CellProfiler-plugins
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CellProfiler
RunDeepProfiler
- [ ] Work out a strategy for installing CellProfiler and DeepProfiler in the same python environment
- [ ] Work out how to run DeepProfiler repeatedly with the same experiment_name but changing image input
Work out how to run DeepProfiler repeatedly with the same experiment_name but changing image input
- So DeepProfiler needs an index.csv file that contains the plate, well, site, and filename for each channel. I created 2 index.csv files with different images as the input. Then, I called
python3 deepprofiler --root=/home/ubuntu/project/ --config filename.json --metadata index.csv --exp experiment_name profileand only changed the --metadata filename. - DeepProfiler runs fine with the same experiment_name but changing index.csv file.
Does this work with the citation generator? Would you please add it into the supported plugins doc? https://github.com/CellProfiler/CellProfiler-plugins/blob/master/documentation/CP-plugins-documentation/supported_plugins.md
Does this work with the citation generator? Would you please add it into the supported plugins doc? https://github.com/CellProfiler/CellProfiler-plugins/blob/master/documentation/CP-plugins-documentation/supported_plugins.md
Yes, it works with the citation generator. Documentation added. Just added a page for RunDeepProfiler as well so we can edit instructions as we change stuff.
@fefossa The install instructions you added don't match the strategy we describe in https://github.com/CellProfiler/CellProfiler-plugins/blob/master/documentation/CP-plugins-documentation/using_plugins.md
Does it not work to use the setup.py-based strategy that Callum has set up? If not, we need to add a description to the using_plugins page telling people to follow alternative instructions for RunDeepProfiler. If it does, can you add the dependencies to setup.py and then I think the whole first section of RunDeepProfiler.md doesn't need to exist as it is a duplication of using_plugins?
@fefossa The install instructions you added don't match the strategy we describe in https://github.com/CellProfiler/CellProfiler-plugins/blob/master/documentation/CP-plugins-documentation/using_plugins.md
Does it not work to use the setup.py-based strategy that Callum has set up? If not, we need to add a description to the using_plugins page telling people to follow alternative instructions for RunDeepProfiler. If it does, can you add the dependencies to
setup.pyand then I think the whole first section of RunDeepProfiler.md doesn't need to exist as it is a duplication ofusing_plugins?
We can use setup.py yes (I'll push that), but there's a git clone and pip install for DeepProfiler itself before doing the setup.py in CP-plugins; do we think these instructions can go inside using_plugins as a note? @ErinWeisbart
Now I've added the option to export the results into a CellProfiler format (within the CSVs).
Because I'm on Windows I still cannot test on analysis mode if the files are being written to the spreadsheet, but I can see on the display window below that the way I'm getting the measurements looks correct.
If you could test on Mac @bethac07 thank you!
@fefossa Sorry, no, I can't get it to run on my computer unless/until we go with the Docker version, so I can't check, sorry! We'll need someone with a non-M1 mac - which might of the current team just be @gnodar01 , we can hopefully have him check later this week!
