{"id":18785260,"url":"https://github.com/andreped/vsi2tif","last_synced_at":"2025-07-18T03:02:58.033Z","repository":{"id":45465912,"uuid":"318510772","full_name":"andreped/vsi2tif","owner":"andreped","description":"Simple tool for converting WSIs from cellSens VSI to pyramidal TIFF","archived":false,"fork":false,"pushed_at":"2025-01-30T19:33:37.000Z","size":619,"stargazers_count":18,"open_issues_count":2,"forks_count":5,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-04-13T05:36:32.979Z","etag":null,"topics":["bftools","bioformats","cellsens","converter","cucim","fast","generic","olympus","openslide","pyfast","pyramidal","pyvips","tif","tiff","vips","vsi","wsi"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/andreped.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-12-04T12:31:51.000Z","updated_at":"2025-04-08T04:17:48.000Z","dependencies_parsed_at":"2023-10-20T17:09:38.100Z","dependency_job_id":"831bc702-9905-4dd8-b7e2-fad9b32575c7","html_url":"https://github.com/andreped/vsi2tif","commit_stats":{"total_commits":16,"total_committers":3,"mean_commits":5.333333333333333,"dds":0.1875,"last_synced_commit":"bc61e7bb6813ff41d0154683970287115b498e66"},"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andreped%2Fvsi2tif","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andreped%2Fvsi2tif/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andreped%2Fvsi2tif/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/andreped%2Fvsi2tif/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/andreped","download_url":"https://codeload.github.com/andreped/vsi2tif/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248670506,"owners_count":21142897,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bftools","bioformats","cellsens","converter","cucim","fast","generic","olympus","openslide","pyfast","pyramidal","pyvips","tif","tiff","vips","vsi","wsi"],"created_at":"2024-11-07T20:46:05.433Z","updated_at":"2025-04-13T12:33:46.302Z","avatar_url":"https://github.com/andreped.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# [vsi2tif](https://github.com/andreped/vsi2tif#vsi2tif)\n\n[![License](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)\n[![Pip Downloads](https://img.shields.io/pypi/dm/vsi2tif?label=pip%20downloads\u0026logo=python)](https://pypi.org/project/vsi2tif/)\n[![PyPI version](https://badge.fury.io/py/vsi2tif.svg)](https://badge.fury.io/py/vsi2tif)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13745169.svg)](https://doi.org/10.5281/zenodo.13745169)\n\u003ca href=\"https://colab.research.google.com/gist/andreped/0e945c30ebb01b309a36162d9ec133ae/vsi2tif-converting-olympus-wsi-to-generic-tiff-ubuntu-linux.ipynb\" target=\"_parent\"\u003e\u003cimg src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/\u003e\u003c/a\u003e\n\nTool for converting WSIs from Olympus' cellSens VSI to Generic TIFF.\n\nTo quickly get started, see these notebooks ([Ubuntu Linux](https://github.com/andreped/vsi2tif/blob/main/notebooks/conversion_tutorial_ubuntu_linux.ipynb), [macOS](https://github.com/andreped/vsi2tif/blob/main/notebooks/conversion_tutorial_macos.ipynb)) for installing the tool, converting your first image, and verifying that the image works with OpenSlide.\n\n## [Continuous integration](https://github.com/andreped/vsi2tif#continuous-integration)\n\n| Build Type | Status |\n| - | - |\n| **Integration Tests** | [![CI](https://github.com/andreped/vsi2tif/workflows/Integration%20Tests/badge.svg)](https://github.com/andreped/vsi2tif/actions) |\n| **Unit Tests** | [![CI](https://github.com/andreped/vsi2tif/workflows/Build%20Package/badge.svg)](https://github.com/andreped/vsi2tif/actions) |\n| **Linting Checks** | [![CI](https://github.com/andreped/vsi2tif/workflows/Check%20Linting/badge.svg)](https://github.com/andreped/vsi2tif/actions) |\n\n## [Requirements](https://github.com/andreped/vsi2tif#requirements)\n\nTo run the tool, you need to configure bftools and vips. To do that, follow the instructions below for the operating system of interest:\n\n\u003cdetails open\u003e\n\u003csummary\u003e\n\n### [Ubuntu](https://github.com/andreped/vsi2tif#ubuntu)\u003c/summary\u003e\n\n1. Download bftools (click [here](http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip))\n\n2. Install vips and JDK\n```\nsudo apt update\nsudo apt-get install openjdk-8-jdk\nsudo apt install libvips-tools\n```\n\n\u003c/details\u003e\n\n\n\u003cdetails\u003e\n\u003csummary\u003e\n\n### [macOS](https://github.com/andreped/vsi2tif#macos)\u003c/summary\u003e\n\n1. Download bftools (click [here](http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip))\n\n2. Install vips and JDK\n```\nbrew install --cask zulu@8\nbrew install vips\n```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n\u003csummary\u003e\n\n### [Windows](https://github.com/andreped/vsi2tif#windows)\u003c/summary\u003e\n\nTo install bftools and vips, I recommend using Powershell as much as possible to automate the installation steps.