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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 "imcRtools" in publications use:'
type: software
license: GPL-3.0-only
title: 'imcRtools: Methods for imaging mass cytometry data analysis'
version: 1.18.1
doi: 10.1038/s41596-023-00881-0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.imcRtools
abstract: This R package supports the handling and analysis of imaging mass cytometry
  and other highly multiplexed imaging data. The main functionality includes reading
  in single-cell data after image segmentation and measurement, data formatting to
  perform channel spillover correction and a number of spatial analysis approaches.
  First, cell-cell interactions are detected via spatial graph construction; these
  graphs can be visualized with cells representing nodes and interactions representing
  edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial
  clustering. Per image/grouping level, interactions between types of cells are counted,
  averaged and compared against random permutations. In that way, types of cells that
  interact more (attraction) or less (avoidance) frequently than expected by chance
  are detected.
authors:
- family-names: Eling
  given-names: Nils
- family-names: Schulz
  given-names: Daniel
  email: daniel.schulz@uzh.ch
  orcid: https://orcid.org/0000-0002-0913-1678
preferred-citation:
  type: article
  title: An end-to-end workflow for multiplexed image processing and analysis
  authors:
  - family-names: Windhager
    given-names: Jonas
  - family-names: Zanotelli
    given-names: Vito R.T.
  - family-names: Schulz
    given-names: Daniel
    email: daniel.schulz@uzh.ch
    orcid: https://orcid.org/0000-0002-0913-1678
  - family-names: Meyer
    given-names: Lasse
  - family-names: Daniel
    given-names: Michelle
  - family-names: Bodenmiller
    given-names: Bernd
  - family-names: Eling
    given-names: Nils
  year: '2023'
  journal: Nature Protocols
  doi: 10.1038/s41596-023-00881-0
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/BodenmillerGroup/imcRtools
commit: 075e056cf3bb8b9f3d49fb78be94d7405893b266
url: https://github.com/BodenmillerGroup/imcRtools
date-released: '2026-05-19'
contact:
- family-names: Schulz
  given-names: Daniel
  email: daniel.schulz@uzh.ch
  orcid: https://orcid.org/0000-0002-0913-1678