Microscopy in Blender

Microscopy Nodes is a Blender add-on for visualizing high-dimensional microscopy data—designed for scientists, or anyone working with biological images 😊.

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.

Usage questions are mainly answered on the image.sc forum

What It Does

Microscopy 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.

Feature	Description
5D Support	Load .tif and .zarr files with any axis order 'tzcyx' or any subset
Channel Interface	Define how to load each channel: volume, surface, label mask
Colors and LUTs	Easy picking of colors per channel or non-linear LUT selection from many colormaps.
Intuitive Slicing	Slice any object by moving the Slicing Cube, as you would move any other Blender object
Scales	3D scale grid for accurate representation and physical Blender scales for easy registration.
Large Volumes	Build your animation and visualization on a downscaled version, render with your massive dataset!

Installation

You can grab the add-on on the Blender Extensions Platform
Or, search Microscopy Nodes in Blender Preferences → Get Extensions. (Blender 4.2+)

For earlier versions, check the legacy install guide.

Once installed, find it under Scene Properties .

Video tutorials

Check out the video tutorials on YouTube for quick guides on:

• Installation
• Loading data
• Fluorescence & EM visualization
• Making presentation-ready renders

First use

1. Load your file (local path or URL) into the Microscopy Nodes panel in Scene Properties
2. The metadata will auto-load, and you can define how each channel is visualized
3. Adjust per-channel options like:
   • Volume or isosurface rendering
   • Label masks
   • Emission, resolution, and colors
4. Customize dataset settings like:
   • Axis order
   • Physical pixel size
   • Reload behavior & storage location

More detail in the full docs.

Show Off Your Vizualizations!

If you create something cool using Microscopy Nodes, share it!
Tag me @aafkegros on Bluesky or use the hashtag #microscopynodes.

If you publish with this add-on, please cite the paper:

@article{gros_microscopy_2026,
	title = {Microscopy {Nodes}: versatile {3D} microscopy visualization with {Blender}},
	volume = {27},
	issn = {1469-3178},
	shorttitle = {Microscopy {Nodes}},
	url = {https://doi.org/10.1038/s44319-025-00654-8},
	doi = {10.1038/s44319-025-00654-8},
	language = {en},
	number = {3},
	urldate = {2026-02-17},
	journal = {EMBO Reports},
	author = {Gros, Aafke and Bhickta, Chandni and Lokaj, Granita and Johnston, Brady and Schwab, Yannick and Köhler, Simone and Banterle, Niccolò},
	month = feb,
	year = {2026},
	keywords = {3D Data, Blender, Data Visualization, Electron Microscopy, Fluorescence Microscopy},
	pages = {581--597},
	file = {Full Text PDF:/Users/oanegros/Zotero/storage/SF7NNTUC/Gros et al. - 2026 - Microscopy Nodes versatile 3D microscopy visualiz.pdf:application/pdf},
}
}