\n\n1. Download bftools (click [here](http://downloads.openmicroscopy.org/latest/bio-formats5.6/artifacts/bftools.zip))\n\n2. Download vips binary from Windows from [here](https://github.com/libvips/build-win64-mxe/releases) or use wget or similar\n```\nhttps://github.com/libvips/build-win64-mxe/releases/download/v8.15.3/vips-dev-w64-all-8.15.3.zip\n```\n\n3. Uncompress downloaded file and place it at an appropriate place, like at home\n```\nunzip ~/Downloads/vips-dev-w64-all-8.15.3.zip\nmv ~/Downloads/vips-dev-w64-all-8.15.3/vips-dev-8.15/ ~/vips-dev-8.15/\n```\n\n4. Add path to `vips.exe` to the PATH (requires powershell administrator)\n```\n$Env:PATH += \";$HOME/vips-dev-8.15/bin/\"\n```\n\n\u003c/details\u003e\n\n\n## [Installation](https://github.com/andreped/vsi2tif#installation)\n\nInstall from source:\n```\npip install git+https://github.com/andreped/vsi2tif\n```\n\n## [Usage](https://github.com/andreped/vsi2tif#usage)\n\nThe conversion tool is available through a command line interface (CLI).\n\nExample for converting a single WSI:\n```\nvsi2tif -i /path/to/olympus/image.vsi -o /path/to/converted/image.tif -b /path/to/bftools/bfconvert\n```\n\nHere is an example to perform batch conversion of a folder of WSIs:\n```\nvsi2tif -i /path/to/olympus/wsis/ -o /path/to/converted/wsis/directory/ -b /path/to/bftools/bfconvert\n```\n\nComprehensive CLI documentation can be seen below:\n\n```\nusage: vsi2tif [-h] -i INPUT -o OUTPUT -b BFCONVERT [-c COMPRESSION] [-s TILESIZE] [-q QUALITY] [-m MAX_MEM] [-v VERBOSE] [--remove-name-spaces] [-p PLANE] [--noskip-converted] [-f EXTENSION]\n\nvsi2tif - simple tool for converting images from cellSens VSI to Generic TIFF\n\noptions:\n  -h, --help            show this help message and exit\n  -i INPUT, --input INPUT\n                        folder with input files\n  -o OUTPUT, --output OUTPUT\n                        folder for output files\n  -b BFCONVERT, --bfconvert BFCONVERT\n                        path to bfconvert tool\n  -c COMPRESSION, --compression COMPRESSION\n                        compression technique for final image - default 'jpeg'\n  -s TILESIZE, --tilesize TILESIZE\n                        tile size to use during both conversion steps - default 1024\n  -q QUALITY, --quality QUALITY\n                        compression quality used with JPEG compression - default 87\n  -m MAX_MEM, --max-mem MAX_MEM\n                        set maximum memory in the java vm - default 32\n  -v VERBOSE, --verbose VERBOSE\n                        set verbosity level - default 1\n  --remove-name-spaces  replace spaces in filename with underscores in batch mode\n  -p PLANE, --plane PLANE\n                        image plane to convert image from. If set to -1, all series are converted and the largest is kept - default 0\n  --noskip-converted    To specifically request existing files to be converted again\n  -f EXTENSION, --extension EXTENSION\n                        extension type to consider (e.g., .vsi)\n```\n\n## [License](https://github.com/andreped/vsi2tif#license)\n\nThis project has [MIT license](https://github.com/andreped/vsi2tif/blob/main/LICENSE).\n\n## [How to cite](https://github.com/andreped/vsi2tif#how-to-cite) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13745169.svg)](https://doi.org/10.5281/zenodo.13745169)\n\nIf you found this tool useful in your research, please cite the following:\n```\n@software{pedersen2024vsi2tif,\n  author       = {André Pedersen and David Bouget and Sebastian Krossa and Erik Smistad},\n  title        = {{andreped/vsi2tif: v0.1.4}},\n  month        = sep,\n  year         = 2024,\n  publisher    = {Zenodo},\n  version      = {v0.1.4},\n  doi          = {10.5281/zenodo.13745169},\n  url          = {https://doi.org/10.5281/zenodo.13745169}\n}\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandreped%2Fvsi2tif","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fandreped%2Fvsi2tif","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fandreped%2Fvsi2tif/lists"}