moenigin / classify_neurons

Neuroglancer tool to classify neurons

Prerequisites

• requires chrome and ChromeDriver to be installed. For ChromeDriver download and unzip the ChromeDriver for your chrome version and include the chrome driver location in your PATH environment variable.

• membership in the Google Cloud Project in which the segmentation is stored

unless a working exe is provided (then installation can be skipped and directly continued to Usage):

• anaconda and git

Installation

Create a folder for the proofreading tool and clone the git repository

cd <dir_path_to_tool>
git clone https://github.com/moenigin/classify_neurons.git

navigate to the proofreading folder and install the downloaded environment.yml,

cd .\classify_neurons
conda env create -f classify_neurons.yml

Usage

To run the program from console, activate the respective environment, navigate to the subfolder of the cloned repo and run

python cli.py

The json file in /data needs to be stored in a folder with known path. When the program is started it opens a dialog window in which the path to directory for saving proofreading data needs to be set to this folder.

For usage instructions see here