I ran cell density on about 100 images but neglected to configure the .csv file name before I started the run. Since I also neglected to save the project before I started the run, I couldn’t kill the process and restart with the .csv file name configured, so I let it run all night. So now I have a bunch of .h5 files that contain the density numbers but in a form I can’t access as a table. Do I have to write Python code to generate the .csv file from the .h5 files? If so, where is the documentation on the .h5 file format? Has anyone else run into this problem and already written a Python script to do this?
PS: It seems rather strange that there is no default .csv file for cell density processing since one is obviously trying to get a single number per image, not a bunch of .h5 files. Indeed, I found no way to inhibit the creation of .h5 (or other image format) files since I don’t want them. Moreover, when I tried doing a batch process it didn’t seem to generate a .csv file even when configured to do so.