cellpainting-gallery.yaml

Name: Cell Painting Gallery
Description: |
  The Cell Painting Gallery is a collection of image datasets created using the [Cell Painting](https://pubmed.ncbi.nlm.nih.gov/27560178/) assay. 
  The images of cells are captured by microscopy imaging, and reveal the response of various labeled cell components to whatever treatments are tested, which can include genetic perturbations, chemicals or drugs, or different cell types. 
  The datasets can be used for diverse applications in basic biology and pharmaceutical research, such as identifying disease-associated phenotypes, understanding disease mechanisms, and predicting a drug’s activity, toxicity, or mechanism of action ([Chandrasekaran et al 2020](https://carpenter-singh-lab.broadinstitute.org/files/anne/files/141_Chandrasekaran_NatRevDrugDiscov_2020.pdf)). 
  This collection is maintained by the [Carpenter–Singh lab](https://carpenter-singh-lab.broadinstitute.org/) and the [Cimini lab](https://cimini-lab.broadinstitute.org/) at the [Broad Institute](https://www.broadinstitute.org/).
  A human-friendly listing of datasets, instructions for accessing them, and other documentation is at the [corresponding GitHub page](https://github.com/broadinstitute/cellpainting-gallery) about the Gallery.
Documentation: https://github.com/broadinstitute/cellpainting-gallery
Contact: cellpainting@broadinstitute.org
ManagedBy: Carpenter-Singh and Cimini Labs at the Broad Institute
UpdateFrequency: Typically when an associated publication is posted on biorxiv
Tags:
  - bioinformatics
  - biology
  - cancer
  - cell biology
  - cell imaging
  - cell painting
  - chemical biology
  - computer vision
  - csv
  - deep learning
  - fluorescence imaging
  - genetic
  - high-throughput imaging
  - image processing
  - image-based profiling
  - imaging
  - machine learning
  - medicine
  - microscopy
  - organelle
License:  CC0 1.0 Universal (CC0 1.0) Public Domain Dedication, but please do cite the corresponding publication for each dataset, as listed [here](https://github.com/broadinstitute/cellpainting-gallery#citation).
Resources:
  - Description: Cell Painting data, comprising fluorescence microscopy cell images (TIFF), extracted features (CSV), and associated metadata (CSV and TXT).
    ARN: arn:aws:s3:::cellpainting-gallery
    Region: us-east-1
    Type: S3 Bucket
    Explore:
      - '[Documentation](https://github.com/broadinstitute/cellpainting-gallery)'
      - '[Browse Bucket](https://cellpainting-gallery.s3.amazonaws.com/index.html)'
DataAtWork:
  Tutorials:
    - Title: Cell Painting wiki
      URL: https://broad.io/cellpaintingwiki
      AuthorName: Multiple Authors
      AuthorURL: https://www.broadinstitute.org/imaging
    - Title: Image-based Profiling Handbook - for processing image-based profiling datasets using CellProfiler and pycytominer
      URL: https://cytomining.github.io/profiling-handbook/
      AuthorName: Multiple Authors
      AuthorURL: https://github.com/cytomining/profiling-handbook/graphs/contributors
    - Title: Scientific Community Image Forum - for software-oriented aspects of scientific imaging including analysis, processing, and acquisition
      URL: https://forum.image.sc
      AuthorName: Multiple Authors
      AuthorURL: https://openbioimageanalysis.org
    - Title: Center for Open Bioimage Analysis (COBA) YouTube Channel - video tutorials of CellProfiler and other softwares
      URL: https://www.youtube.com/c/COBACenterforOpenBioimageAnalysis/videos
      AuthorName: Multiple Authors
      AuthorURL: https://openbioimageanalysis.org
    - Title: Image-based profiling introductory exercise - data and an exercise on exploring image-based profiles, including understanding the various data levels
      URL: https://github.com/broadinstitute/BBBC021_Morpheus_Exercise/blob/main/MorpheusExerciseWritten.pdf
      AuthorName: Beth Cimini
      AuthorURL: https://github.com/broadinstitute/BBBC021_Morpheus_Exercise/graphs/contributors    
  Tools & Applications:
    - Title: Pycytominer - Data processing functions for profiling perturbations
      URL: https://github.com/cytomining/pycytominer
      AuthorName: Multiple Authors
      AuthorURL: https://github.com/cytomining/pycytominer/graphs/contributors
    - Title: Distributed CellProfiler - Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure
      URL: https://github.com/CellProfiler/Distributed-CellProfiler
      AuthorName: Multiple Authors
      AuthorURL: https://github.com/CellProfiler/Distributed-CellProfiler/graphs/contributors
    - Title: Deep Profiler - Morphological profiling using deep learning
      URL: https://github.com/cytomining/DeepProfiler
      AuthorName: Multiple Authors
      AuthorURL: https://github.com/cytomining/DeepProfiler/graphs/contributors
    - Title: Image-based Profiling Recipe
      URL: https://github.com/cytomining/profiling-recipe
      AuthorName: Multiple Authors
      AuthorURL: https://github.com/cytomining/profiling-recipe/graphs/contributors
  Publications:
    - Title: Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
      URL: https://pubmed.ncbi.nlm.nih.gov/27560178/
      AuthorName: Bray M-A, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, & Carpenter AE
    - Title: Systematic morphological profiling of human gene and allele function via Cell Painting
      URL: https://elifesciences.org/content/6/e24060
      AuthorName: Rohban MH, Singh S, Wu X, Berthet JB, Bray M-A, Shrestha Y, Varelas X, Boehm JS, & Carpenter AE
    - Title: Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects
      URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0131370
      AuthorName: Singh S, Wu X, Ljosa V, Bray M-A, Piccioni F, Root DE, Doench JG, Boehm JS, & Carpenter AE
    - Title: A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay
      URL: https://academic.oup.com/gigascience/article/6/12/1/2865213
      AuthorName: Bray M-A, Gustafsdottir SM, Rohban MH, Singh S, Ljosa V, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancik V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, & Carpenter AE
    - Title: Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling
      URL: http://www.pnas.org/content/111/30/10911
      AuthorName: Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, BodycombeNE, Marton MA, Sokolnicki KL, Bray M-A, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CSK, Duvall JR, Wilson JA, Bittker JA, Dancik V, Narayan R, Subramanian A, Winckler W, Golub TR, Carpenter AE, Shamji AF, Schreiber SL, & Clemons PA
    - Title: Multiplex Cytological Profiling Assay to Measure Diverse Cellular States
      URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080999
      AuthorName: Gustafsdottir SM, Ljosa V, Sokolnicki KL, Wilson JA, Walpita D, Kemp MM, Seiler KP, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, and Shamji AF
    - Title: Cell Painting predicts impact of lung cancer variants
      URL: https://www.molbiolcell.org/doi/10.1091/mbc.E21-11-0538
      AuthorName: Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, & Singh S