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khanlab / SPIMprep

A Snakemake workflow for pre-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
MIT License
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Integrate QC report generation into the workflow #40

Closed BenGros closed 1 month ago

BenGros commented 2 months ago

QC reports are generated for flat-field correction, whole slice viewing and a 3D volume rendered model. These reports are accessible through a locally run HTML file. Also added a script for producing test datasets that are subsets of an original dataset.

The ff correction and whole slice viewing use locally stored images that are created. The 3D viewer generates a JSON file containing the data and generates the model from that.

akhanf commented 2 months ago

I added the commits I made to fix some things and an example of splitting off the rule..

Karl5766 commented 1 month ago

Code looks good to me, but some documentation could be better. Can you add documentation to briefly describe how to run the .js files? In docs/ or/and using docstring """ """ at the top of the file (as in PEP 257) would be fine.

Also may I ask what's the purpose of the dataset created by testing/create_test_dataset.py? I was looking around but not sure what it's used in. I think it may be good to add a description of this as docstrings as well.

Other .py files can benefit from docstrings as well but I think these two will be most helpful.

Edit: Just saw the issue to add documentation - if it's not part of the PR and will be done in the future then I believe we can merge the PR now.

BenGros commented 1 month ago

I can add the documentation for running the js files in this pull request. And the create_test_dataset.py is used to create a subset of a large raw dataset to be able to test the workflow quickly.

akhanf commented 1 month ago

@BenGros this looks good to merge now, when you're ready you can do a Squash and Merge to clean the history, and provide a commit message and summarizes the PR.