[ome-devel] Fwd: Bio-Formats/C++/Python

[Jason Swedlow]

Dear All-

Michael Held (ETH Zurich) wrote this comment about Python  
implementation of Bio-Formats.  Any comments, feedback, or other  
similar experiences out there?

In general, our own preference would be to ensure there is a  
**single** resource for file format translation.  Maintaining more  
than one just duplicates effort on something that is very difficult  
and tedious, even at the best of times.  While I do agree that making  
a Python HCS-only reader is possible, and probably not terribly hard,  
it's the maintenance and updates of this resource that is really time  
consuming in the end.  Until the various vendors coalesece around a  
single standard, that is just true.  So, if possible, let's reuse as  
much as we have, and work together on a **single** resource, whatever  
it is.

Regarding the timings quoted, I'll let Curtis respond, but something  
sounds pretty wrong.

Comments??

Cheers,

Jason




Begin forwarded message:

> - The access to image formats via the Java-based bioformats has a  
> big performance issue when accessing from C++/Python (or any non- 
> Java system). People at Sybit/Switzerland tried there own Jace-based  
> wrapper via BLITZ (libBlitzBioFormats), but had to improve Jace  
> first, since the import of ONE! 512x512 image took ~60s.  
> CellProfiler has its own way by launching a Java VM from Python.
> The simple question behind this is: how to make the access to  
> bioformats simpler and faster, which is an issue for the growing  
> Python community.
> I see two solutions for that.
> 1. Using the CellProfiler implementation as a standalone package.  
> Performance is unknown to me. Short term issue.
> 2. I was wondering with Carolina Wählby from the Broad how much work  
> it really is to collect the most needed formats for HC/HT screening  
> and rewrite bioformats as a pure C++ library using the highly  
> developed libtiff/libpng/libjpeg while providing a Python interface.  
> For TIFF derivate formats (and there are many) this would be a  
> simple job and there a C++ libs out there solving the problem already.
> I guess CellProfiler has the same problem. Any opinions?



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