Microscopy Nodes

Microscopy Nodes helps load microscopy data and visualize it for easy, accurate, and intuitive data visualization of microscopy!

Currently, Microscopy Nodes supports the import of up to 5D tif files (xyz, time and channels), from tif or OME-Zarr files.

Usage questions are mainly answered on the image.sc forum

OME-Zarr

OME-Zarr is an upcoming microscopy format, allowing you to load bigger or smaller versions of the data (pyramidal, such as google maps resolutions) - in Microscopy Nodes, this allows you to create your scene with a smaller volume, and render with your giant full-scale microscopy stack. OME-Zarr can also easily be hosted and loaded online, so if you are looking for example/toy data, you can check out open repositories such as the IDR.

Example datasets to try: https://s3.embl.de/microscopynodes/RPE1_4x.zarr and https://s3.embl.de/microscopynodes/FIBSEM_dino.zarr - over 4GB Cycles is a lot more efficient.

Features

In short, Microscopy Nodes supports:

• Up to 5D files (tzcyx, in any order)
• Handling of both fluorescence and electron microscopy
• Channel-dependent loading
• Automatic µm-scale axes
• Arbitrary slicing, multiple slicing objects
• Pyramidal data support and data replacement

All data rendered needs to fit within RAM, but Microscopy Nodes will load lazily for multiple channels or timepoints, and not load all into RAM at the same time. The entire dataset does need to fit on disk.

Microscopy Nodes used to be known as 'Tif2Blender'. Tutorials for Microscopy Nodes can be found on https://www.youtube.com/@oanegros

Usage

The Microscopy Nodes panel can be found in Scene Properties:

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