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flimfit / FLIMfit

State of the art fluorescence lifetime imaging analysis software
http://flimfit.org
GNU General Public License v2.0
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Loading Abberior Instruments .msr Files #365

Open AndreasSchoenle opened 3 years ago

AndreasSchoenle commented 3 years ago

Loading AI .msr/.obf files currently fails with the message 'No time resolved data'.

Imspector holds time resolved data internally as LT,X,Y... stacks. Our BioFormats reader uses 'moduloZ' to load the image correctly with the 'lifetime' dimension as planes. How does FLIMfit recognize a stack with time resolved data? Are there specific meta-data tags we need to have in place, so it will recognize the situation?

Alternatively, I believe I could produce an MR that would allow reading the files directly, using MATLAB tools that come with every Imspector Installation. Would it be acceptable to allow configuring this location and using the .m and .mex files there if present. Otherwise FLIMfit could fall back to the bioformats approach. The advantage would be that multiple FLIM stacks could be recognized as channels and that reading would be significantly sped up.

seanwarren commented 3 years ago

Hi Andreas,

FLIMfit should be able to read ome.tif data where the modulo dimension used has a type annotation containing the string 'lifetime'. I'm not sure if this has been tested with real data other than moduloT though.

I'm afraid I'm not actively working on FLIMfit so I don't think I'd be able to help with the second approach. However it should be noted that compiled matlab executables can't use external .m or mex files (as far as I understand) so this would only work with versions of FLIMfit run from within Matlab.

Best regards, Sean

imunro commented 3 years ago

Hi Andreas Am i to understand that you have modified the bio-formats. .msr reader to handle FLIM data? If this has happened recently it may simply be that the version of bio-formats in FLIMfit need to be updated.