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<img src="vignettes/imgs/cytoviewer_sticker.png" align="right" alt="" width="100" /> # cytoviewer <!-- badges: start --> [![docs](]( [![codecov](]( <!-- badges: end --> An interactive multi-channel image viewer for R. This shiny application allows users to interactively visualize multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques. The `cytoviewer` package is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with [SingleCellExperiment]( / [SpatialExperiment]( and [CytoImageList]( objects for metadata and image visualization and supports image downloads. Read the **BMC Bioinformatics paper** here: []( ## Check status | Bioc branch | Checks | |:------------------------------------------:|:--------------------------:| | Release | [![build-checks-release](]( | | Devel | [![build-checks-devel](]( | ## Requirements The `cytoviewer` package requires R version \>= 4.0. It builds on data objects and functions contained in the [cytomapper]( package. ## Installation The `cytoviewer` package can be installed from `Bioconductor` via: ``` r if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("cytoviewer") ``` The development version of `cytoviewer` can be installed from Github via: ``` r if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes") remotes::install_github("BodenmillerGroup/cytoviewer") ``` To load the package in your R session, type the following: ``` r library(cytoviewer) ``` ## Basic usage ``` r library(cytoviewer) # Load example datasets library(cytomapper) data("pancreasImages") data("pancreasMasks") data("pancreasSCE") # Use cytoviewer with images, masks and object app <- cytoviewer(image = pancreasImages, mask = pancreasMasks, object = pancreasSCE, img_id = "ImageNb", cell_id = "CellNb") if (interactive()) { shiny::runApp(app) } ``` For more detailed information on package usage and functionality, please refer to []( ## Contributing For feature requests, please open an issue [here]( Alternatively, feel free to fork the repository, add your changes and issue a pull request. ## Citation If you are using `cytoviewer` in your work, please cite the paper as: ``` Meyer, L., Eling, N., & Bodenmiller, B. (2024). cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data. BMC Bioinformatics, ``` ## Authors [Lasse Meyer]( lasse.meyer 'at' [Nils Eling]( nils.eling 'at'