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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "SPIAT" in publications use:'
type: software
license: Artistic-2.0
title: 'SPIAT: Spatial Image Analysis of Tissues'
version: 1.7.1
identifiers:
- type: doi
  value: 10.32614/CRAN.package.SPIAT
abstract: SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package
  with a suite of data processing, quality control, visualization and data analysis
  tools. SPIAT is compatible with data generated from single-cell spatial proteomics
  platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the
  form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT
  includes six analysis modules that allow visualization, calculation of cell colocalization,
  categorization of the immune microenvironment relative to tumor areas, analysis
  of cellular neighborhoods, and the quantification of spatial heterogeneity, providing
  a comprehensive toolkit for spatial data analysis.
authors:
- family-names: Trigos
  given-names: Anna
  email: anna.trigos@petermac.org
  orcid: https://orcid.org/0000-0002-5915-2952
- family-names: Feng
  given-names: Yuzhou
  email: yuzhou.feng@petermac.org
  orcid: https://orcid.org/0000-0002-2955-4053
- family-names: Yang
  given-names: Tianpei
  email: yangtp3344@gmail.com
- family-names: Li
  given-names: Mabel
- family-names: Zhu
  given-names: John
- family-names: Ozcoban
  given-names: Volkan
  email: volkanozcoban1@gmail.com
- family-names: Doyle
  given-names: Maria
  email: maria.doyle@petermac.org
preferred-citation:
  type: manual
  title: 'SPIAT: Spatial Image Analysis of Cells in Tissues'
  authors:
  - family-names: Trigos
    given-names: Anna S
  - family-names: Feng
    given-names: Yuzhou
    email: yuzhou.feng@petermac.org
    orcid: https://orcid.org/0000-0002-2955-4053
  - family-names: Yang
    given-names: Tianpei
    email: yangtp3344@gmail.com
  - family-names: Li
    given-names: Mabel
  - family-names: Zhu
    given-names: John
  - family-names: Ozcoban
    given-names: Volkan
    email: volkanozcoban1@gmail.com
  - family-names: Doyle
    given-names: Maria
    email: maria.doyle@petermac.org
  notes: R package version 1.7.1
  year: '2024'
  url: https://trigosteam.github.io/SPIAT/
repository: https://bioc.r-universe.dev
repository-code: https://github.com/trigosteam/SPIAT
commit: 77e929b251ea3d033ae1703b92104da37634ef16
url: https://trigosteam.github.io/SPIAT/
contact:
- family-names: Feng
  given-names: Yuzhou
  email: yuzhou.feng@petermac.org
  orcid: https://orcid.org/0000-0002-2955-4053
references:
- type: article
  title: Spatial analysis with SPIAT and spaSim to characterize and simulate tissue
    microenvironments
  authors:
  - family-names: Feng
    given-names: Yuzhou
  - family-names: Yang
    given-names: Tianpei
  - family-names: Zhu
    given-names: John
  - family-names: Li
    given-names: Mabel
  - family-names: Doyle
    given-names: Maria
  - family-names: Ozcoban
    given-names: Volkan
  - family-names: Bass
    given-names: Greg T
  - family-names: Pizzolla
    given-names: Angela
  - family-names: Cain
    given-names: Lachlan
  - family-names: Weng
    given-names: Sirui
  - family-names: Pasam
    given-names: Anupama
  - family-names: Kocovski
    given-names: Nikolce
  - family-names: Huang
    given-names: Yu-Kuan
  - family-names: Keam
    given-names: Simon P
  - family-names: Speed
    given-names: Terence P
  - family-names: Neeson
    given-names: Paul J
  - family-names: Pearson
    given-names: Richard B
  - family-names: Sandhu
    given-names: Shahneen K
  - family-names: Goode
    given-names: David L
  - family-names: Trigos
    given-names: Anna S
  journal: Nature Communications
  volume: '14'
  issue: '2697'
  year: '2023'
  doi: 10.1038/s41467-023-37822-0