Visualization of large volumetric microscopy datasets and geometric objects using Fiji/BigVolumeBrowser

In this practical course, you will learn how to explore and visualize in 3D multiple (and single) large (and small) volumetric microscopy datasets using the open-source software Fiji and the BigVolumeBrowser plugin. We will combine it with simultaneous visualization of meshes or point clouds (transcriptomics, SMLM data). We will be using walkthroughs and examples from the plugin’s documentation.

Learning objectives:

• Understanding and adjusting different modes of 3D volume rendering
• Clipping and transformation of datasets in 3D
• Combining datasets render with meshes and point clouds
• Optimizing loading of very large datasets (exceeding RAM and GPU memory)
• Creating animations

We will work through various examples, including:

• Comparing 3D datasets of different modalities (expansion microscopy, EM, (lattice) light-sheet microscopy, SMLM)
• Adding 3D annotations (moving arrows, scale bars, captions)
• Segmented 3-D electron microscopy datasets, with data hosted remotely at the Janelia Research Farm
• Working with MoBIE and segmentation data

Bring your own 3D data, there would be time to work on it and ask questions.

Event details

• Location: Zoom
• Duration: 1 day
• Morning session 9:30 – 12:00: Tutorial using prepared data
• Afternoon session 13:00 – 16:00: Apply on your own data
• Requirements: No previous knowledge needed
• IT setup: You will work on own laptop; please have Fiji/BigVolumeBrowser installed.

Bookings