[ome-devel] bfconvert 5 produces 16-bit tiff files that cannot be read by freeimage

[Tjelvar Olsson (JIC)]

Dear OME,

I have for some time now been finding myself switching back to bfconvert version 4 when dealing with 16-bit microscopy images.

The reason for this is that bfconvert version 5 produces tiff images that cannot be parsed by the freeimage library.

Today I thought I'd spend a little bit of time trying to work out what is going on and send a query to your mailing list.

The error that I get from freeimage is:

FreeImage error: Unable to handle this format: bitspersample = 16, samplesperpixel = 1, photometric = 3

I suspect that this has to do with the photmetric flag, which I don't really know anything about.
However, looking through the freeimage source code I think it can be traced to the
"IsValidBitsPerSample" function on line 1079

https://github.com/imazen/freeimage/blob/master/Source/FreeImage/PluginTIFF.cpp#L1097

In particular the check for the whether or not the "photometric" is a "PHOTOMETRIC_PALETTE" on line 1111.

https://github.com/imazen/freeimage/blob/master/Source/FreeImage/PluginTIFF.cpp#L1111

Inspecting the content of the TIFF files generated using bfconvert it seems that one difference between version 4 and 5 is that the former has a photometric interpretation "BlackIsZero" and the latter "RGB Palette".

Was this change in going from version 4 to 5 intentional?
What was the rationale?

I would love to be able to use newer versions of bfconvert on 16-bit micoscopy files and parse the files using freeimage.

Do you think this will be possible in the future?

Versions used here:

Version: 4.4.2
VCS revision: c2322fc
Build date: 25 August 2012

Version: 5.0.6
VCS revision: 33b1150
Build date: 10 November 2014

Kind regards,

Tjelvar


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