RunDeepProfiler

[fefossa]

No description provided.

[callum-jpg]

• 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

[fefossa]

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 profile and only changed the --metadata filename.
• DeepProfiler runs fine with the same experiment_name but changing index.csv file.

[bethac07]

Awesome! A couple tiny comments around print statements, hardcoding of Windows-style paths, and subprocess nuance, but otherwise, works great!

[bethac07]

I approve on the code basis, but someone else (@ErinWeisbart ?) should check if anything else is needed on our list of things we ask for in a submission now

[ErinWeisbart]

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

[fefossa]

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.

[ErinWeisbart]

@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]

@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?

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

[fefossa]

@ErinWeisbart instructions are updated!

[fefossa]

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!

[bethac07]

@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!

[bethac07]

Actually, @ErinWeisbart, do you have a non-M1 mac?

[ErinWeisbart]

I do have a non-M1 Mac. I can test this later today. Stay tuned...