nilseling
commented
1 year ago Hi @chinoeke
the .h5 files generated for Ilastik training contain all channels that you specified in the panel file. In the lower left part of the Ilastik user interface there is a menu item called "Raw input". There you can switch through the different channels. The order of the channels can be seen in the _ilastik.csv files in the analysis/ilastik folder. Please refer to the documentation for more info.
Hi, I was wondering if there was a way to generate a .h5 file for each of the channels that are originally present in the .mcd file. For example, our panel includes 191_Ir, CD20, CD4, CD3, etc and the .h5 output for Illastik only seems to contain the 191_Ir marker for the visual. I was wondering if there was a way to create unique .h5 files for a given marker to visualize in Illastik as a separate .h5 image?
Thanks!