Package: simpleSeg 1.7.1

Ellis Patrick

simpleSeg: A package to perform simple cell segmentation

Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.

Authors:Nicolas Canete [aut], Alexander Nicholls [aut], Ellis Patrick [aut, cre]

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simpleSeg.pdf |simpleSeg.html✨
simpleSeg/json (API)
NEWS

# Install 'simpleSeg' in R:

install.packages('simpleSeg', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sydneybiox/simpleseg/issues

On BioConductor:simpleSeg-1.7.1(bioc 3.20)simpleSeg-1.6.1(bioc 3.19)

bioconductor-package

2 exports 1.38 score 141 dependencies

Last updated 2 months agofrom:1283f9dc53

Exports:normalizeCells simpleSeg

Dependencies:abind askpass base64enc beeswarm BH Biobase BiocFileCache BiocGenerics BiocParallel bit bit64 bitops blob bslib cachem cli codetools colorspace commonmark cpp11 crayon curl cytomapper DBI dbplyr DelayedArray deldir digest dplyr EBImage evaluate fansi farver fastmap fftwtools filelock fontawesome formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggplot2 glue gridExtra gtable HDF5Array highr htmltools htmlwidgets httpuv httr IRanges isoband jpeg jquerylib jsonlite knitr labeling lambda.r later lattice lifecycle locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnls openssl pillar pkgconfig plogr png polyclip promises purrr R6 rappdirs raster RColorBrewer Rcpp RCurl rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales shiny shinydashboard SingleCellExperiment snow sourcetools sp SparseArray SpatialExperiment spatstat.data spatstat.geom spatstat.utils stringi stringr SummarizedExperiment svglite svgPanZoom sys systemfonts terra tibble tidyr tidyselect tiff tinytex UCSC.utils utf8 vctrs vipor viridis viridisLite withr xfun xtable XVector yaml zlibbioc

Segmenting and normalizing multiplexed imaging data with simpleSeg

Alexander Nicholls, Ellis Patrick, Nicolas Canete

Rendered fromsimpleSeg.Rmdusingknitr::rmarkdownon Jun 20 2024.

Last update: 2024-05-21
Started: 2022-05-30

Help page	Topics
Utility function to generate BPPARM object.	generateBPParam
Normalizes and transforms cell data in preparation for clustering (accepts dataframe, SingleCellExperiment and SpatialExperiment).	normalizeCells
Perform simple segmentation of multiplexed cellular images	simpleSeg

Package: simpleSeg 1.7.1

simpleSeg: A package to perform simple cell segmentation

Segmenting and normalizing multiplexed imaging data with simpleSeg

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