ninjatō

neuroimaging joint annotation tool

Web-based segmentation tool for 3D tissue cleared microscopy images of nuclei.

Development Setup

This section provides guidance for setting up docker-based girder server and React-based client development and deployment environments for the ninjatō tool.

Prerequisite

Docker and Docker Compose need to be installed. On Windows 10 and above, native Docker may be installed and used. Otherwise, a Linux VM is needed.

Steps to set up and run the tool in local development environment

• git clone source code from this repo.

  git clone https://github.com/RENCI/ninjato.git
  cd ninjato
  
  

• Get the client and server containers running with test data loaded into the girder backend database container.

  ./up.sh
  

• Remove the client and server containers

  ./down.sh