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2022_Cimini_NatureProtocols

DOI

This repo contains supporting analyses and files for Cimini et al "Optimizing the Cell Painting assay for image-based profiling".

Experiment metadata

This paper contains a large number of analyses taken from many experiments over the course of more than a year. We have endeavored to add as much metadata as possible; a static copy is present in the repo, and a live copy is available online and should contain the most up-to-date information.

Downloading data

Cell Painting images and single-cell profiles are available at the Cell Painting Gallery on the Registry of Open Data on AWS (https://registry.opendata.aws/cellpainting-gallery/) under accession numbers cpg0000-jump-pilot and cpg0001-cellpainting-protocol.

Download cell images

Cell images are available on an S3 bucket. The images can be downloaded using the command

plate=BR00117011__2020-11-08T19_57_47-Measurement1
aws s3 cp \
  --no-sign-request \
  --recursive \
  s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/${plate} .

You can test out download for a single file using:

suffix=BR00117011__2020-11-08T19_57_47-Measurement1/Images/r01c01f01p01-ch1sk1fk1fl1.tiff

aws s3 cp \
  --no-sign-request \
  s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/images/${suffix} .

Download illumination correction files

Illumination correction files, produced by running illum.cppipe on the cell images, are available on an S3 bucket. The images can be downloaded using the command

plate=BR00117011
aws s3 cp \
  --no-sign-request \
  --recursive \
  s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/images/2020_11_04_CPJUMP1/illum/${plate} .

Download sample per-well profiles

Per-well profiles generated by running the profiling script, created from the provided sample images are available on an S3 bucket. Download the .csv using the command

aws s3 cp \
  --no-sign-request \
  s3://cellpainting-gallery/cpg0000-jump-pilot/source_4/workspace/backend/2020_11_04_CPJUMP1/BR00117011/BR00117011.csv .

Image metadata

The image metadata will be automatically extracted from the images using the pipelines provided. An orientation to the metadata is as follows:

The folder for the 384-well plate contains images from nine sites for each well. There are eight images per site (five from the fluorescent channels and three brightfield images). The names of the image files follow the naming convention - rXXcXXfXXp01-chXXsk1fk1fl1.tiff where