cai-lab-at-university-of-michigan Goto Github PK

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

imagej-hdf5-viewer

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.

mmcoreanddevices

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

ncorrect

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

neuron_volume_tools

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.

ntracer2

plscm_v1

Documentation for the parallel-line scanning confocal microscope design

public_tracing_datasets

Publicly-released neuron tracing datasets from Cai Lab papers.

pysisf

A Python library for manipulating SISF images.

simpledac

An open source hardware interface for experimental automation

sisf_cdn

A tool for remote access of SISF Files

stage_controller

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.