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# CITATION.cff 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 "bgnormR" in publications use:'
type: software
license: MIT
title: 'bgnormR: Background Normalisation for Multiplex Spatial Proteomics'
version: 0.99.5
doi: 10.64898/2026.08.05.743141
abstract: Implements bgnorm, a generative statistical framework for background correction,
  normalisation, and quality control in multiplex spatial proteomics. The method models
  fluorescence pixel intensities as a three-component mixture of log-normal convolutions
  representing background, non-specific binding, and biological signal. A deconvolution
  step separates the signal component from background sources, and a model-based quantile
  normalisation (bgnormQ) unifies measurements across markers, samples, and three-dimensional
  tissue slices. A Jensen-Shannon Divergence metric provides automated quality control.
  A Java-free reader for Akoya PhenoCycler-Fusion QPTIFF, OME-TIFF, and OME-Zarr (OME-NGFF)
  images is included.
authors:
- family-names: Bhuva
  given-names: Dharmesh D.
  email: d.bhuva@uq.edu.au
  orcid: https://orcid.org/0000-0002-6398-9157
- family-names: Tubelleza
  given-names: Rafael
  email: r.tubelleza@uq.edu.au
  orcid: https://orcid.org/0009-0007-1414-547X
- family-names: Kharbanda
  given-names: Malvika
  email: malvika.kharbanda@adelaide.edu.au
  orcid: https://orcid.org/0000-0001-9726-3023
- family-names: Salim
  given-names: Agus
  email: salim.a@unimelb.edu.au
  orcid: https://orcid.org/0000-0003-3999-7701
preferred-citation:
  type: article
  title: 'bgnorm: A Generative Statistical Framework for Background Correction, Normalisation,
    and Quality Control in Multiplex Spatial Proteomics'
  authors:
  - family-names: Kharbanda
    given-names: Malvika
    orcid: https://orcid.org/0000-0001-9726-3023
    email: malvika.kharbanda@adelaide.edu.au
  - family-names: Tubelleza
    given-names: Rafael
    orcid: https://orcid.org/0009-0007-1414-547X
    email: r.tubelleza@uq.edu.au
  - family-names: Tan
    given-names: Yuqi
    orcid: https://orcid.org/0000-0002-7200-3222
  - family-names: Tan
    given-names: Chin Wee
    orcid: https://orcid.org/0000-0001-9695-7218
  - family-names: Janke
    given-names: Cooper
    orcid: https://orcid.org/0009-0002-0544-8966
  - family-names: Sebina
    given-names: Ismail
    orcid: https://orcid.org/0000-0003-3232-3472
  - family-names: Belz
    given-names: Gabrielle T.
    orcid: https://orcid.org/0000-0002-9660-9587
  - family-names: Kulasinghe
    given-names: Arutha
    orcid: https://orcid.org/0000-0003-3224-7350
  - family-names: Salim
    given-names: Agus
    orcid: https://orcid.org/0000-0003-3999-7701
    email: salim.a@unimelb.edu.au
  - family-names: Bhuva
    given-names: Dharmesh D.
    orcid: https://orcid.org/0000-0002-6398-9157
    email: d.bhuva@uq.edu.au
  journal: bioRxiv
  year: '2026'
  doi: 10.64898/2026.08.05.743141
  url: https://www.biorxiv.org/content/10.64898/2026.08.05.743141v1
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/BhuvaLab/bgnormR
commit: b187a5be699d2bb126555d0af1734c6852d6adf4
url: https://github.com/BhuvaLab/bgnormR
date-released: '2026-11-08'
contact:
- family-names: Bhuva
  given-names: Dharmesh D.
  email: d.bhuva@uq.edu.au
  orcid: https://orcid.org/0000-0002-6398-9157