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

# 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)

immunooncology singlecell spatial dataimport clustering imc single-cell

8.78 score 33 stars 417 scripts 23 exports 172 dependencies

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

Target	Result	Time
bioc-checks	WARNING	287
linux-devel-x86_64	WARNING	1088
source / vignettes	OK	490
linux-release-x86_64	WARNING	967
macos-release-arm64	WARNING	569
macos-oldrel-arm64	WARNING	770
windows-devel	WARNING	1153
windows-release	WARNING	1141
windows-oldrel	WARNING	1190
wasm-release	OK	275

Exports:aggregateNeighbors binAcrossPixels buildSpatialGraph countInteractions detectCommunity detectSpatialContext distToCells filterPixels filterSpatialContext findBorderCells patchDetection patchSize plotInteractions plotSpatial plotSpatialContext plotSpotHeatmap read_cpout read_steinbock readImagefromTXT readSCEfromTIFF readSCEfromTXT show_cpout_features testInteractions

Dependencies:abind askpass assorthead base64enc beachmat beeswarm BH Biobase BiocFileCache BiocGenerics biocmake BiocNeighbors BiocParallel bit bit64 bitops blob bslib cachem class classInt cli clipr codetools commonmark concaveman cpp11 crayon crosstalk curl cytomapper data.table DBI dbplyr DelayedArray digest dir.expiry distances dplyr DT e1071 EBImage evaluate farver fastmap fftwtools filelock fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggbeeswarm ggforce ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable h5mread HDF5Array highr hms htmltools htmlwidgets httpuv httr2 igraph IRanges isoband jpeg jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lazyeval lifecycle locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mime nnls openssl otel pheatmap pillar pkgconfig png polyclip prettyunits progress promises proxy purrr R6 rappdirs raster RColorBrewer Rcpp RcppArmadillo RCurl readr rhdf5 rhdf5filters Rhdf5lib Rigraphlib rjson rlang rmarkdown RSQLite RTriangle s2 S4Arrays S4Vectors S7 sass scales scrapper Seqinfo sf shiny shinydashboard SingleCellExperiment snow sourcetools sp SparseArray SpatialExperiment stringi stringr SummarizedExperiment svglite svgPanZoom sys systemfonts terra textshaping tibble tidygraph tidyr tidyselect tiff tinytex tweenr tzdb units utf8 V8 vctrs vipor viridis viridisLite vroom withr wk xfun xtable XVector yaml

Tools for IMC data analysis

Rendered fromimcRtools.Rmdusingknitr::rmarkdown

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

Help page	Topics
Function to aggregate all neighbors of each cell.	aggregateNeighbors
Aggregate consecutive pixels per single-metal spot	binAcrossPixels
Builds an interaction graph based on the cells' locations	buildSpatialGraph
Summarizes cell-cell interactions within grouping levels (e.g. images)	countInteractions
Detect the spatial community of each cell	detectCommunity
Detect the spatial context of each cell based on its neighborhood	detectSpatialContext
Function to calculate distance to cells of interest	distToCells
Filter pixels based on their assigned masses	filterPixels
Filter spatial contexts	filterSpatialContext
Find cells at the image border	findBorderCells
Function to detect patches containing defined cell types	patchDetection
Function to compute the area of c3ll patches	patchSize
Plot interaction graph	plotInteractions
Visualizes the spatial locations and interactions of cells	plotSpatial
Plot spatial context graph	plotSpatialContext
Summarizes and visualizes the pixel intensities per spot and channel	plotSpotHeatmap
Reads in single-cell data generated by the ImcSegmentationPipeline	read_cpout
Reads in single-cell data generated by the steinbock pipeline	read_steinbock
Reads one or multiple .txt files into a CytoImageList object	readImagefromTXT
Generates a SingleCellExperiment from .tiff files	readSCEfromTIFF
Generates a SingleCellExperiment from .txt files	readSCEfromTXT
Display all features measured by CellProfiler.	show_cpout_features
Tests if cell types interact more or less frequently than random	testInteractions

Package: imcRtools 1.19.1

imcRtools: Methods for imaging mass cytometry data analysis

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