{
  "_id": "6a1be8481d7bb097a0a1beba",
  "Package": "cellmigRation",
  "Type": "Package",
  "Title": "Track Cells, Analyze Cell Trajectories and Compute Migration\nStatistics",
  "Version": "1.21.0",
  "Date": "2021-05-11",
  "Authors@R": "c(\nperson(\ngiven = \"Salim\",\nfamily = \"Ghannoum\",\nrole = c(\"aut\", \"cph\"),\nemail = \"salim.ghannoum@medisin.uio.no\"\n),\nperson(\ngiven = \"Damiano\",\nfamily = \"Fantini\",\nrole = c(\"aut\", \"cph\")\n),\nperson(\ngiven = \"Waldir\",\nfamily = \"Leoncio\",\nrole = c(\"cre\", \"aut\"),\nemail = \"w.l.netto@medisin.uio.no\"\n),\nperson(\ngiven = \"Øystein\",\nfamily = \"Sørensen\",\nrole = c(\"aut\")\n)\n)",
  "Description": "Import TIFF images of fluorescently labeled cells, and\ntrack cell movements over time. Parallelization is supported\nfor image processing and for fast computation of cell\ntrajectories. In-depth analysis of cell trajectories is enabled\nby 15 trajectory analysis functions.",
  "biocViews": "CellBiology, DataRepresentation, DataImport",
  "License": "GPL-2",
  "Encoding": "UTF-8",
  "LazyData": "false",
  "RoxygenNote": "7.1.1",
  "VignetteBuilder": "knitr",
  "BugReports": "https://github.com/ocbe-uio/cellmigRation/issues",
  "URL": "https://github.com/ocbe-uio/cellmigRation/",
  "Config/pak/sysreqs": "cmake make libicu-dev libjpeg-dev libtiff-dev\nlibuv1-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:55:39 UTC",
  "RemoteUrl": "https://github.com/bioc/cellmigRation",
  "RemoteRef": "HEAD",
  "RemoteSha": "ed6d00a32e56c3d89aba55b861d58ae58aca2109",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-31 06:42:46 UTC",
    "User": "root"
  },
  "Author": "Salim Ghannoum [aut, cph],\nDamiano Fantini [aut, cph],\nWaldir Leoncio [cre, aut],\nØystein Sørensen [aut]",
  "Maintainer": "Waldir Leoncio <w.l.netto@medisin.uio.no>",
  "MD5sum": "e00e6c10f8d02b1d9c86ec42e2f6d5e2",
  "_user": "bioc",
  "_type": "src",
  "_file": "cellmigRation_1.21.0.tar.gz",
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  "_filesize": 1223553,
  "_sha256": "a63ae8417611edc2d242d5615f84b58908dc4a206ddbe9bd9cfcb0466896e672",
  "_created": "2026-05-31T06:42:46.000Z",
  "_published": "2026-05-31T07:50:32.653Z",
  "_jobs": [
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  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 9
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26705545600",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/cellmigRation",
  "_commit": {
    "id": "ed6d00a32e56c3d89aba55b861d58ae58aca2109",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380939
  },
  "_maintainer": {
    "name": "Waldir Leoncio",
    "email": "w.l.netto@medisin.uio.no",
    "login": "wleoncio",
    "description": "Research Software Engineer @ocbe-uio",
    "uuid": 8234768
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Depends"
    },
    {
      "package": "foreach",
      "role": "Depends"
    },
    {
      "package": "tiff",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "matrixStats",
      "role": "Imports"
    },
    {
      "package": "FME",
      "role": "Imports"
    },
    {
      "package": "SpatialTools",
      "role": "Imports"
    },
    {
      "package": "sp",
      "role": "Imports"
    },
    {
      "package": "vioplot",
      "role": "Imports"
    },
    {
      "package": "FactoMineR",
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    {
      "package": "Hmisc",
      "role": "Imports"
    },
    {
      "package": "knitr",
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      "package": "ggplot2",
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    {
      "package": "BiocGenerics",
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    {
      "package": "BiocManager",
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    {
      "package": "kableExtra",
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    {
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  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
