Cai Lab at University of Michigan
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.
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A Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology.
MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.
Rolling release code for the nTracer ImageJ/Fiji plugin, as published in: Roossien DH, et. al, Bioinformatics 2019.
A HDF5 filter for compression images using ffmpeg video libraries
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.
Publicly-released neuron tracing datasets from Cai Lab papers.
Repositories
31WebGL-based viewer for volumetric data
Documentation for RE-JOIN Portal Wiki
Documentation for Microendoscope Portal Wiki
Shared Portal Community Wiki
A tool for remote access of SISF Files
A HDF5 filter for compression images using ffmpeg video libraries
A Python library for manipulating SISF images.
A Python library which provides a collection of tools for the measurement, quantification, and visualization of neuron morphology.
Padlock design pipeline for multiplexed assay with multiple probes per target in cDNA-based expression profiling
No description provided.
napari GUI widgets library
napari GUI to use nnInteractive for 3D Object Annotation
MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.
No description provided.
An open source hardware interface for experimental automation
Documentation for the parallel-line scanning confocal microscope design
No description provided.
No description provided.
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.
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.
register lossy ffmpeg compression filters to h5py
No description provided.
No description provided.
Figure source code for Duan, et al. 2024
No description provided.
A toolkit for the correction and normalization of SWC files from neuron morphology experiments.
Publicly-released neuron tracing datasets from Cai Lab papers.
Rolling release code for the nTracer ImageJ/Fiji plugin, as published in: Roossien DH, et. al, Bioinformatics 2019.
Analysis scripts for "A Comparison of Lossless Compression Methods for Microscopy Data Storage" (Walker 2023)
Micro-Manager's device control layer, written in C++