CSBDeep / CSBDeep_fiji

BSD 2-Clause "Simplified" License
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Run plugin from command line #13

Closed HedgehogCode closed 5 years ago

HedgehogCode commented 6 years ago

Running the plugin from the command line doesn't work because the result isn't shown until clicking somewhere with the mouse.

Example script:

cd /path/to/Fiji.app
./ImageJ-linux64 --ij2 -macro ~/CARE_denoise.ijm

Example macro:

open("~/image.tif");
run("3D Denoising - Planaria", "datasetview=net.imagej.display.DefaultDatasetView@6ca6979e ntiles=16 overlap=32");
selectWindow("result");
saveAs("Tiff", "~/image_denoised.tif");
run("Quit");

@tboo, thank you for reporting this bug!

frauzufall commented 5 years ago

Should not be an issue anymore. There is also an example script.