awesome-janelia-software
github.com/janeliascicomp/awesome-janelia-software ↗A curated list of awesome Janelia software
Use this list with your AI agent
Add the Context Awesome MCP server to Claude, Cursor, or any MCP client, then ask:
"Show me end-user applications resources from awesome-janelia-software"
Installation instructions →What's inside
End-User Applications
- APT
Animal Part Tracker
- CATMAID
Web application for collaborative neural circuit reconstruction and analysis
- Cellpose
Deep learning tool for cell segmentation
- Facemap
mouse facial behavior analysis
- G4 Display Tools
Collection of tools for using Modular LED Displays (4th generation)
- HippoSeq
Interactive analysis tool for RNA-seq data in the mouse hippocampus
ImgLib2, BDV and N5 Ecosystem
- BigDataViewer
Re-slicing browser for terabyte-sized multi-view image sequences
- Hot-Knife
ImgLib2 code for processing very large EM and Lightsheet data
- ImgLib2
ImgLib2 project (lots of subprojects)
- N5
Specification for the N5 file format
- N5 Spark
Tools for working with N5 on a Spark cluster
- N5 Viewer
Viewer for visualizing N5 data sets
Fiji Plugins
- BigDataViewer
Re-slicing browser for terabyte-sized multi-view image sequences
- BigStitcher
ImgLib2/BDV implementation of Stitching for large datasets
- BigWarp
Pointwise deformable 2D and 3D registration of large image data
- ColorMIP Mask Search
Fiji plugin for color depth search
- H5J Loader
Fiji plugin for loading images in lossy H5J format
- n5-ij
Fiji plugin for loading and saving image data as N5 data sets
Python Libraries
- BigStream
Distributed piecewise affine and deformable alignment for big 3D datasets
- CircuitSeeker
Distributed complex alignment tasks for big 4D datasets
- FishSpot
Fully automated PSF estimation and spot detection for punctate data (e.g. FISH spots)
- Python Dist Demo
Examples of bundling Python scripts and dependencies into execultables for easy sharing
- xarray-multiscale
Library for generating multiscale pyramids with Dask
Visualization Tools
- Blender Spherical Video
Scripts for rendering 360-degree spherical videos in Blender
- Janelia Unity Toolkit
Unity game engine packages enabling animal studies in VR
- neuVid
Generate biology videos from high-level descriptions using Blender and VVDViewer
- VVD Viewer
Interactive 3D volume viewer for large microscopy data
- Web Vol Viewer
Direct volume rendering in a browser using WebGL 2
Julia Packages
- Blosc2_jll
Contributed build script for cross-compilation of C-Blosc2
- ClusterManagers
Contributed Julia support for interacting with IBM Platform LSF
- ImarisWriter
Julia API for writing files in Imaris5 file format
- UInt12Arrays
Handle 12-bit unsigned integers in Julia with SIMD (AVX2 and AVX512) support
GitHub Organizations
High Performance Computing
- Burst Compute
AWS service for highly parallel Lambda processing
- Daisy
Block-size task scheduling for large volumes
- JACS
RESTful services for running jobs at scale
- Java LSF
Java library for interacting with a HPC compute cluster running IBM Platform LSF
Showing a sample of 81 resources. View the full list on GitHub →