{"id":25237177,"url":"https://github.com/aafkegros/MicroscopyNodes","last_synced_at":"2025-10-26T12:30:42.371Z","repository":{"id":198018166,"uuid":"699879669","full_name":"oanegros/MicroscopyNodes","owner":"oanegros","description":"Loading and handling microscopy data in blender","archived":false,"fork":false,"pushed_at":"2025-01-23T08:54:39.000Z","size":515244,"stargazers_count":108,"open_issues_count":18,"forks_count":8,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-01-23T09:33:33.754Z","etag":null,"topics":["blender","blender-addon","microscopy","volume-rendering"],"latest_commit_sha":null,"homepage":"https://oanegros.github.io/MicroscopyNodes/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/oanegros.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":"2023-10-03T14:19:28.000Z","updated_at":"2025-01-23T08:54:20.000Z","dependencies_parsed_at":"2023-11-06T23:02:32.349Z","dependency_job_id":"133e3a05-14d3-47df-af58-1705af108a38","html_url":"https://github.com/oanegros/MicroscopyNodes","commit_stats":null,"previous_names":["oanegros/tif2bpy","oanegros/tif2blender","oanegros/microscopynodes"],"tags_count":16,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oanegros%2FMicroscopyNodes","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oanegros%2FMicroscopyNodes/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oanegros%2FMicroscopyNodes/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/oanegros%2FMicroscopyNodes/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/oanegros","download_url":"https://codeload.github.com/oanegros/MicroscopyNodes/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238320478,"owners_count":19452560,"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":["blender","blender-addon","microscopy","volume-rendering"],"created_at":"2025-02-11T15:33:32.174Z","updated_at":"2025-10-26T12:30:42.359Z","avatar_url":"https://github.com/oanegros.png","language":"Python","funding_links":[],"categories":["🌻 Visualization"],"sub_categories":[],"readme":"# \u003cimg src=\"./docs/grey_icons/icon_microscopy_nodes.svg\" width=\"40\" style=\"vertical-align:-0.4em;\"/\u003e Microscopy in Blender\n\n**Microscopy Nodes** is a Blender add-on for visualizing high-dimensional microscopy data—designed for scientists, or anyone working with biological images 😊.\n\n For any type of microscopy: fluorescence, electron microscopy, or anything in between! This tool helps you turn complex 3D+ datasets into stunning, accurate, and animatable visualizations. \n\nUsage questions are mainly answered on the [image.sc forum](https://forum.image.sc/tag/microscopy-nodes)\n\n## \u003cimg src=\"./docs/grey_icons/blender_icon_settings.svg\" width=\"20\" style=\"vertical-align:-0.2em;\"/\u003e  What It Does\n\nMicroscopy Nodes supports importing **up to 5D** microscopy datasets (XYZ + time + channels) from `.tif` and **OME-Zarr** files, setting easy and adaptable settings to start with visualizing your data.\n\n\n| Feature | Description |\n|--------|-------------|\n| **5D Support** | Load `.tif` and `.zarr` files with any axis order 'tzcyx' or any subset |\n| **Channel Interface** | Define how to load each channel: \u003cimg src=\"./docs/grey_icons/blender_icon_outliner_data_volume.svg\" width=\"15\" style=\"vertical-align:-0.2em;\"/\u003e volume, \u003cimg src=\"./docs/grey_icons/blender_icon_outliner_data_surface.svg\" width=\"15\" style=\"vertical-align:-0.2em;\"/\u003e surface, \u003cimg src=\"./docs/grey_icons/blender_icon_outliner_data_pointcloud.svg\" width=\"15\" style=\"vertical-align:-0.2em;\"/\u003e label mask |\n| **Colors and LUTs** | Easy picking of colors per channel or non-linear LUT selection from [many colormaps](https://cmap-docs.readthedocs.io/en/stable/).  |\n| **Intuitive Slicing** | Slice any object by moving the Slicing Cube, as you would move any other Blender object |\n| **Scales** | 3D scale grid for accurate representation and physical Blender scales for easy registration.  |\n| **Large Volumes** | Build your animation and visualization on a downscaled version, render with your massive dataset! |\n\n\n## \u003cimg src=\"./docs/grey_icons/blender_icon_file.svg\" width=\"20\" style=\"vertical-align:-0.2em;\"/\u003e Installation\n\nYou can grab the add-on on the [Blender Extensions Platform](https://extensions.blender.org/add-ons/microscopynodes/)  \nOr, search **Microscopy Nodes** in Blender Preferences → Get Extensions. (Blender 4.2+)\n\nFor earlier versions, check the [legacy install guide](https://aafkegros.github.io/MicroscopyNodes/outdated).\n\nOnce installed, find it under Scene Properties \u003cimg src=\"./docs/grey_icons/blender_icon_scene_data.svg\" width=\"15\" style=\"vertical-align:-0.2em;\"/\u003e .\n\n## \u003cimg src=\"./docs/grey_icons/blender_icon_camera_data.svg\" width=\"20\" style=\"vertical-align:-0.2em;\"/\u003e  Video tutorials\n\nCheck out the [video tutorials](https://www.youtube.com/@aafkegros) on YouTube for quick guides on:\n- Installation\n- Loading data\n- Fluorescence \u0026 EM visualization\n- Making presentation-ready renders\n\n\u003cp align=\"center\"\u003e\u003cimg src=\"./figures/newprettyside.png\" width=\"400\"/\u003e\u003c/p\u003e\n\n\n## First use\n\n1. Load your file (local path or URL) into the **Microscopy Nodes** panel in Scene Properties \u003cimg src=\"./docs/grey_icons/blender_icon_scene_data.svg\" width=\"15\" style=\"vertical-align:-0.2em;\"/\u003e \n2. The metadata will auto-load, and you can define how each channel is visualized\n3. Adjust per-channel options like:\n   - Volume or isosurface rendering\n   - Label masks\n   - Emission, resolution, and colors\n4. Customize dataset settings like:\n   - Axis order\n   - Physical pixel size\n   - Reload behavior \u0026 storage location\n\nMore detail in the [full docs](https://aafkegros.github.io/MicroscopyNodes/).\n\n## Show Off Your Vizualizations!\n\nIf you create something cool using `Microscopy Nodes`, share it!  \nTag me [@aafkegros on Bluesky](https://bsky.app/profile/aafkegros.bsky.social) or use the hashtag `#microscopynodes`.\n\nIf you publish with this add-on, please cite [the preprint](https://www.biorxiv.org/content/10.1101/2025.01.09.632153v1):\n```\n@article {Gros2025.01.09.632153,\n\tauthor = {Gros, Oane and Bhickta, Chandni and Lokaj, Granita and Schwab, Yannick and K{\\\"o}hler, Simone and Banterle, Niccol{\\`o}},\n\ttitle = {Microscopy Nodes: versatile 3D microscopy visualization with Blender},\n\telocation-id = {2025.01.09.632153},\n\tyear = {2025},\n\tdoi = {10.1101/2025.01.09.632153},\n\tpublisher = {Cold Spring Harbor Laboratory},\n\tURL = {https://www.biorxiv.org/content/early/2025/01/14/2025.01.09.632153},\n\teprint = {https://www.biorxiv.org/content/early/2025/01/14/2025.01.09.632153.full.pdf},\n\tjournal = {bioRxiv}\n} \n```\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faafkegros%2FMicroscopyNodes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Faafkegros%2FMicroscopyNodes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Faafkegros%2FMicroscopyNodes/lists"}