Cai Lab at University of Michigan
The Cai Laboratory develops and uses interdisciplinary techniques to study the development and fine tuning of neural circuits in the mouse brain.
Ann Arbor, Michigan, USA
Pinned Repositories
compression_paper_walker2023
Analysis scripts for "A Comparison of Lossless Compression Methods for Microscopy Data Storage" (Walker 2023)
ffmpeg_HDF5_filter
A HDF5 filter for compression images using ffmpeg video libraries
hdf5plugin
register lossy ffmpeg compression filters to h5py
lossy_image_storage_2024
Figure source code for Duan, et al. 2024
MiCV
MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.
nCorrect
A toolkit for the correction and normalization of SWC files from neuron morphology experiments.
nGauge
A Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology.
nTracer
Rolling release code for the nTracer ImageJ/Fiji plugin, as published in: Roossien DH, et. al, Bioinformatics 2019.
public_tracing_datasets
Publicly-released neuron tracing datasets from Cai Lab papers.
TraceMontage
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.
Cai Lab at University of Michigan's Repositories
Cai-Lab-at-University-of-Michigan/MiCV
MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.
Cai-Lab-at-University-of-Michigan/nGauge
A Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology.
Cai-Lab-at-University-of-Michigan/nTracer
Rolling release code for the nTracer ImageJ/Fiji plugin, as published in: Roossien DH, et. al, Bioinformatics 2019.
Cai-Lab-at-University-of-Michigan/public_tracing_datasets
Publicly-released neuron tracing datasets from Cai Lab papers.
Cai-Lab-at-University-of-Michigan/nCorrect
A toolkit for the correction and normalization of SWC files from neuron morphology experiments.
Cai-Lab-at-University-of-Michigan/TraceMontage
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.
Cai-Lab-at-University-of-Michigan/ffmpeg_HDF5_filter
A HDF5 filter for compression images using ffmpeg video libraries
Cai-Lab-at-University-of-Michigan/compression_paper_walker2023
Analysis scripts for "A Comparison of Lossless Compression Methods for Microscopy Data Storage" (Walker 2023)
Cai-Lab-at-University-of-Michigan/hdf5plugin
register lossy ffmpeg compression filters to h5py
Cai-Lab-at-University-of-Michigan/lossy_image_storage_2024
Figure source code for Duan, et al. 2024
Cai-Lab-at-University-of-Michigan/mmCoreAndDevices
Micro-Manager's device control layer, written in C++
Cai-Lab-at-University-of-Michigan/neuron_volume_tools
Cai-Lab-at-University-of-Michigan/plscm_v1
Documentation for the parallel-line scanning confocal microscope design
Cai-Lab-at-University-of-Michigan/imagej-hdf5-viewer
Cai-Lab-at-University-of-Michigan/nTracer2
Cai-Lab-at-University-of-Michigan/pySISF
A Python library for manipulating SISF images.
Cai-Lab-at-University-of-Michigan/SimpleDAC
An open source hardware interface for experimental automation
Cai-Lab-at-University-of-Michigan/SISF_CDN
A tool for remote access of SISF Files
Cai-Lab-at-University-of-Michigan/stage_controller