Package: imcRtools 1.19.1

Daniel Schulz

imcRtools: Methods for imaging mass cytometry data analysis

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:Nils Eling [aut], Tobias Hoch [ctb], Vito Zanotelli [ctb], Jana Fischer [ctb], Daniel Schulz [ctb, cre], Lasse Meyer [ctb], Lutz Marlene [ctb], Schiller Chiara [ctb], Ibañez Victor [ctb]

imcRtools_1.19.1.tar.gz
imcRtools_1.19.1.zip(r-4.7)imcRtools_1.19.1.zip(r-4.6)imcRtools_1.19.1.zip(r-4.5)
imcRtools_1.19.1.tgz(r-4.6-any)imcRtools_1.19.1.tgz(r-4.5-any)
imcRtools_1.19.1.tar.gz(r-4.7-any)imcRtools_1.19.1.tar.gz(r-4.6-any)
imcRtools_1.19.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
imcRtools/json (API)
NEWS

# Install 'imcRtools' in R:
install.packages('imcRtools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bodenmillergroup/imcrtools/issues

On BioConductor:imcRtools-1.19.1(bioc 3.24)imcRtools-1.18.1(bioc 3.23)

immunooncologysinglecellspatialdataimportclusteringimcsingle-cell

8.84 score 31 stars 426 scripts 592 downloads 23 exports 172 dependencies

Last updated from:6b31abd5ac. Checks:8 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING288
linux-devel-x86_64WARNING1070
source / vignettesOK528
linux-release-x86_64WARNING989
macos-release-arm64WARNING557
macos-oldrel-arm64WARNING663
windows-develWARNING1530
windows-releaseWARNING1043
windows-oldrelWARNING1555
wasm-releaseOK260

Exports:aggregateNeighborsbinAcrossPixelsbuildSpatialGraphcountInteractionsdetectCommunitydetectSpatialContextdistToCellsfilterPixelsfilterSpatialContextfindBorderCellspatchDetectionpatchSizeplotInteractionsplotSpatialplotSpatialContextplotSpotHeatmapread_cpoutread_steinbockreadImagefromTXTreadSCEfromTIFFreadSCEfromTXTshow_cpout_featurestestInteractions

Dependencies:abindaskpassassortheadbase64encbeachmatbeeswarmBHBiobaseBiocFileCacheBiocGenericsbiocmakeBiocNeighborsBiocParallelbitbit64bitopsblobbslibcachemclassclassIntclicliprcodetoolscommonmarkconcavemancpp11crayoncrosstalkcurlcytomapperdata.tableDBIdbplyrDelayedArraydigestdir.expirydistancesdplyrDTe1071EBImageevaluatefarverfastmapfftwtoolsfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtableh5mreadHDF5Arrayhighrhmshtmltoolshtmlwidgetshttpuvhttr2igraphIRangesisobandjpegjquerylibjsonliteKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimennlsopensslotelpheatmappillarpkgconfigpngpolyclipprettyunitsprogresspromisesproxypurrrR6rappdirsrasterRColorBrewerRcppRcppArmadilloRCurlreadrrhdf5rhdf5filtersRhdf5libRigraphlibrjsonrlangrmarkdownRSQLiteRTriangles2S4ArraysS4VectorsS7sassscalesscrapperSeqinfosfshinyshinydashboardSingleCellExperimentsnowsourcetoolsspSparseArraySpatialExperimentstringistringrSummarizedExperimentsvglitesvgPanZoomsyssystemfontsterratextshapingtibbletidygraphtidyrtidyselecttifftinytextweenrtzdbunitsutf8V8vctrsviporviridisviridisLitevroomwithrwkxfunxtableXVectoryaml

Tools for IMC data analysis

Nils Eling, Lasse Meyer, Daniel Schulz

Rendered fromimcRtools.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-03-30
Started: 2020-12-17

Readme and manuals

Help Manual

Help pageTopics
Function to aggregate all neighbors of each cell.aggregateNeighbors
Aggregate consecutive pixels per single-metal spotbinAcrossPixels
Builds an interaction graph based on the cells' locationsbuildSpatialGraph
Summarizes cell-cell interactions within grouping levels (e.g. images)countInteractions
Detect the spatial community of each celldetectCommunity
Detect the spatial context of each cell based on its neighborhooddetectSpatialContext
Function to calculate distance to cells of interestdistToCells
Filter pixels based on their assigned massesfilterPixels
Filter spatial contextsfilterSpatialContext
Find cells at the image borderfindBorderCells
Function to detect patches containing defined cell typespatchDetection
Function to compute the area of c3ll patchespatchSize
Plot interaction graphplotInteractions
Visualizes the spatial locations and interactions of cellsplotSpatial
Plot spatial context graphplotSpatialContext
Summarizes and visualizes the pixel intensities per spot and channelplotSpotHeatmap
Reads in single-cell data generated by the ImcSegmentationPipelineread_cpout
Reads in single-cell data generated by the steinbock pipelineread_steinbock
Reads one or multiple .txt files into a CytoImageList objectreadImagefromTXT
Generates a SingleCellExperiment from .tiff filesreadSCEfromTIFF
Generates a SingleCellExperiment from .txt filesreadSCEfromTXT
Display all features measured by CellProfiler.show_cpout_features
Tests if cell types interact more or less frequently than randomtestInteractions