{ "_id": "6ae84505818c9e3ef6dbd5af", "Package": "AiES", "Type": "Package", "Title": "Axon Integrity Evaluation System for Microscopy Images", "Version": "1.0.0", "Authors@R": "c(\nperson(\"Shinji\", \"Tokunaga\", email = \"tokunaga@ncnp.go.jp\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-8398-3054\")),\nperson(\"Masabumi\", \"Funakoshi\", email = \"funakoshi@ncnp.go.jp\", role = \"ctb\"),\nperson(\"Toshiyuki\", \"Araki\", email = \"taraki@ncnp.go.jp\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3625-2042\")),\nperson(\"National Center of Neurology and Psychiatry\", role = \"cph\")\n)", "Description": "Provides tools for the quantitative analysis of axon\nintegrity in phase-contrast microscopy images. 'AiES' (Axon\nintegrity Evaluation System) implements image pre-processing,\nadaptive thresholding, feature extraction, and support vector\nmachine-based classification to compute indices such as the\nAxon Integrity Index (AII) and Degeneration Index (DI). Two\nbuilt-in models are provided, and classifiers can be re-trained\non user data. The package is designed for reproducible and\nautomated analysis in neuroscience research.", "License": "BSD_3_clause + file LICENSE", "Copyright": "2025 National Center of Neurology and Psychiatry", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "URL": "https://github.com/BreezyCave/AiES", "BugReports": "https://github.com/BreezyCave/AiES/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "cmake libfftw3-dev make libjpeg-dev libpng-dev\nlibtiff-dev libuv1-dev", "Repository": "https://breezycave.r-universe.dev", "Date/Publication": "2026-11-02 06:14:15 UTC", "RemoteUrl": "https://github.com/breezycave/aies", "RemoteRef": "HEAD", "RemoteSha": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "NeedsCompilation": "no", "Packaged": { "Date": "2026-11-02 07:54:59 UTC", "User": "root" }, "Author": "Shinji Tokunaga [aut, cre] (ORCID:\n),\nMasabumi Funakoshi [ctb],\nToshiyuki Araki [ctb] (ORCID: ),\nNational Center of Neurology and Psychiatry [cph]", "Maintainer": "Shinji Tokunaga ", "_user": "breezycave", "_type": "src", "_file": "AiES_1.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/d50d4f689cdf29592686fa52d22ed7ddd6df53fe51084816ab2c5e8f1f57b9bf", "_filesize": 1456448, "_sha256": "d50d4f689cdf29592686fa52d22ed7ddd6df53fe51084816ab2c5e8f1f57b9bf", "_expires": "2027-02-10T08:08:35.000Z", "_created": "2026-11-02T07:54:59.000Z", "_published": "2026-11-02T08:08:37.204Z", "_upstream": "https://github.com/breezycave/aies", "_status": "success", "_maintainer": { "name": "Shinji Tokunaga", "email": "tokunaga@ncnp.go.jp", "orcid": "0000-0001-8398-3054" }, "_jobs": [ { "job": 125158724165, "time": 143, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13124633340" }, { "job": 125158723878, "time": 118, "config": "linux-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13125041955" }, { "job": 125158723819, "time": 110, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "13125896117" }, { "job": 125158723796, "time": 114, "config": "macos-release-arm64", "r": "4.6.2", "check": "OK", "artifact": "13125296829" }, { "job": 125157699540, "time": 179, "config": "source", "r": "4.6.2", "check": "OK", "artifact": "13124229622" }, { "job": 125158723823, "time": 97, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "13124359427" }, { "job": 125158723818, "time": 88, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "13124742063" }, { "job": 125158723946, "time": 86, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "13124433942" }, { "job": 125158723861, "time": 78, "config": "windows-release-x86_64", "r": "4.6.2", "check": "OK", "artifact": "13125475149" } ], "_buildurl": "https://github.com/r-universe/breezycave/actions/runs/41409020808", "_commit": { "id": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "author": "Shinji TOKUNAGA <34032561+BreezyCave@users.noreply.github.com>", "committer": "GitHub ", "message": "Delete R/axDistmap_v1_00_15.R", "time": 1793600055 }, "_distro": "resolute", "_host": "GitHub-Actions", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.6.0", "role": "Depends" }, { "package": "EBImage", "role": "Imports" }, { "package": "e1071", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "fs", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "data.table", "role": "Imports" }, { "package": "rstudioapi", "role": "Imports" }, { "package": "tiff", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "tcltk", "role": "Suggests" }, { "package": "svDialogs", "role": "Suggests" } ], "_owner": "breezycave", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-44", "n": 1 }, { "week": "2026-45", "n": 1 } ], "_tags": [], "_stars": 0, "_contributors": [ { "user": "breezycave", "count": 85, "uuid": 34032561 } ], "_userbio": { "uuid": 34032561, "type": "user", "name": "Shinji TOKUNAGA", "followers": 0 }, "_downloads": { "count": 351, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/AiES" }, "_devurl": "https://github.com/breezycave/aies", "_searchresults": 