Scripts for Current Protocols paper.
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To run the notebooks (support notebooks and Basic_Protocol_2), use Google Colab or create an environment using environment.yml file;
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Clone this repository and cd to the folder;
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Open Anaconda prompt and paste the following:
conda env create -f environment.yml -
Will create an environment with the dependencies specified. To activate:
conda activate interpret_profiles
To visualize random or representative cell in a given group and field of view, make a copy of the notebook in your Google Drive and follow the instructions available in the Basic Protocol 2 [1]:
Please cite our paper if using this repository
[1] Garcia-Fossa F, Cruz MC, Haghighi M, de Jesus MB, Singh S, Carpenter AE, Cimini BA. Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization. Curr Protoc. 2023 Mar;3(3):e713. doi: 10.1002/cpz1.713. PMID: 36921124; PMCID: PMC10027367.