Add analysis notebook using MCMICRO

erindiel commented 3 months ago

This notebook covers an example of image analysis using fluorescence WSI data from IDC as input to MCMICRO. Some caveats include:

Nextflow and Docker need to be installed, as they are requirements for running MCMICRO. To my knowledge, Docker cannot be used within Google Colab, so these notebooks must be downloaded and run locally.
As noted in https://github.com/ImagingDataCommons/IDC-Tutorials/pull/67 commands like wget will not work on Windows, so some sections may need alternatives provided.
MCMICRO does not appear to support DICOM as input, given the expectations for multi-file filesets https://mcmicro.org/troubleshooting/faq.html#q-mcmicro-doesnt-seem-to-recognize-my-file-format-how-do-i-tell-it-what-files-to-look-for For this reason, the IDC DICOM data was converted to OME-TIFF before running the analysis. This has the advantage of optionally cropping the analysis input for quick testing.

Note that the markers.csv and params.yml files needed for MCMICRO analysis are included in this PR as well.

cc @melissalinkert @dclunie @fedorov

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DanielaSchacherer commented 2 weeks ago

Hey Erin, I am Daniela, also part of the IDC team and Andrey asked me to check out your notebook and let you know my feedback! First of all, MCMICRO seems to be a pretty cool tool, that I did not come across so far. I tried to run the notebook locally on Windows and Linux. On Windows I was not successful unfortunately, s5cmd and docker did not work at all. However, on Linux, I was able to run your notebook with some adaptations (had to run part of the code from the command line instead from within the notebook).

I agree with all your points mentioned above. I think it could be valuable to have a list of requirements (nextflow, docker, java...) and maybe separate notebooks for Windows and Linux (can't say anything about MacOS). Alternatively, notebooks could be converted to a script + README, that explains what to expect from the code.

fedorov commented 2 weeks ago

@DanielaSchacherer thank you for the review!

@erindiel I am working on my review, and adding some small features to idc-index to help simplify some steps. I will follow up shortly.

DanielaSchacherer commented 2 weeks ago

As an update to what I had to adapt in the code: I had to manually create the folder /raw in MCMICRO-example-IDC/OME-TIFF and move markers.csv into MCMICRO-example-IDC/OME-TIFF. I guess that's not something I was supposed to do, is it?

ImagingDataCommons / IDC-Tutorials

Add analysis notebook using MCMICRO #69