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Images and other data from the JUMP Cell Painting Consortium
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Locating data obtained from channels associated with different cellular components #119

Open EmiliyaStol opened 2 months ago

EmiliyaStol commented 2 months ago

I was wondering, in the cpg0016-jump dataset, where can I locate the image data associated with each of the five channels and six fluorescent dyes described in the Chandrasekaran et al. 2023 preprint. In the Images.csv files, I have found columns that are labeled with "AGP", "DNA", "ER", "Mito", and "RNA". I was wondering where can I find the documentation information for these columns in the Images.csv files.

williamdee1 commented 2 months ago

Hi @EmiliyaStol , not an official response, but I have functions for loading the raw image and/or the mage-based profile data for this work on my GitHub repo at: https://github.com/williamdee1/Cell-Vision-Fusion. Hopefully they might be of some help.

shntnu commented 1 month ago

If you are looking for the meaning of these channel names, please look up https://github.com/carpenter-singh-lab/2023_Cimini_NatureProtocols/wiki/What-do-Cell-Painting-features-mean%3F

If you are looking to figure out how to download these files please use https://github.com/broadinstitute/cpg/tree/main/cpgdata

Also see the "Load Images" section of this notebook https://github.com/jump-cellpainting/datasets/blob/main/sample_notebook.ipynb to orient yourself