Linux

scenery is a scenegraphing and rendering library. It allows you to quickly create high-quality 3D visualisations based on mesh data. scenery contains both a OpenGL 4.1 and Vulkan renderer. The rendering pipelines of both renderers are configurable using YAML files, so it's easy to switch between e.g. Forward Shading and Deferred Shading, as well as stereo rendering. Rendering pipelines can be switched on-the-fly.

Both renderers support rendering to head-mounted VR goggles like the HTC Vive or Oculus Rift via OpenVR/SteamVR.

The Multiview Reconstruction software package enables users to register, fuse, deconvolve and view multiview microscopy images. The software is designed for lightsheet fluorescence microscopy (LSFM), but is applicable to any form of three or higher dimensional imaging modalities like confocal timeseries or multicolor stacks. 

The BigDataViewer is a re-slicing browser for terabyte-sized multi-view image sequences. BigDataViewer was developed with multi-view light-sheet microscopy data in mind and integrates well with Fiji's SPIMage processing pipeline.

"The plugin analyzes fluorescence microscopy images of neurites and nuclei of dissociated cultured neurons. Given user-defined thresholds, the plugin counts neuronal nuclei, and traces and measures neurite length."[...]" NeuriteTracer is a fast simple-to-use ImageJ plugin for the analysis of outgrowth in two-dimensional fluorescence microscopy images of neuronal cultures. The plugin performed well on images from three different types of neurons with distinct morphologies."

This plugin requires parameter setting: Threshold levels and scale (see more details on the related publication)

Integrates hardware control of Leica microscopes (via CAM), image analysis (e.g. via ImageJ, Matlab), and adaptive automatic screening of identified regions of interest.