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 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.

The add-on will then show up as a window in the Scene Properties.

Video tutorials

See the video introductions 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:

@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 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

• per-channel load options:

  • load volumetric data
  • load Blender isosurface
  • load labelmask

• per-channel visuzalization options:

  • emission
  • surface resolution

• extra options

  • data storage location
  • overwrite existing local files
  • preset environment