► NeuronBridge
Find neuron matches across modalities
► HortaCloud
A cloud-based collaborative annotation system for terabyte-scale sparse volume annotation
► VVD Viewer
Volumetric renderer for 3D/4D microscopy data
► EASI-FISH pipeline
Portable pipeline for end-to-end analysis of spatial transcriptomics data
► Render
Web services for image transformation
► RS-FISH
Precise, interactive, fast, and scalable FISH spot detection
► BigStitcher
Efficient alignment of multi-tile and multi-angle image datasets
See also this curated list of Janelia software that is actively maintained either by Scientific Computing or individual labs.