple" of channels in its own window. So for rotifer488spectral, you would get 11 windows, with the first 10 being RGB, and the last being grayscale. With test 1, there would be 2 windows, with the first being RGB and the second being grayscale.

#4 fixed Bio-Formats native solution curtis curtis

Reported by curtis, 13 years ago.


Many developers, especially those working on applications for acquisition (e.g., Nico Stuurman and Nenad Amodaj), could benefit from an easy way to access Bio-Formats from native code. Since most of the I/O is done with our own classes (RandomAccessStream, RAFile, etc.) it should be fairly straightforward to port Bio-Formats to C++, though still a substantial amount of effort.

We would also need a native version of the OME-XML library (org.openmicroscopy.xml), but that port is largely a matter of replacing instances of Java DOM library usage with a C++ DOM library such as Microsoft's DOM implementation.

How to maintain two parallel implementations is another matter. SWIG is probably not the answer because it merely wraps C++ code with Java native bindings.

A possibility along different lines might be to point developers to something like  NewJ, a native Java implementation allowing easy porting of Java to C++, but unfortunately that solution is not free, and would restrict adoption. Or  GCJ might be useful, as it can  compile Java to native code, but my understanding is that such code is incompatible with Microsoft Visual C++.

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