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  ],
  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "1.21.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.20.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "cellbiology",
    "datarepresentation",
    "dataimport",
    "bioconductor-package",
    "cell-tracking",
    "shiny",
    "trajectory-analysis"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "wleoncio",
      "count": 896,
      "uuid": 8234768
    },
    {
      "user": "systemsbiologist",
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  ],
  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 328,
    "source": "https://www.bioconductor.org/packages/stats/bioc/cellmigRation"
  },
  "_devurl": "https://github.com/ocbe-uio/cellmigration",
  "_searchresults": 6,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/cellmigRation.html",
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ocbe-uio/cellmigration",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aggregateFR",
    "aggregateTrackedCells",
    "CellMig",
    "CellMigPCA",
    "CellMigPCAclust",
    "CellMigPCAclustALL",
    "CellTracker",
    "ComputeTracksStats",
    "DiAutoCor",
    "DiRatio",
    "DiRatioPlot",
    "EstimateDiameterRange",
    "FilterTrackedCells",
    "FinRes",
    "FMI",
    "ForwardMigration",
    "getAvailableAggrMetrics",
    "getCellImages",
    "getCellMigSlot",
    "getCellsMeta",
    "getCellsStats",
    "getCellTrackMeta",
    "getCellTracks",
    "getCellTrackStats",
    "getDACtable",
    "getDiRatio",
    "getFMItable",
    "getForMigtable",
    "getImageCentroids",
    "getImageStacks",
    "getMSDtable",
    "getOptimizedParameters",
    "getOptimizedParams",
    "getPerAndSpeed",
    "getPopulationStats",
    "getProcessedImages",
    "getProcessingStatus",
    "getResults",
    "getTracks",
    "getVACtable",
    "LoadTiff",
    "MSD",
    "OptimizeParams",
    "PerAndSpeed",
    "plot3DAllTracks",
    "plot3DTracks",
    "plotAllTracks",
    "plotSampleTracks",
    "PlotTracksSeparately",
    "rmPreProcessing",
    "setAnalyticParams",
    "setCellMigSlot",
    "setCellsMeta",
    "setCellTracks",
    "setExpName",
    "setOptimizedParams",
    "setProcessedImages",
    "setProcessingStatus",
    "setTrackedCellsMeta",
    "setTrackedCentroids",
    "setTrackedPositions",
    "setTrackingStats",
    "VeAutoCor",
    "visualizeCellTracks",
    "VisualizeImg",
    "VisualizeStackCentroids",
    "wsaPreProcessing"
  ],
  "_datasets": [
    {
      "name": "preProcCellMig",
      "title": "Trajectories of 11 cells",
      "object": "preProcCellMig",
      "file": "preProcCellMig.rda",
      "class": [
        "CellMig"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ThreeConditions",
      "title": "Intermediates and Results from Cell Tracking Analyses",
      "object": "ThreeConditions",
      "file": "ThreeConditions.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "TrackCellsDataset",
      "title": "Sample Stack of Fluorescent Cells",
      "object": "TrackCellsDataset",
      "file": "TrackCellsDataset.rda",
      "class": [
        "trackedCells"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "TrajectoryDataset",
      "title": "Trajectories of 350 cells",
      "object": "TrajectoryDataset",
      "file": "TrajectoryDataset.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "X",
        "Y",
        "Track"
      ],
      "rows": 50216,
      "table": true,
      "tojson": true
    },
    {
      "name": "WSADataset",
      "title": "Trajectories of 147 cells",
      "object": "WSADataset",
      "file": "WSADataset.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "ID",
        "X",
        "Y",
        "track"
      ],
      "rows": 11970,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "aggregateFR",
      "title": "Aggregating the outcome of several experiments or conditions.",
      "topics": [
        "aggregateFR"
      ]
    },