5, "_rbuild": "4.6.2", "_assets": [ "extra/AiES.html", "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", "LICENSE" ], "_homeurl": "https://github.com/breezycave/aies", "_realowner": "breezycave", "_cranurl": true, "_releases": [ { "version": "0.99.6", "date": "2025-06-06" } ], "_exports": [ "axDistmap", "axQnt", "axSvm" ], "_help": [ { "page": "AiES-package", "title": "AiES: Axon Integrity Evaluation System", "topics": [ "AiES-package", "AiES" ] }, { "page": "Axdistmap", "title": "Create distance map and binary image from image file", "topics": [ "axDistmap" ] }, { "page": "AxQnt", "title": "Quantify Axon Integrity and Degeneration Indices from Images or Feature Data", "topics": [ "axQnt" ] }, { "page": "Axsvm", "title": "Build SVM Classifier for Axon Image Feature Classification", "topics": [ "axSvm" ] } ], "_readme": "https://github.com/breezycave/aies/raw/HEAD/README.md", "_rundeps": [ "abind", "base64enc", "BiocGenerics", "bitops", "bslib", "cachem", "class", "cli", "data.table", "digest", "e1071", "EBImage", "evaluate", "fastmap", "fftwtools", "fontawesome", "fs", "generics", "highr", "htmltools", "htmlwidgets", "jpeg", "jquerylib", "jsonlite", "knitr", "lattice", "lifecycle", "locfit", "memoise", "mime", "png", "proxy", "R6", "rappdirs", "RCurl", "rlang", "rmarkdown", "rstudioapi", "sass", "tiff", "tinytex", "xfun", "yaml" ], "_vignettes": [ { "source": "Introduction_to_AiES.Rmd", "filename": "Introduction_to_AiES.html", "title": "Introduction to AiES: Axon integrity Evaluation System", "author": "Shinji Tokunaga, Masabumi Funakoshi, Toshiyuki Araki", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Typical Workflow", "1. Feature Extraction from Images (axDistmap)", "2. Building an SVM Classifier (axSvm)", "3. Quantitative Analysis (axQnt)", "Advanced Usage", "Built-in models", "Pixel size and image formats", "Exporting all features", "Training and applying a custom model", "Sampling and reproducibility", "Quantifying from feature tables", "Upgrading from AiES 0.99.x", "Summary", "Source code and issues" ], "created": "2026-11-01 12:58:29", "modified": "2026-11-01 12:58:29", "commits": 1 } ], "_score": 4, "_indexed": true, "_nocasepkg": "aies", "_universes": [ "breezycave" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.0", "date": "2026-11-02T07:57:27.000Z", "distro": "resolute", "commit": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "fileid": "https://r2.ropensci.org/8c8861452eac2e1c2887730d1205ee9ee09b835d5659b9c3a76dc0e5a2022c3f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breezycave/actions/runs/41409020808" }, { "r": "4.6.2", "os": "linux", "version": "1.0.0", "date": "2026-11-02T07:56:50.000Z", "distro": "resolute", "commit": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "fileid": "https://r2.ropensci.org/5e4cf3d71c66a45473516b647b742a91ab5cd964f123ac2ff64daa3519557a14", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breezycave/actions/runs/41409020808" }, { "r": "4.5.3", "os": "mac", "version": "1.0.0", "date": "2026-11-02T08:07:51.000Z", "commit": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "fileid": "https://r2.ropensci.org/1b3d3ce6d6b0b03d33aa03bb3487deb9f1679644765a01997bb6904c3222f1a4", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breezycave/actions/runs/41409020808" }, { "r": "4.6.2", "os": "mac", "version": "1.0.0", "date": "2026-11-02T08:04:47.000Z", "commit": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "fileid": "https://r2.ropensci.org/9b7f67da588c8d677c18232427ea6c78fe7d81daa1d50d126b274695139c6d46", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breezycave/actions/runs/41409020808" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.0", "date": "2026-11-02T07:56:54.000Z", "commit": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "fileid": "https://r2.ropensci.org/9ff8584fd898997f04aabf81dab88e12b425c7866c77b9a202e8cdaa76a07710", "status": "success", "buildurl": "https://github.com/r-universe/breezycave/actions/runs/41409020808" }, { "r": "4.7.0", "os": "win", "version": "1.0.0", "date": "2026-11-02T07:56:14.000Z", "commit": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "fileid": "https://r2.ropensci.org/36829805842ec95587bdefa1bce44b16aa8cd86e3c48903f9f72d1699bd4a512", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breezycave/actions/runs/41409020808" }, { "r": "4.5.3", "os": "win", "version": "1.0.0", "date": "2026-11-02T07:56:13.000Z", "commit": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "fileid": "https://r2.ropensci.org/480f419a8210d0def8ff5a6647820c360bfcd22e0ada557959c79939841aac14", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breezycave/actions/runs/41409020808" }, { "r": "4.6.2", "os": "win", "version": "1.0.0", "date": "2026-11-02T07:56:00.000Z", "commit": "2f9c9d0160fb673a57f2c915a5b53cb012634490", "fileid": "https://r2.ropensci.org/ec842f3ab9f9a657924e4fb86d6297022fed6c165ee07484c4071efca0d3b2ef", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/breezycave/actions/runs/41409020808" } ] }