Jonas Wagner
Selected projects

01 Scientific software · Immersive imaging

Fiji VR

A Fiji plugin for examining the 3D structure and time evolution of microscopy samples in a browser or on a compatible VR headset.

Try the sample stack

Motivation

See what lies between slices

Stepping through a microscopy stack makes it hard to see how structures connect in depth. I built Fiji VR to let researchers move between an individual source plane and a view of the whole volume from the same Fiji image.

Implementation

Keep the original pixels

The plugin reads Fiji’s channel, depth, and time axes and streams native-resolution image blocks to a browser viewer. You can rotate the volume, inspect source planes, and play time series. The immersive viewer is a prototype and headset testing is pending.

Interactive figure

One stack, two views

Scrub through the source planes to find the shell and the off-center core. Then switch to maximum intensity to see what happens when the brightest signal along each depth column is projected onto a single image.

Maximum-intensity projection of the synthetic shell volume

Synthetic shell

64 × 64 × 64 voxels from the Fiji VR demo.

FIG. 01 A browser illustration using the project’s synthetic demo data. The full plugin can render and rotate the volume in three dimensions.

Inside the viewer

Fiji VR desktop interface with a cyan synthetic volume, rendering controls, and channel, depth, and time sliders
FIG. 02 The desktop prototype showing a synthetic time series. The controls keep channel, source plane, and time available while the stack is rendered in 3D.