Repositories list

• pySISF

  Public
  A Python library for manipulating SISF images.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•44 pull requests•Updated Jun 15, 2026Jun 15, 2026

• SISF_CDN

  Public
  A tool for remote access of SISF Files

  C++

  •

  MIT License

  •33 forks•00 stars•00 issues•00 pull requests•Updated Jun 15, 2026Jun 15, 2026

• nTracer2

  Public
  Python

  •33 forks•00 stars•00 issues•11 pull request•Updated Jun 14, 2026Jun 14, 2026

• Savaii-Deployment-Doc

  Public
  TeX

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 8, 2026Jun 8, 2026

• neuroglancer

  Public
  WebGL-based viewer for volumetric data

  TypeScript

  •

  Apache License 2.0

  •366366 forks•11 star•00 issues•00 pull requests•Updated May 12, 2026May 12, 2026

• napari-nninteractive

  Public
  napari GUI to use nnInteractive for 3D Object Annotation

  Python

  •

  Apache License 2.0

  •1616 forks•11 star•00 issues•11 pull request•Updated Apr 17, 2026Apr 17, 2026

• nnInteractive

  Public
  nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points, scribbles, bounding boxes, and lasso. Trained on 120+ di…

  Python

  •

  Apache License 2.0

  •4747 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2026Apr 10, 2026

• RE_JOIN_PORTAL_WIKI

  Public
  Documentation for RE-JOIN Portal Wiki

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 10, 2026Mar 10, 2026

• MICROENDOSCOPE_PORTAL_WIKI

  Public
  Documentation for Microendoscope Portal Wiki

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 10, 2026Mar 10, 2026

• portal_wiki

  Public
  Shared Portal Community Wiki

  MIT License

  •11 fork•22 stars•00 issues•11 pull request•Updated Mar 10, 2026Mar 10, 2026

• ffmpeg_HDF5_filter

  Public
  A HDF5 filter for compression images using ffmpeg video libraries

  Java

  •

  MIT License

  •00 forks•44 stars•44 issues•11 pull request•Updated Jan 17, 2026Jan 17, 2026

• SimpleDAC

  Public
  An open source hardware interface for experimental automation

  C++

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 14, 2025Dec 14, 2025

• webproxy-login-portal

  Public
  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 25, 2025Sep 25, 2025

• multi_padlock_design

  Public
  Padlock design pipeline for multiplexed assay with multiple probes per target in cDNA-based expression profiling

  Python

  •

  MIT License

  •1616 forks•00 stars•00 issues•00 pull requests•Updated Sep 3, 2025Sep 3, 2025

• plSCMV1_code

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 30, 2025May 30, 2025

• napari_toolkit

  Public
  napari GUI widgets library

  Python

  •

  Apache License 2.0

  •33 forks•22 stars•00 issues•00 pull requests•Updated Apr 15, 2025Apr 15, 2025

• stitching_gui

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 28, 2025Mar 28, 2025

• nGauge

  Public
  A Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology.

  visualizationpython-librarymeasurement+ 2

  visualizationpython-librarymeasurementquantificationneuron-morphology

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •11 fork•88 stars•44 issues•00 pull requests•Updated Jan 17, 2025Jan 17, 2025

• plSCMv1_Design

  Public
  Documentation for the parallel-line scanning confocal microscope design

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 19, 2024Dec 19, 2024

• hdf5plugin

  Public
  register lossy ffmpeg compression filters to h5py

  C

  •

  Other

  •3333 forks•00 stars•00 issues•00 pull requests•Updated Dec 9, 2024Dec 9, 2024

• stage_controller

  Public
  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 5, 2024Aug 5, 2024

• lossy_image_storage_2024

  Public
  Figure source code for Duan, et al. 2024

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 18, 2024Jun 18, 2024

• imagej-hdf5-viewer

  Public
  Java

  •00 forks•00 stars•55 issues•00 pull requests•Updated Jan 18, 2024Jan 18, 2024

• MiCV

  Public
  MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.

  clusteringgene-expressionmarker-genes+ 6

  clusteringgene-expressionmarker-genesleidenpseudotimescanpyanndatapseudotime-trajectoryumap-projection

  CSS

  •

  Apache License 2.0

  •00 forks•77 stars•00 issues•22 pull requests•Updated Jan 23, 2023Jan 23, 2023

• compression_paper_walker2023

  Public
  Analysis scripts for "A Comparison of Lossless Compression Methods for Microscopy Data Storage" (Walker 2023)

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 24, 2022Oct 24, 2022

• nCorrect

  Public
  A toolkit for the correction and normalization of SWC files from neuron morphology experiments.

  data-analysisswcneuron-morphology

  data-analysisswcneuron-morphology

  Java

  •

  GNU General Public License v3.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 30, 2022Aug 30, 2022

• CCF_Registration_Pipeline

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 29, 2022Aug 29, 2022

• mmCoreAndDevices

  Public
  Micro-Manager's device control layer, written in C++

  C++

  •138138 forks•00 stars•00 issues•00 pull requests•Updated Mar 25, 2022Mar 25, 2022

• nTracer

  Public
  Rolling release code for the nTracer ImageJ/Fiji plugin, as published in: Roossien DH, et. al, Bioinformatics 2019.

  javaneuronsimage-analysis-and-processing+ 1

  javaneuronsimage-analysis-and-processingneuron-morphology

  Java

  •00 forks•55 stars•00 issues•00 pull requests•Updated Sep 19, 2021Sep 19, 2021

• neuron_volume_tools

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 7, 2020Dec 7, 2020