qupath-extension-sp-classify/CITATION.cff at main · mikemcka/qupath-extension-sp-classify · GitHub

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cff-version: 1.2.0
message: >-
  If you use this software, please cite it as below. Please also cite the CellTune
  paper (doi:10.1038/s41592-026-03162-2), whose human-in-the-loop workflow this
  extension derives functions from. Depending on which features you use, please
  also cite the relevant method papers listed under "references".
title: "SP Classify: an active-learning cell classifier extension for QuPath"
abstract: >-
  A QuPath extension for classifying cells in highly multiplexed images. It trains two
  different gradient-boosted models on manually labelled cells, then uses their disagreement
  to pick the most informative cells for review, so a usable classifier can be built from a
  few hundred labels rather than thousands.
type: software
authors:
  - family-names: Mckay
    given-names: Michael
    orcid: "https://orcid.org/0009-0002-2447-9506"
    affiliation: "Walter and Eliza Hall Institute of Medical Research"
# Concept DOI — always resolves to the latest release. Use this rather than a
# version-specific DOI so citations do not go stale.
doi: 10.5281/zenodo.21782421
version: 0.3.3
date-released: "2026-10-16"
license: GPL-3.0-only
repository-code: "https://github.com/mikemcka/qupath-extension-sp-classify"
keywords:
  - QuPath
  - multiplexed imaging
  - cell classification
  - active learning
  - spatial biology
  - image analysis
  - machine learning
  - bioimage analysis
# Method papers whose algorithms this extension reimplements. Cite the ones whose
# corresponding feature you actually use in your analysis.
references:
  - type: article
    title: "CellTune"
    notes: "The human-in-the-loop cell classification workflow this extension derives functions from (Keren Lab). Cite whenever you use this extension."
    authors:
      - name: "Keren Lab"
    doi: 10.1038/s41592-026-03162-2
    journal: "Nature Methods"
    year: 2026
  - type: article
    title: "Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front"
    notes: "Cite if you use the Cellular Neighborhoods (CN) analysis."
    authors:
      - family-names: "Schürch"
        given-names: "Christian M."
      - family-names: "Bhate"
        given-names: "Salil S."
      - family-names: "Barlow"
        given-names: "Graham L."
    doi: 10.1016/j.cell.2020.07.005
    journal: "Cell"
    volume: 182
    issue: 5
    year: 2020
  - type: article
    title: "From Louvain to Leiden: guaranteeing well-connected communities"
    notes: "Cite if you use graph-based (Leiden) clustering."
    authors:
      - family-names: "Traag"
        given-names: "Vincent A."
      - family-names: "Waltman"
        given-names: "Ludo"
      - family-names: "van Eck"
        given-names: "Nees Jan"
    doi: 10.1038/s41598-019-41695-z
    journal: "Scientific Reports"
    volume: 9
    year: 2019
  - type: article
    title: "SCANPY: large-scale single-cell gene expression data analysis"
    notes: "Cite if graph-based clustering (which mirrors the scanpy recipe) is central to your analysis."
    authors:
      - family-names: "Wolf"
        given-names: "F. Alexander"
      - family-names: "Angerer"
        given-names: "Philipp"
      - family-names: "Theis"
        given-names: "Fabian J."
    doi: 10.1186/s13059-017-1382-0
    journal: "Genome Biology"
    volume: 19
    year: 2018
  - type: article
    title: "Efficient and robust approximate nearest neighbor search using Hierarchical Navigable Small World graphs"
    notes: "Cite if you use cohort/all-cells Leiden clustering (which builds an HNSW kNN graph)."
    authors:
      - family-names: "Malkov"
        given-names: "Yu A."
      - family-names: "Yashunin"
        given-names: "Dmitry A."
    doi: 10.1109/TPAMI.2018.2889473
    journal: "IEEE Transactions on Pattern Analysis and Machine Intelligence"
    volume: 42
    issue: 4
    year: 2020
  - type: article
    title: "Single-cell metabolic profiling of human cytotoxic T cells"
    notes: "Cite if you use the recommended arcsinh cofactor (0.05) for MIBI mass-spectrometry data."
    authors:
      - family-names: "Hartmann"
        given-names: "Felix J."
      - family-names: "Mrdjen"
        given-names: "Dunja"
      - family-names: "McCaffrey"
        given-names: "Erin"
    doi: 10.1038/s41587-020-0651-8
    journal: "Nature Biotechnology"
    volume: 39
    year: 2021
  - type: article
    title: "UniFORM: Towards Universal Immunofluorescence Normalization for Multiplex Tissue Imaging"
    notes: "Cite if you use the Batch Normalisation (UniFORM) feature."
    authors:
      - family-names: "Wang"
        given-names: "Kunlun"
      - family-names: "Ait-Ahmad"
        given-names: "Karim"
      - family-names: "Kupp"
        given-names: "Sara"
    doi: 10.1101/2024.12.06.626879
    journal: "bioRxiv"
    year: 2024