[SciPy-User] Microscopy TIFF files

[Chris Weisiger]

Apologies for the somewhat off-topic nature of this post, but I'm not aware
of any more-pertinent communities. Please feel free to redirect me
elsewhere.

Our microscope control software currently outputs files in MRC format. In
the interests of interoperability with the rest of the microscope
community, it would be nice if we had TIFF support as well. There exist
programs that convert MRC to TIFF and vice versa, but a native solution is
always preferable if only to reduce the number of steps involved.
Personally I have next to no experience with the TIFF format as used in
microscopy, so I'm starting out by doing some research.

There exist Python libraries for writing TIFF files, of course; my concern
with them is that they perform writes "atomically" (that is, the entire
image data is written at once). This requires you to *have* all of the
image data at the time you perform the writing, and means that for large
datasets you need lots of RAM (to hold the dataset in memory) and lots of
time (to write the data to disk all at once). I prefer to stream data to
disk as it comes in, which greatly reduces RAM requirements and also
improves performance by allowing writes to happen in parallel with data
acquisition. However, I'm not aware of a Python/TIFF library that allows
for this.

I've taken a brief look at the TIFF spec (
http://partners.adobe.com/public/developer/en/tiff/TIFF6.pdf ). Is this
actually the same format that is used for microscopy data? I've seen
OME-TIFF as well (
http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/ ) but I
don't know how widely it is supported (though I do see that Micro-Manager
supports it). The Adobe TIFF standard specifies a limit in filesize of 4GB,
which could be potentially troublesome. I don't know if OME-TIFF has
similar limitations.

I'd appreciate any advice on this topic. I'm missing a lot of context, I'm
sure, which will make it a lot harder to implement a working and useful
solution.

-Chris
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