    {
      "page": "aggregateTrackedCells",
      "title": "Aggregate trackedCells Objects",
      "topics": [
        "aggregateTrackedCells"
      ]
    },
    {
      "page": "CellMig-class",
      "title": "The CellMig Class.",
      "topics": [
        "CellMig",
        "CellMig-class",
        "initialize,CellMig-method"
      ]
    },
    {
      "page": "CellMigPCA",
      "title": "PCA",
      "topics": [
        "CellMigPCA"
      ]
    },
    {
      "page": "CellMigPCAclust",
      "title": "PCA Clusters",
      "topics": [
        "CellMigPCAclust"
      ]
    },
    {
      "page": "CellMigPCAclustALL",
      "title": "PCA Clusters of different conditions",
      "topics": [
        "CellMigPCAclustALL"
      ]
    },
    {
      "page": "CellTracker",
      "title": "Compute Cell Tracks",
      "topics": [
        "CellTracker"
      ]
    },
    {
      "page": "ComputeTracksStats",
      "title": "Compute Tracks Stats",
      "topics": [
        "ComputeTracksStats"
      ]
    },
    {
      "page": "DiAutoCor",
      "title": "Direction AutoCorrelation",
      "topics": [
        "DiAutoCor"
      ]
    },
    {
      "page": "DiRatio",
      "title": "Directionality Table",
      "topics": [
        "DiRatio"
      ]
    },
    {
      "page": "DiRatioPlot",
      "title": "Directionality Ratio plots",
      "topics": [
        "DiRatioPlot"
      ]
    },
    {
      "page": "EstimateDiameterRange",
      "title": "Detect Paricle Diameters in a Numeric matrix",
      "topics": [
        "EstimateDiameterRange"
      ]
    },
    {
      "page": "FilterTrackedCells",
      "title": "Filter an Aggregated Table of Cell Tracks",
      "topics": [
        "FilterTrackedCells"
      ]
    },
    {
      "page": "FinRes",
      "title": "Final Results",
      "topics": [
        "FinRes"
      ]
    },
    {
      "page": "FMI",
      "title": "Forward Migration Index",
      "topics": [
        "FMI"
      ]
    },
    {
      "page": "ForwardMigration",
      "title": "Forward Migration",
      "topics": [
        "ForwardMigration"
      ]
    },
    {
      "page": "getAvailableAggrMetrics",
      "title": "Get Available Aggregate Cell Metrics",
      "topics": [
        "getAvailableAggrMetrics"
      ]
    },
    {
      "page": "getCellImages",
      "title": "Method getCellImages",
      "topics": [
        "getCellImages",
        "getCellImages,trackedCells-method"
      ]
    },
    {
      "page": "getCellMigSlot",
      "title": "Method getCellMigSlot",
      "topics": [
        "getCellMigSlot",
        "getCellMigSlot,CellMig,character-method"
      ]
    },
    {
      "page": "getCellsMeta",
      "title": "Get MetaData",
      "topics": [
        "getCellsMeta"
      ]
    },
    {
      "page": "getCellsStats",
      "title": "Get Cell migration stats",
      "topics": [
        "getCellsStats"
      ]
    },
    {
      "page": "getCellTrackMeta",
      "title": "Method getCellTrackMeta",
      "topics": [
        "getCellTrackMeta",
        "getCellTrackMeta,trackedCells-method"
      ]
    },
    {
      "page": "getCellTracks",
      "title": "Method getCellTracks",
      "topics": [
        "getCellTracks",
        "getCellTracks,trackedCells-method"
      ]
    },
    {
      "page": "getCellTrackStats",
      "title": "Method getCellTrackStats",
      "topics": [
        "getCellTrackStats",
        "getCellTrackStats,trackedCells-method"
      ]
    },
    {
      "page": "getDACtable",
      "title": "Getting the Direction AutoCorrelation",
      "topics": [
        "getDACtable"
      ]
    },
    {
      "page": "getDiRatio",
      "title": "Getting the Directionality Table",
      "topics": [
        "getDiRatio"
      ]
    },
    {
      "page": "getFMItable",
      "title": "Getting the Forward Migration Index",
      "topics": [
        "getFMItable"
      ]
    },
    {
      "page": "getForMigtable",
      "title": "Getting the Forward Migration",
      "topics": [
