This is a data repository storing instructions on how to:
- Download the Cell Health Cell Painting dataset (IDR0080)
- Perform segmentation
- Define a new single-cell focused dataset of isolated single cells
- Compute single cell embeddings
- Using CellProfiler
- Using DeepProfiler
- Process both kinds of embeddings using pycytominer
These data were originally used as part of the publication Way et al. 2021.
Predicting cell health phenotypes using image-based morphology profiling Gregory P. Way, Maria Kost-Alimova, Tsukasa Shibue, William F. Harrington, Stanley Gill, Federica Piccioni, Tim Becker, Hamdah Shafqat-Abbasi, William C. Hahn, Anne E. Carpenter, Francisca Vazquez, and Shantanu Singh Molecular Biology of the Cell 2021 32:9, 995-1005
Note: Not all data are stored in this repository. Some data are too large.
See 0.image-download
for more details.
# Make sure to follow all steps in `0.data-download/README.md` first
# This includes one step to test and confirm download configuration
cd 0.image-download
bash download_images.sh