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pelkmanslab / iBRAIN_BRUTUS

A version of canonical iBRAIN (2015) deployed on BRUTUS cluster
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Problem with Nikon image renaming/handling #39

Closed victoriagreen closed 8 years ago

victoriagreen commented 8 years ago

iBRAIN is not correctly renaming images from the Visiscope placed in a Nikon folder. Not renaming .stk files to .tiff, so no conversion to .png or processing to MIPs. See project here for example (and I have two more examples run on different days): /Volumes/biol_uzh_pelkmans_s5/Data/Users/Vicky/iBrain/160601_NSP5movie1

ewiger commented 8 years ago

the problem is in 

renameImages: (360) files have been processed (using bulk copy operation)'
unpackStack: OutputDir for the unpacked STK images is '/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Vicky/iBrain/160601_NSP5movie1/TMPNKDIR'
readNDFile: processing input directory '/BIOL/sonas/biol_uzh_pelkmans_s5/Data/Users/Vicky/iBrain/160601_NSP5movie1/NIKON'
unpackStack: dataset has been recognized as an acquisition with ZDimension'
unpackStack: inventarising .stk files in provided directory (strOutputDir)'

ans =

unpackStack: unpacking the 1. of 360 stk files'

Undefined function 'tiffread' for input arguments of type 'char'.

Error in microscopetool.nikon.unpackStack (line 77)
            sctSTKFile = tiffread(cellFp2Unstack{i,1})';

Error in microscopetool.nikon.renameImages (line 151)
microscopetool.nikon.unpackStack(strOutputDir, strInputDir, strOutputDir);