Repositories list

• pySISF

  Public
  A Python library for manipulating SISF images.

  Python

  •

  MIT License

  •0•0•0•1•Updated Jun 18, 2025Jun 18, 2025

• SimpleDAC

  Public
  An open source hardware interface for experimental automation

  C

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 18, 2025Jun 18, 2025

• ffmpeg_HDF5_filter

  Public
  A HDF5 filter for compression images using ffmpeg video libraries

  Java

  •

  MIT License

  •0•2•5•0•Updated Jun 18, 2025Jun 18, 2025

• plSCMV1_code

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 30, 2025May 30, 2025

• nTracer2

  Public
  Python

  •3•0•0•0•Updated May 7, 2025May 7, 2025

• napari-nninteractive

  Public
  napari GUI to use nnInteractive for 3D Object Annotation

  Python

  •

  Apache License 2.0

  •11•0•0•0•Updated May 1, 2025May 1, 2025

• nnInteractive

  Public
  nnInteractive is a framework for 3D interactive segmentation, supporting intuitive prompts like points, scribbles, bounding boxes, and lasso. Trained on 120+ diverse 3D datasets, it sets a new standard in accuracy, usability, and adaptability for clinical and research applications.

  Python

  •

  Apache License 2.0

  •18•0•0•0•Updated Apr 23, 2025Apr 23, 2025

• napari_toolkit

  Public
  napari GUI widgets library

  Python

  •

  Apache License 2.0

  •3•1•0•0•Updated Apr 15, 2025Apr 15, 2025

• SISF_CDN

  Public
  A tool for remote access of SISF Files

  C++

  •

  MIT License

  •2•0•0•0•Updated Apr 10, 2025Apr 10, 2025

• nGauge

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

  visualizationpython-librarymeasurement+ 2quantificationneuron-morphology

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•7•4•0•Updated Jan 17, 2025Jan 17, 2025

• plSCMv1_Design

  Public
  Documentation for the parallel-line scanning confocal microscope design

  MIT License

  •0•0•0•0•Updated Dec 19, 2024Dec 19, 2024

• hdf5plugin

  Public
  register lossy ffmpeg compression filters to h5py

  C

  •

  Other

  •25•0•0•0•Updated Dec 9, 2024Dec 9, 2024

• stage_controller

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Aug 5, 2024Aug 5, 2024

• lossy_image_storage_2024

  Public
  Figure source code for Duan, et al. 2024

  Jupyter Notebook

  •0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

• imagej-hdf5-viewer

  Public
  Java

  •0•0•5•0•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+ 6leidenpseudotimescanpyanndatapseudotime-trajectoryumap-projection

  CSS

  •

  Apache License 2.0

  •0•6•0•2•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

  •0•0•0•0•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

  Java

  •

  GNU General Public License v3.0

  •0•2•0•0•Updated Aug 30, 2022Aug 30, 2022

• CCF_Registration_Pipeline

  Public
  Python

  •0•0•0•0•Updated Aug 29, 2022Aug 29, 2022

• mmCoreAndDevices

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

  C++

  •116•0•0•0•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+ 1neuron-morphology

  Java

  •0•5•0•0•Updated Sep 19, 2021Sep 19, 2021

• neuron_volume_tools

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Dec 7, 2020Dec 7, 2020

• public_tracing_datasets

  Public
  Publicly-released neuron tracing datasets from Cai Lab papers.

  neuron-morphology

  0•3•0•0•Updated Nov 10, 2020Nov 10, 2020

• TraceMontage

  Public
  A ImageJ/Fiji plugin for the merging of multiple neuron traces between two images, as published in: Dizaji SA, Walker L, and Cai D, Journal of Neuroscience Methods 2019.

  image-analysisneuron-morphology

  Java

  •0•3•0•0•Updated Oct 6, 2020Oct 6, 2020