        "getForMigtable"
      ]
    },
    {
      "page": "getImageCentroids",
      "title": "Method getImageCentroids",
      "topics": [
        "getImageCentroids",
        "getImageCentroids,trackedCells-method"
      ]
    },
    {
      "page": "getImageStacks",
      "title": "Get Image Stacks",
      "topics": [
        "getImageStacks"
      ]
    },
    {
      "page": "getMSDtable",
      "title": "Getting the Mean Square Displacement",
      "topics": [
        "getMSDtable"
      ]
    },
    {
      "page": "getOptimizedParameters",
      "title": "Get Auto Optimized Parameters",
      "topics": [
        "getOptimizedParameters"
      ]
    },
    {
      "page": "getOptimizedParams",
      "title": "Method getOptimizedParams",
      "topics": [
        "getOptimizedParams",
        "getOptimizedParams,trackedCells-method"
      ]
    },
    {
      "page": "getPerAndSpeed",
      "title": "Getting the table of Persistence and Speed.",
      "topics": [
        "getPerAndSpeed"
      ]
    },
    {
      "page": "getPopulationStats",
      "title": "Get Cell population stats",
      "topics": [
        "getPopulationStats"
      ]
    },
    {
      "page": "getProcessedImages",
      "title": "Method getProcessedImages",
      "topics": [
        "getProcessedImages",
        "getProcessedImages,trackedCells-method"
      ]
    },
    {
      "page": "getProcessingStatus",
      "title": "Method getProcessingStatus",
      "topics": [
        "getProcessingStatus",
        "getProcessingStatus,trackedCells-method"
      ]
    },
    {
      "page": "getResults",
      "title": "Final Results",
      "topics": [
        "getResults"
      ]
    },
    {
      "page": "getTracks",
      "title": "Get Track Data",
      "topics": [
        "getTracks"
      ]
    },
    {
      "page": "getVACtable",
      "title": "Getting the Velocity AutoCorrelation",
      "topics": [
        "getVACtable"
      ]
    },
    {
      "page": "LoadTiff",
      "title": "Import Image from TIFF",
      "topics": [
        "LoadTiff"
      ]
    },
    {
      "page": "MSD",
      "title": "Mean Square Displacement",
      "topics": [
        "MSD"
      ]
    },
    {
      "page": "OptimizeParams",
      "title": "Optimize Detection Params",
      "topics": [
        "OptimizeParams"
      ]
    },
    {
      "page": "PerAndSpeed",
      "title": "Persistence and Speed",
      "topics": [
        "PerAndSpeed"
      ]
    },
    {
      "page": "plot3DAllTracks",
      "title": "A 3D rose-plot of all cells",
      "topics": [
        "plot3DAllTracks"
      ]
    },
    {
      "page": "plot3DTracks",
      "title": "A 3D rose-plot",
      "topics": [
        "plot3DTracks"
      ]
    },
    {
      "page": "plotAllTracks",
      "title": "A 2D rose-plot",
      "topics": [
        "plotAllTracks"
      ]
    },
    {
      "page": "plotSampleTracks",
      "title": "A 2D rose-plot of sample cells",
      "topics": [
        "plotSampleTracks"
      ]
    },
    {
      "page": "PlotTracksSeparately",
      "title": "A graphical display of the track of each cell.",
      "topics": [
        "PlotTracksSeparately"
      ]
    },
    {
      "page": "rmPreProcessing",
      "title": "Data preprocessing for random migration (RM)",
      "topics": [
        "rmPreProcessing"
      ]
    },
    {
      "page": "setAnalyticParams",
      "title": "Method setAnalyticParams",
      "topics": [
        "setAnalyticParams",
        "setAnalyticParams,trackedCells,list-method"
      ]
    },
    {
      "page": "setCellMigSlot",
      "title": "Method setCellMigSlot",
      "topics": [
        "setCellMigSlot",
        "setCellMigSlot,CellMig,character,ANY-method",
        "setCellMigSlot,CellMig,character-method"
      ]
    },
    {
      "page": "setCellsMeta",
      "title": "Set MetaData",
      "topics": [
        "setCellsMeta"
      ]
    },
    {
      "page": "setCellTracks",
      "title": "Method setCellTracks",
