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https://github.com/oanegros/MicroscopyNodes
Loading and handling microscopy data in blender
https://github.com/oanegros/MicroscopyNodes
blender blender-addon microscopy volume-rendering
Last synced: about 9 hours ago
JSON representation
Loading and handling microscopy data in blender
- Host: GitHub
- URL: https://github.com/oanegros/MicroscopyNodes
- Owner: oanegros
- License: gpl-3.0
- Created: 2023-10-03T14:19:28.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-01-23T08:54:39.000Z (20 days ago)
- Last Synced: 2025-01-23T09:33:33.754Z (20 days ago)
- Topics: blender, blender-addon, microscopy, volume-rendering
- Language: Python
- Homepage: https://oanegros.github.io/MicroscopyNodes/
- Size: 491 MB
- Stars: 108
- Watchers: 5
- Forks: 8
- Open Issues: 18
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-scientific-image-analysis - tif2blender
- awesome-scientific-image-analysis - tif2blender
README
# Microscopy in Blender
This is a project building bioimage support for the open source software blender. This currently exists as the Blender add-on `microscopynodes`, previously named `tif2blender`. This is able to easily load tif files as volumetric objects in Blender.
Please make some pretty figures with this add-on!
You can download and install the add-on on the [Blender extensions platform](https://extensions.blender.org/add-ons/microscopynodes/) or by searching for Microscopy Nodes in the Extensions in your Blender preferences. For installing with earlier Blender versions than 4.2, follow the [legacy install instructions]( https://oanegros.github.io/MicroscopyNodes/outdated).
The add-on will then show up as a window in the `Scene Properties`.
For usage questions please use the [image.sc forum](https://forum.image.sc/tag/microscopy-nodes) 😁
For bug reports/feature requests please [open an issue](https://github.com/oanegros/MicroscopyNodes/issues).
## Video tutorials
See the [video introductions](https://www.youtube.com/playlist?list=PLAv6_GEMrbKdpje81juHowSCw-gWOJwy5) to the microscopynodes add-on on youtube. There's multiple playlists on the account, and they'll show you how to go from installing to rendering a presentation-ready video for fluorescence and electron microscopy.
## Current Features
The `microscopynodes` Blender addon supports:
- up to 5D (up to tzcyx in any axis order) tifs and OME-Zarr files can be loaded.
- Channel interface to define how to load data
- Replacing a pyramidal dataset with it's higher resolution version
- Accurate scale bars
- Load per-index label masks
- Lazy loading of giant files (no data is loaded in RAM outside what's rendered)
## Citing this addon
If you publish with this add-on, please cite [the preprint](https://www.biorxiv.org/content/10.1101/2025.01.09.632153v1):
```
@article {Gros2025.01.09.632153,
author = {Gros, Oane and Bhickta, Chandni and Lokaj, Granita and Schwab, Yannick and K{\"o}hler, Simone and Banterle, Niccol{\`o}},
title = {Microscopy Nodes: versatile 3D microscopy visualization with Blender},
elocation-id = {2025.01.09.632153},
year = {2025},
doi = {10.1101/2025.01.09.632153},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2025/01/14/2025.01.09.632153},
eprint = {https://www.biorxiv.org/content/early/2025/01/14/2025.01.09.632153.full.pdf},
journal = {bioRxiv}
}
```
## Using `microscopynodes`
Please checkout the further documentation on the [website](https://oanegros.github.io/MicroscopyNodes/) or the youtube tutorials.
Load any tif or zarr file by inputting the path or URL in the appropriate window in the `Microscopy Nodes` panel. This will read out metadata and prompt you to define how you want to load the data.
- generic options
- axis order
- pixel size in µm
- dataset (for pyramidal Zarr data)
- [reload data]( https://oanegros.github.io/MicroscopyNodes/settings#reload)
- per-channel load options:
- load [volumetric data]( https://oanegros.github.io/MicroscopyNodes/objects#volumes)
- load [Blender isosurface]( https://oanegros.github.io/MicroscopyNodes/objects#surfaces)
- load [labelmask]( https://oanegros.github.io/MicroscopyNodes/objects#masks)
- per-channel visuzalization options:
- [emission]( https://oanegros.github.io/MicroscopyNodes/settings#emission)
- [surface resolution]( https://oanegros.github.io/MicroscopyNodes/settings#surface-resolution)
- extra options
- [data storage location]( https://oanegros.github.io/MicroscopyNodes/settings#resave-location)
- [overwrite existing local files]( https://oanegros.github.io/MicroscopyNodes/settings#overwrite)
- [preset environment]( https://oanegros.github.io/MicroscopyNodes/settings#preset-environment)