broadinstitute/luad-cell-painting

Repository for analysis of CellPainting data in the LUAD dataset

luad-cell-painting's Issues

No Cells to Profile

I have managed to follow profiling steps 1-3 (requirements installation, data download, data preparation) without any apparent issues.
However, when I run the command shown in step 4 to extract features, I encounter 2 issues:

1. First, I get KeyError: label_smoothing. This was easily resolved by adding "label_smoothing": 0.0 under train: model: params
2. After resolving issue 1, the profile command runs but says No cells to profile for each image (ex: No cells to profile: .//outputs/efn_pretrained/features//52649/p10/3.npz)

I have tried running step 4 with both the latest commit of DeepProfiler as well as commit c91b9d8 which is mentioned in this repository.

Why is DeepProfiler not able to detect any cells to profile?

Annotate the legend for sc UMAP plots where label = plate

From https://broadinstitute.github.io/luad-cell-painting/variants/BRAF_p.W450L/

It's not obvious what the numbers 52662 etc refer to (they are plates)

Update biorxiv link when available

luad-cell-painting/index.html

Line 46 in 7123bf1

<li class="flow-text">Here is a <a href="#">link</a> to the preprint in bioRxiv with more