Profiling using Pycytominer

Perform image-based profiling using Pycytominer application [a].

Materials

1. Presentation about single-cell data to well-aggregated data:

   • video in PT

2. Retrieve information from a database file from CellProfiler:

   • video in PT and Q&A

   • Jupyter notebook 1_Samples_retrieval_database.ipynb

3. How to perform profiling using Pycytominer:

   • theory about profiling and pycytominer, video in PT

   • practice video: using Pycytominer with Jupyter notebook and Q&A

   • Jupyter notebook 2_AggAnnNormFeat.ipynb

a. Serrano, E., Chandrasekaran, N., Bunten, D., Brewer, K., Tomkinson, J., Kern, R., Bornholdt, M., Fleming, S., Pei, R., Arevalo, J., Tsang, H., Rubinetti, V., Tromans-Coia, C., Becker, T., Weisbart, E., Bunne, C., Kalinin, A. A., Senft, R., Taylor, S. J., Jamali, N., Adeboye, A., Abbasi, H. S., Goodman, A., Caicedo, J., Carpenter, A. E., Cimini, B. A., Singh, S., & Way, G. P. Reproducible image-based profiling with Pycytominer. https://doi.org/10.48550/arXiv.2311.13417