2022_Cimini_NatureProtocols

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

rXX is the row number of the well that was imaged. rXX ranges from r01 to r16.
cXX is the column number of the well that was imaged. cXX ranges from c01 to c24.
fXX corresponds to the site that was imaged. fXX ranges from f01 to f09.
chXX corresponds to the fluorescent channels imaged. chXX ranges from ch01 to ch08.
- ch01 - Alexa 647
- ch02 - Alexa 568
- ch03 - Alexa 488 long
- ch04 - Alexa 488
- ch05 - Hoechst 33342
- ch06-8 - three brightfield z planes.

daisukekubota0823/2023_Cimini_NatureProtocols