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    19 repositories

    • nTracer2

      Public
      Python
      •2•0•0•0•Updated Nov 21, 2024Nov 21, 2024

    • pySISF

      Public
      A Python library for manipulating SISF images.
      Python
      •
      MIT License
      •0•0•0•2•Updated Nov 19, 2024Nov 19, 2024

    • SISF_CDN

      Public
      A tool for remote access of SISF Files
      C++
      •
      MIT License
      •2•0•0•0•Updated Oct 25, 2024Oct 25, 2024

    • hdf5plugin

      Public
      register lossy ffmpeg compression filters to h5py
      C
      •
      Other
      •25•0•0•0•Updated Aug 9, 2024Aug 9, 2024

    • ffmpeg_HDF5_filter

      Public
      A HDF5 filter for compression images using ffmpeg video libraries
      C
      •
      MIT License
      •0•1•5•0•Updated Aug 9, 2024Aug 9, 2024

    • stage_controller

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • SimpleDAC

      Public
      An open source hardware interface for experimental automation
      C
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 7, 2024Jul 7, 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

    • plscm_v1

      Public
      Documentation for the parallel-line scanning confocal microscope design
      0•0•0•0•Updated Jan 31, 2024Jan 31, 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-genesleidenpseudotimescanpyanndatapseudotime-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

    • mmCoreAndDevices

      Public
      Micro-Manager's device control layer, written in C++
      C++
      •112•0•0•0•Updated Mar 25, 2022Mar 25, 2022

    • nGauge

      Public
      A Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology.
      visualizationpython-librarymeasurementquantificationneuron-morphology
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•5•4•0•Updated Jan 2, 2022Jan 2, 2022

    • nTracer

      Public
      Rolling release code for the nTracer ImageJ/Fiji plugin, as published in: Roossien DH, et. al, Bioinformatics 2019.
      javaneuronsimage-analysis-and-processingneuron-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•2•0•0•Updated Oct 6, 2020Oct 6, 2020