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! If you post using this addon on social media please either tag me (@GrosOane on twitter) or use hashtag #microscopynodes.

You can now also find the add-on on the Blender extensions platform under https://extensions.blender.org/approval-queue/microscopynodes/ (currently still awaiting review by blender).

Video introduction

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 is still under active development, but some notable features are already supported:

• up to 5D (up to tzcyx in any axis order) tifs are supported.
• Axes order and pixel size will be attempted to be read out automatically
• Otsu initial volumetric emission material is applied
• Scale bars are added to the Geometry Nodes container of your volumetric data

Installing microscopynodes

You can now find the add-on on the Blender extensions platform under https://extensions.blender.org/approval-queue/microscopynodes/ (currently still awaiting review by blender). You can download this and drag it into the Blender 4.2 window.

For older versions than Blender 4.2:

• Download blender from https://www.blender.org/download/. Check the supported blender version next to the release!

• Download the microscopynodes zip file from the releases page.

Start blender.

Install the microscopynodes Add-On:

• In Blender go to Edit > Preferences
• Go to Add-Ons tab in Preferences
• Press Install and give the tif_loader.zip file (as .zip)
• In the added microscopynodes add-on window in Preferences: press the tick box to enable, and the arrow to unfold the details
• in the details press install tifffile
• (if this fails please try restarting blender and seeing if it can then find tifffile)

This should create the microscopynodes panel in Scene Properties.

Using microscopynodes

Load in tif-files in the file explorer from the panel in Scene Properties.

Loading with preset environment recently had a small bug, fixed on 7th nov 18:45. So either uncheck this or update your tif_loader(see below), if you have this issue. For any other problems, please open an issue.

• The microscopynodes panel should be able to automatically read out your axis order and pixel size, but these can otherwise also manually be entered
• Any tif stack from zyx to tzcyx (in any axis order) is supported
• The microscopynodes resaves your tif as a .vdb file (in a blender_volumes subfolder) and loads this as a volume object in your blender scene, connected to a Container object.
• With large files (over 2048 px in an axis), the volumes will be split to avoid blender crashes.
• With the Import option: Force Remake you will force remaking the vdb files, if this is unchecked and the vdb files exist, these will be loaded.
• With the Import option: Preset Environment some default environment variables will be set. These overwrite current other environment settings, but are useful for quickly looking at data:
  • Sets background to black (as emission material is default)
  • Sets Eevee volumetric tile_size to 2 px (might be heavy for enormous data)
  • Sets Cycles Samples to manageable numbers for volumetric data
  • Sets View Transform to Standard (the default Filmic crunches dynamic range post-render)

Upon load, multiple defaults are applied, but all of these can be changed as granularly as you want.

Updating microscopynodes

To update the microscopynodes add-on (future versions may have bugfixes, new features) a few steps need to be taken:

• In Blender go to Edit > Preferences
• Go to Add-Ons tab in Preferences and find the microscopynodes add-on
• Press Remove
• Restart Blender
• Install the new version.