{
  "_id": "6acf8ef5e2d863f6629527d4",
  "Package": "simpleSeg",
  "Type": "Package",
  "Title": "A package to perform simple cell segmentation",
  "Description": "Image segmentation is the process of identifying the\nborders of individual objects (in this case cells) within an\nimage. This allows for the features of cells such as marker\nexpression and morphology to be extracted, stored and analysed.\nsimpleSeg provides functionality for user friendly, watershed\nbased segmentation on multiplexed cellular images in R based on\nthe intensity of user specified protein marker channels.\nsimpleSeg can also be used for the normalization of single cell\ndata obtained from multiple images.",
  "Version": "1.15.2",
  "Date": "2026-10-14",
  "Authors@R": "c(person(\"Nicolas\", \"Canete\", email = \"nicolas.canete@sydney.edu.au\",\nrole = c(\"aut\")),\nperson(\"Alexander\", \"Nicholls\", email = \"alexanderwnicholls@gmail.com\",\nrole = c(\"aut\")),\nperson(\"Ellis\", \"Patrick\", email = \"ellis.patrick@sydney.edu.au\",\nrole = c(\"aut\", \"cre\")))",
  "VignetteBuilder": "knitr",
  "Encoding": "UTF-8",
  "biocViews": "Classification, Survival, SingleCell, Normalization, Spatial",
  "License": "GPL-3",
  "Config/testthat/edition": "3",
  "BugReports": "https://github.com/SydneyBioX/simpleSeg/issues",
  "URL": "https://sydneybiox.github.io/simpleSeg/\nhttps://github.com/SydneyBioX/simpleSeg",
  "Config/roxygen2/version": "8.0.0",
  "RoxygenNote": "7.3.3",
  "Config/pak/sysreqs": "cmake libfftw3-dev libfontconfig1-dev\nlibfreetype6-dev libfribidi-dev libgdal-dev gdal-bin\nlibgeos-dev make libharfbuzz-dev libmagick++-dev gsfonts\nlibicu-dev libjpeg-dev libpng-dev libtiff-dev libuv1-dev\nlibssl-dev libproj-dev libsqlite3-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-10-14 06:20:17 UTC",
  "RemoteUrl": "https://github.com/bioc/simpleSeg",
  "RemoteRef": "HEAD",
  "RemoteSha": "5304f331faac14c64f7ede972b0409ba14e555ee",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-14 13:53:35 UTC",
    "User": "root"
  },
  "Author": "Nicolas Canete [aut],\nAlexander Nicholls [aut],\nEllis Patrick [aut, cre]",
  "Maintainer": "Ellis Patrick <ellis.patrick@sydney.edu.au>",
  "_user": "bioc",
  "_type": "src",
  "_file": "simpleSeg_1.15.2.tar.gz",
  "_fileid": "https://r2.ropensci.org/8a8124e2738d5ad05dbf865b50189cb86e8e959a81e1b5e47078cbd3f9e33698",
  "_filesize": 4691388,
  "_sha256": "8a8124e2738d5ad05dbf865b50189cb86e8e959a81e1b5e47078cbd3f9e33698",
  "_expires": "2027-01-22T14:17:23.000Z",
  "_created": "2026-10-14T13:53:35.000Z",
  "_published": "2026-10-14T14:17:25.477Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 9
  },
  "_upstream": "https://github.com/bioc/simpleSeg",
  "_commit": {
    "id": "5304f331faac14c64f7ede972b0409ba14e555ee",
    "author": "EllisPatrick <ellis.patrick@sydney.edu.au>",
    "committer": "EllisPatrick <ellis.patrick@sydney.edu.au>",
    "message": "Cell body models on 1,000,000 sampled pixels; no-data pixels keep their value\n\nCo-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>\nClaude-Session: https://claude.ai/code/session_01Y1YeeuxPhptPfm3pWGocSU\n",
    "time": 1791958817
  },
  "_maintainer": {
    "name": "Ellis Patrick",
    "email": "ellis.patrick@sydney.edu.au",
    "login": "ellispatrick",
    "twitter": "@TheEllisPatrick",
    "description": "",
    "uuid": 8390021
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 115892689797,
      "time": 255,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11899319191"
    },
    {
      "job": 115892690368,
      "time": 508,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11901475474"
    },
    {
      "job": 115892690017,
      "time": 673,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11902385681"
    },
    {
      "job": 115892690074,
      "time": 499,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11901320493"
    },
    {
      "job": 115892690059,
      "time": 586,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11901945630"
    },
    {
      "job": 115892690555,
      "time": 640,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11900767055"
    },
    {
      "job": 115892689900,
      "time": 1326,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11902597569"
    },
    {
      "job": 115892690269,
      "time": 727,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11902235938"
    },
    {
      "job": 115892689911,
      "time": 1128,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11902696774"
    },
    {
      "job": 115888836319,
      "time": 453,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11899048738"
    },
    {
