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hilldr / permeability_imaging

convert time-lapse VSI-format microscopy images into a table containing the mean, median, minimum, and maximum intensity
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barrier-pipeline.sh can't find ./bin/ij.jar #1

Closed hilldr closed 5 years ago

hilldr commented 5 years ago 
david@spence-linux:~$ xvfb-run -a ./permeability_imaging/src/barrier-pipeline.sh /media/david/Elements/live_imaging/190117/ microbe_panel/results/barrier/
[START] converting VSI files in /media/david/Elements/live_imaging/190117/ to tif files for experiment 190117
Error: Unable to access jarfile ./bin/ij.jar
[FINISHED] converting VSI files to TIF
[START] Computing fluorescence intensity values...
This may take a while. Now would be a good time for a coffee break.
ls: cannot access '/media/david/Elements/live_imaging/190117//*.tif': No such file or directory
ls: cannot access '/media/david/Elements/live_imaging/190117//*.tif': No such file or directory
0 of 0 tif files remaining in /media/david/Elements/live_imaging/190117/
Error: Unable to access jarfile ./bin/ij.jar
rm: cannot remove '/media/david/Elements/live_imaging/190117//*.tif': No such file or directory
[FINISHED] Computing fluorescence intensity values
[IMAGE PROCESSING FINISHED]
Printing first 10 lines of output
#################################
Filename        Area    Mean    Min     Max     Median
hilldr commented 5 years ago

Need to start in permeability_imaging dir