Article

GammaGateR: semi-automated marker gating for single-cell multiplexed imaging

2023-09-23

Abstract excerpt

<h4>Motivation</h4> Multiplexed immunofluorescence (mIF) is an emerging assay for multichannel protein imaging that can decipher cell-level spatial features in tissues. However, existing automated cell phenotyping methods, such as clustering, face challenges in achieving consistency across experiments and often require subjective evaluation. As a result, mIF analyses often revert to marker gating based on manual...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 930b2b16-446d-5f41-b046-4cdca4b70bcb
DOI: 10.1101/2023.09.20.558645

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

GammaGateR: semi-automated marker gating for single-cell multiplexed imagingDOI 10.1101/2023.09.20.558645Read

ImmuNet: A Segmentation-Free Machine Learning Pipeline for Immune Landscape Phenotyping in Tumors by Muliplex ImagingSemantic proximity Read

UMITIC: An unsupervised framework for the joint characterization of cellular phenotypes and spatial neighborhoods in multiplex and hyperplex immunofluorescence imaging dataSemantic proximity Read

Dice-XMBD: Deep learning-based cell segmentation for imaging mass cytometrySemantic proximity Read

Deep cell phenotyping and spatial analysis of multiplexed imaging with TRACERx-PHLEX.Semantic proximity Read

Tribus: Semi-automated discovery of cell identities and phenotypes from multiplexed imaging and proteomic dataSemantic proximity Read

PhenoBIC: operator-free single-cell spatial phenotyping in multiplex imaging data using deep learning of cell staining patternsSemantic proximity Read

<i>cytomapper</i> : an R/Bioconductor package for visualisation of highly multiplexed imaging dataSemantic proximity Read

DIANNE: Segmentation-Free Localization of Histology Differential AttributesSemantic proximity Read

Multi-modal digital pathology for colorectal cancer diagnosis by high-plex immunofluorescence imaging and traditional histology of the same tissue sectionSemantic proximity Read

<i>7-UP:</i> generating <i>in silico</i> CODEX from a small set of immunofluorescence markersSemantic proximity Read

Self-Supervised AI Reveals a Hidden Landscape of Prognostic Spatial Patterns in Multiplex Immunofluorescence ImagesSemantic proximity Read

Optimizing multiplexed imaging experimental design through tissue spatial segregation estimationSemantic proximity Read