CITATION.cff

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---
cff-version: 1.2.0
title: CytoDataFrame
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: David
    family-names: Bunten
    orcid: 'https://orcid.org/0000-0001-6041-3665'
  - given-names: Jenna
    family-names: Tomkinson
    orcid: 'https://orcid.org/0000-0003-2676-5813'
  - given-names: Vincent
    family-names: Rubinetti
    orcid: 'https://orcid.org/0000-0002-4655-3773'
  - given-names: Gregory
    family-names: Way
    orcid: 'https://orcid.org/0000-0002-0503-9348'
repository-code: 'https://github.com/cytomining/CytoDataFrame'
identifiers:
  - description: Software DOI
    type: doi
    value: "10.5281/zenodo.14797074"
abstract: >-
  An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.
keywords:
  - python
  - single-cell-analysis
  - profiling
  - dataframes
  - data-analysis
  - way-lab
license: BSD-3-Clause
references:
  - authors:
      - name: "Way Lab CFReT_data Team"
    date-accessed: "2024-05-13"
    title: Way Lab CFReT_data CytoTable Data
    type: data
    repository-code: "https://github.com/WayScience/CFReT_data"
    url: "https://github.com/WayScience/CFReT_data/blob/main/3.process_cfret_features/data/converted_profiles/localhost231120090001_converted.parquet"
    scope: "localhost231120090001_converted.parquet"
    notes: >-
      Data from CFReT_data project is used to help validate
      expected results. Data is generated from CellProfiler
      and CytoTable.
    identifiers:
      - description: "Github Link with Contributors"
        type: url
        value: "https://github.com/WayScience/CFReT_data/graphs/contributors"
  - authors:
      - name: "Way Lab NF1_cellpainting_data Team"
    date-accessed: "2024-06-28"
    title: Way Lab NF1_cellpainting_data CytoTable Data
    type: data
    repository-code: "https://github.com/WayScience/nf1_cellpainting_data"
    notes: >-
      Data from NF1_cellpainting_data project is used to help validate
      expected results. Data is generated from CellProfiler
      and CytoTable. We use the following files from the repository:
      - "Plate_2_nf1_analysis.sqlite"
      - "Plate_2.parquet"
    identifiers:
      - description: "Github Link with Contributors"
        type: url
        value: "https://github.com/WayScience/nf1_cellpainting_data/graphs/contributors"
  - title: >-
      Plate 2 (Cell Painting images from Plate 2 for NF1_cellpainting_data project)
    type: data
    url: https://figshare.com/articles/dataset/Plate_2/22233700
    notes: >-
      Image data for related NF1_cellpainting_data parquet sqlite.
    authors:
    - family-names: Tomkinson
      given-names: Jenna
    - family-names: Mattson-Hoss
      given-names: Michelle
    - family-names: Sarnoff
      given-names: Herb
    - family-names: Way
      given-names: Gregory
    date-published: "2023-04-12"
    identifiers:
    - type: doi
      value: 10.6084/m9.figshare.22233700.v4
  - authors:
      - name: "Way Lab and Alexander Lab Nuclear Speckles Collaboration"
    date-accessed: "2024-09-04"
    title: Way Lab and Alexander Lab Nuclear Speckles Collaboration Data
    type: data
    repository-code: https://github.com/WayScience/nuclear_speckle_image_profiling
    notes: >-
      Data from a collaborative project focusing on nuclear speckles
      with the Way Lab and Alexander Lab s used to help validate
      expected results. Parquet data is generated from CellProfiler
      and CytoTable. Images courtesy of Katherine Alexander
      and the Alexander Lab.
    identifiers:
      - description: "Github Link with Contributors"
        type: url
        value: "https://github.com/WayScience/nuclear_speckle_image_profiling/graphs/contributors"
  - authors:
      - family-names: Chandrasekaran
        given-names: Srinivas Niranj
      - family-names: Cimini
        given-names: Beth A.
      - family-names: Goodale
        given-names: Amy
      - family-names: Miller
        given-names: Lisa
      - family-names: Kost-Alimova
        given-names: Maria
      - family-names: Jamali
        given-names: Nasim
      - family-names: Doench
        given-names: John G.
      - family-names: Fritchman
        given-names: Briana
      - family-names: Skepner
        given-names: Adam
      - family-names: Melanson
        given-names: Michelle
      - family-names: Kalinin
        given-names: Alexandr A.
      - family-names: Arevalo
        given-names: John
      - family-names: Haghighi
        given-names: Marzieh
      - family-names: Caicedo
        given-names: Juan C.
      - family-names: Kuhn
        given-names: Daniel
      - family-names: Hernandez
        given-names: Desiree
      - family-names: Berstler
        given-names: James
      - family-names: Shafqat-Abbasi
        given-names: Hamdah
      - family-names: Root
        given-names: David E.
      - family-names: Swalley
        given-names: Susanne E.
      - family-names: Garg
        given-names: Sakshi
      - family-names: Singh
        given-names: Shantanu
      - family-names: Carpenter
        given-names: Anne E.
    date-accessed: "2024-08-21"
    title: >-
      Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations
    type: article
    issn: 1548-7105
    issue: 6
    journal: Nature Methods
    pages: 1114-1121
    volume: 21
    url: https://doi.org/10.1038/s41592-024-02241-6
    date-published: "2024-06-01"
    identifiers:
      - type: doi
        value: 10.1038/s41592-024-02241-6
    notes: >-
      JUMP (cpg0000-jump-pilot) was used to help demonstrate CytoDataFrame performance
      with large data. See here for more information:
      https://github.com/broadinstitute/cellpainting-gallery
  - type: article
    authors:
      - family-names: Blin
        given-names: Guillaume
      - family-names: Sadurska
        given-names: Dominika
      - family-names: Portero Migueles
        given-names: Rafael
      - family-names: Chen
        given-names: Ni
      - family-names: Watson
        given-names: James A.
      - family-names: Lowell
        given-names: Sally
    title: "Nessys: A new set of tools for the automated detection of nuclei within intact tissues and dense 3D cultures"
    journal: PLoS Biology
    volume: "17"
    issue: "8"
    pages: e3000388
    year: 2019
    doi: "10.1371/journal.pbio.3000388"
    url: "https://doi.org/10.1371/journal.pbio.3000388"
    notes: >
      This work used the file "6001240_labels.zarr" from the DISCEPTS imaging
      dataset, available through the Image Data Resource (IDR) under accession
      number idr0062.
  - type: data
    title: "3D Noise Nuclei Segmentation Tutorial"
    authors:
      - name: "CellProfiler Tutorials Team"
    url: "https://tutorials.cellprofiler.org/#3d-noise-nuclei-segmentation"
    publisher:
      name: "CellProfiler Organization"
    notes: >
      This work uses data that were slightly modified from the
      CellProfiler 3D Noise Nuclei Segmentation tutorial.