wholebrain by tractatus
R package for segmentation, registration and generating web-based brain atlases from microscope images
created at Oct. 29, 2015, 5:43 p.m.
cellfinder by brainglobe
Automated 3D cell detection in very large images
created at Jan. 17, 2020, 2:14 p.m.
pycytominer by cytomining
Python package for processing image-based profiling data
created at July 3, 2019, 6:22 p.m.
brainglobe-atlasapi by brainglobe
A lightweight python module to interact with atlases for systems neuroscience
created at April 30, 2020, 11:10 a.m.
axondeepseg by axondeepseg
Axon/Myelin segmentation using Deep Learning
created at Sept. 26, 2016, 2:20 p.m.
plant-seg by kreshuklab
A tool for cell instance aware segmentation in densely packed 3D volumetric images
created at Oct. 18, 2019, 10:56 a.m.
nd2reader by Open-Science-Tools
Pure Python library for reading NIS Elements ND2 images and metadata
created at Feb. 14, 2017, 3:47 p.m.
Image processing toolbox for Rbrainreg by brainglobe
Automated 3D brain registration with support for multiple species and atlases.
created at May 26, 2020, 2:36 p.m.
OpenMicroscopy by HohlbeinLab
Non-comprehensive list of projects and resources related to open microscopy.
created at Sept. 28, 2021, 8:51 a.m.
FAST-Pathology by AICAN-Research
⚡ Open-source software for deep learning-based digital pathology
created at July 9, 2019, 12:28 p.m.
ark-analysis by angelolab
Integrated pipeline for multiplexed image analysis
created at Jan. 7, 2019, 4:31 a.m.
python-microscopy by python-microscopy
The python-microscopy environment - an open-source package for light microscopy
created at Nov. 28, 2019, 2:12 a.m.
Cell_ACDC by SchmollerLab
A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data
created at Feb. 25, 2021, 4:14 p.m.
big-fish by fish-quant
Toolbox for the analysis of smFISH images.
created at Dec. 17, 2018, 12:26 p.m.
DIRT by Computational-Plant-Science
Digital Imaging of Root Traits: Extract trait measurements from images of monocot and dicot roots.
created at Sept. 9, 2014, 10:56 p.m.