/autoseg

A package for automated deep-learning 3D image segmentation algorithms for connectomic brain mapping.

Primary LanguagePythonApache License 2.0Apache-2.0

autoseg

A package for automated deep-learning 3D image segmentation algorithms for connectomic brain mapping. Developed for X-Ray Nanoholography data.

  • Free software: Apache 2.0 License

Installation

Install Rust and Cargo via RustUp:

curl https://sh.rustup.rs -sSf | sh

Install MongoDB:

curl -fsSL https://pgp.mongodb.com/server-6.0.asc | sudo gpg -o /usr/share/keyrings/mongodb-server-6.0.gpg --dearmor

And initialize a MongoDB server in a screen on your machine:

screen
mongod

Install graph_tool

conda install -c conda-forge -c ostrokach-forge -c pkgw-forge graph-tool

Install autoseg:

pip install git+https://github.com/brianreicher/autoseg.git

Features

Usage

Credits

This package builds upon segmentation techniques & algorithms developed by Arlo Sheridan, Brian Reicher, Jeff Rhoades, Vijay Venu, and William Patton.