      "job": 115892689943,
      "time": 215,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11900855514"
    },
    {
      "job": 115892691187,
      "time": 771,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11900422898"
    },
    {
      "job": 115892690224,
      "time": 615,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11901345798"
    },
    {
      "job": 115892690449,
      "time": 563,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11901965528"
    },
    {
      "job": 115892690694,
      "time": 556,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11901445613"
    },
    {
      "job": 115892690542,
      "time": 570,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11900836626"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "BiocParallel",
      "role": "Imports"
    },
    {
      "package": "EBImage",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "RhpcBLASctl",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "cytomapper",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "terra",
      "role": "Suggests"
    },
    {
      "package": "SpatialExperiment",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-42",
      "n": 9
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.15.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.14.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "classification",
    "survival",
    "singlecell",
    "normalization",
    "spatial",
    "spatial-statistics",
    "cpp"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "nick-robo",
      "count": 126,
      "uuid": 17681331
    },
    {
      "user": "ellispatrick",
      "count": 73,
      "uuid": 8390021
    },
    {
      "user": "anic0077",
      "count": 36,
      "uuid": 82946312
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "nickcee",
      "count": 4,
      "uuid": 22989881
    },
    {
      "user": "shreyarajeshrao",
      "count": 1,
      "uuid": 99242186
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 477,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 557,
    "source": "https://www.bioconductor.org/packages/stats/bioc/simpleSeg"
  },
  "_devurl": "https://github.com/sydneybiox/simpleseg",
  "_pkgdown": "https://sydneybiox.github.io/simpleSeg/",
  "_searchresults": 28,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/simpleSeg.html"
  ],
  "_homeurl": "https://github.com/sydneybiox/simpleseg",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "normalizeCells",
    "simpleSeg"
  ],
  "_help": [
    {
      "page": "normalizeCells",
      "title": "Normalizes and transforms cell data in preparation for clustering (accepts dataframe, SingleCellExperiment and SpatialExperiment).",
      "topics": [
        "normalizeCells"
      ]
    },
    {
      "page": "simpleSeg",
      "title": "Perform simple segmentation of multiplexed cellular images",
      "topics": [
        "simpleSeg"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/simpleSeg/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "askpass",
    "base64enc",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocFileCache",
    "BiocGenerics",
    "biocmake",
    "BiocParallel",
    "bit",
    "bit64",
    "bitops",
    "blob",
    "bslib",
    "cachem",
    "cli",
    "codetools",
    "commonmark",
    "cpp11",
    "curl",
    "cytomapper",
    "DBI",
    "dbplyr",
    "DelayedArray",
    "digest",
    "dir.expiry",
    "dplyr",
    "EBImage",
    "evaluate",
    "farver",
    "fastmap",
    "fftwtools",
    "filelock",
    "fontawesome",
    "formatR",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggbeeswarm",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "h5mread",
    "HDF5Array",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "httr2",
    "IRanges",
    "isoband",
    "jpeg",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "lambda.r",
    "later",
    "lattice",
    "lifecycle",
    "locfit",
    "magick",
    "magrittr",
    "Matrix",
    "MatrixGenerics",
    "matrixStats",
    "memoise",
    "mime",
    "nnls",
    "openssl",
    "otel",
    "pillar",
    "pkgconfig",
    "png",
    "promises",
    "purrr",
    "R6",
    "rappdirs",
    "raster",
    "RColorBrewer",
    "Rcpp",
    "RCurl",
    "rhdf5",
    "rhdf5filters",
    "Rhdf5lib",
    "RhpcBLASctl",
    "rjson",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "Seqinfo",
    "shiny",
    "shinydashboard",
    "SingleCellExperiment",
    "snow",
    "sourcetools",
    "sp",
    "SparseArray",
    "SpatialExperiment",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "svglite",
    "svgPanZoom",
    "sys",
    "systemfonts",
    "terra",