      "topics": [
        "setCellTracks",
        "setCellTracks,trackedCells,matrix-method"
      ]
    },
    {
      "page": "setExpName",
      "title": "Method setExpName",
      "topics": [
        "setExpName",
        "setExpName,CellMig,character-method"
      ]
    },
    {
      "page": "setOptimizedParams",
      "title": "Method setOptimizedParams",
      "topics": [
        "setOptimizedParams",
        "setOptimizedParams,trackedCells,ANY,ANY-method",
        "setOptimizedParams,trackedCells-method"
      ]
    },
    {
      "page": "setProcessedImages",
      "title": "Method setProcessedImages",
      "topics": [
        "setProcessedImages",
        "setProcessedImages,trackedCells,list-method"
      ]
    },
    {
      "page": "setProcessingStatus",
      "title": "Method setProcessingStatus",
      "topics": [
        "setProcessingStatus",
        "setProcessingStatus,trackedCells,character,numeric-method"
      ]
    },
    {
      "page": "setTrackedCellsMeta",
      "title": "Method setTrackedCellsMeta",
      "topics": [
        "setTrackedCellsMeta",
        "setTrackedCellsMeta,trackedCells,list-method"
      ]
    },
    {
      "page": "setTrackedCentroids",
      "title": "Method setTrackedCentroids",
      "topics": [
        "setTrackedCentroids",
        "setTrackedCentroids,trackedCells,list-method"
      ]
    },
    {
      "page": "setTrackedPositions",
      "title": "Method setTrackedPositions",
      "topics": [
        "setTrackedPositions",
        "setTrackedPositions,trackedCells,data.frame-method"
      ]
    },
    {
      "page": "setTrackingStats",
      "title": "Method setTrackingStats",
      "topics": [
        "setTrackingStats",
        "setTrackingStats,trackedCells,ANY,ANY-method",
        "setTrackingStats,trackedCells-method"
      ]
    },
    {
      "page": "trackedCells-class",
      "title": "The trackedCells Class.",
      "topics": [
        "initialize,trackedCells-method",
        "trackedCells",
        "trackedCells-class"
      ]
    },
    {
      "page": "TrajectoryDataset",
      "title": "Trajectories of 350 cells",
      "topics": [
        "TrajectoryDataset"
      ]
    },
    {
      "page": "VeAutoCor",
      "title": "Velocity AutoCorrelation",
      "topics": [
        "VeAutoCor"
      ]
    },
    {
      "page": "visualizeCellTracks",
      "title": "Visualize Cell Tracks originating at an Image Stack",
      "topics": [
        "visualizeCellTracks"
      ]
    },
    {
      "page": "VisualizeStackCentroids",
      "title": "Visualize Cells in an Image Stack",
      "topics": [
        "VisualizeStackCentroids"
      ]
    },
    {
      "page": "wsaPreProcessing",
      "title": "Data preprocessing for wound scratch assay (WSA).",
      "topics": [
        "wsaPreProcessing"
      ]
    }
  ],
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    "timeDate",
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  ],
  "_vignettes": [
    {
      "source": "cellmigRation.Rmd",
      "filename": "cellmigRation.html",
      "title": "cellmigRation",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Summary",
        "Notes and Acknowledgmenets",
        "More resources",
        "Reproducibility",
        "Installation",
        "cellmigRation Pipeline",
        "Required libraries",
        "Module 1",
        "Importing TIFF files",
        "Optimizing Tracking Params",
        "Tracking Cell Movements",
        "Basic migration stats",
        "Basic Visualizations",
        "Aggregate Cell Tracks",
        "Module 2",
        "Import and Pre-process Cell Tracks",
        "Plotting tracks (2D and 3D)",
        "3D Plots",
        "Deep Trajectory Analysis",
        "Final Results",
        "Principal Component Analysis (PCA) and Cell Clustering",
        "Session & Environment"
      ],
      "created": "2021-03-05 08:45:16",
      "modified": "2021-03-19 11:23:13",
      "commits": 2
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