    "textshaping",
    "tibble",
    "tidyr",
    "tidyselect",
    "tiff",
    "tinytex",
    "utf8",
    "vctrs",
    "vipor",
    "viridis",
    "viridisLite",
    "withr",
    "xfun",
    "xtable",
    "XVector",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "simpleSeg.Rmd",
      "filename": "simpleSeg.html",
      "title": "Segmenting and normalizing multiplexed imaging data with simpleSeg",
      "author": "Alexander Nicholls, Ellis Patrick, Nicolas Canete",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installation",
        "Overview",
        "Load example data",
        "Segmentation",
        "Visualise separation",
        "Visualise outlines",
        "Methods of Watershedding",
        "Methods of cell body identification",
        "Parallel Processing",
        "Summarise cell features",
        "Segmenting image files",
        "Normalising cells",
        "QC normalisation",
        "Session Info"
      ],
      "created": "2022-05-30 04:01:29",
      "modified": "2026-10-14 06:20:17",
      "commits": 39
    }
  ],
  "_score": 4.845098040014257,
  "_indexed": true,
  "_nocasepkg": "simpleseg",
  "_universes": [
    "bioc",
    "ellispatrick",
    "sydneybiox"
  ],
  "_previous": "1.15.1",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.15.2",
      "date": "2026-10-14T13:57:45.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/d8712fb8d058c6a6c21c90e327fe93398d06dd004ac0ae81f6c9bf4d0ec954dc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.15.2",
      "date": "2026-10-14T13:58:33.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/ae0c716c21efa634f5cbcdfdd49a1355c386c50d607fa1a32b46ed6e16079c07",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.15.2",
      "date": "2026-10-14T13:57:38.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/4059a938e29df1a18a7db6a9095ad7c01d4e6877e8c3dd6694a7220fa977986c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.15.2",
      "date": "2026-10-14T13:58:30.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/787e2731cd166e5a3f7ff65bc07552212849a23ac02fde1ad1ebd800be2a793c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.15.2",
      "date": "2026-10-14T13:56:38.000Z",
      "arch": "aarch64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/5c28b83a0ae84239f9c2d99b86f1435bdce8e2a9b260214ff0a92fc07cc88808",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.15.2",
      "date": "2026-10-14T14:00:21.000Z",
      "arch": "x86_64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/6f341109143a2e000413d56211456a7af8e1d9019d00543e65298b7218f83af6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.15.2",
      "date": "2026-10-14T13:56:51.000Z",
      "arch": "aarch64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/510c2c73becdee60edb0d71cad7eddccca608ce1d86a2c0064a6b15d18e570b0",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.15.2",
      "date": "2026-10-14T13:59:12.000Z",
      "arch": "x86_64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/d86b566a78aeb8d6d55892907c155d2bde64258001772b8d1012062ac784fa01",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.15.2",
      "date": "2026-10-14T13:58:09.000Z",
      "arch": "emscripten",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/a4304d4ec90f9e2291c2a197019229aa369c2c011d93e4a206c052ba048995e1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.15.2",
      "date": "2026-10-14T14:01:33.000Z",
      "arch": "aarch64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/9c890ee40fba646b231feb5a58840175a4a8af9c95e0864480bb6f9302be0ba4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.15.2",
      "date": "2026-10-14T13:56:08.000Z",
      "arch": "x86_64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/8de7c2cb33a79d1ffc76839f678700d019a75cfbf88840678945a9d714b351bb",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.15.2",
      "date": "2026-10-14T13:56:11.000Z",
      "arch": "x86_64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/23353f505e931cf8dcb7fd2d2237bb367d3c83fe5684eb4d72c3275104b8aa90",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.15.2",
      "date": "2026-10-14T13:57:52.000Z",
      "arch": "aarch64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/3e05c50daf22d08b3c00527459f740dc145918ee12ff1e0091ce5a996423fc6e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.15.2",
      "date": "2026-10-14T13:56:47.000Z",
      "arch": "x86_64",
      "commit": "5304f331faac14c64f7ede972b0409ba14e555ee",
      "fileid": "https://r2.ropensci.org/324b545f4ab5f569c389da9389957ac628a9c6ef80e79030ad22eb2958d27323",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/38574716637"
    }
  ]
}