Prerequisites: The proofreading tool needs 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.
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If necessary download and install anaconda. Open anaconda prompt and install git:
conda install git
Create a folder for the proofreading tool and clone the git repository
cd <dir_path_to_tool>
git clone https://github.com/moenigin/agglomeration-proofreading.git
navigate to the proofreading folder and install the downloaded environment.yml,
cd agglomeration-proofreading
conda env create -f apr.yml
activate the environment and install the remaining requirements
conda activate apr
pip install -r requirements.txt
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It is recommended to work in to create a dedicated environment for the proofreading tool. It requires Python 3.7 and git to be installed.
git clone --recurse https://github.com/moenigin/agglomeration-proofreading.git
navigate to the agglomeration-proofreading subfolder and install requirements
cd agglomeration-proofreading
pip install -r requirements.txt
To run the proofreading tool type in the prompt
python run_proofreading.py
The configuration of the proofreading tool can be adapted either through editing the proofreading.ini or by passing arguments directly in the prompt. For list of arguments see
python run_proofreading.py -h
ATTENTION: On Windows10 Ctrl-C will not work to exit the program because the tool uses threading.Event. For more information see here.
for usage instructions see manual
The tool requires users to be registered with Viewer role to a Google cloud project that stores the segmentation data. Additional access to the BrainMaps API requires a service account file with Editor role.
During authentication to neuroglancer an .apitoken file is created in the user folder. Per default this file will be deleted when exiting the program. In consequence the user needs to authenticate every time the program is started. Users, that wish to avoid this and maintain the apitoken, should start the program with -remove_token False from the command prompt or set the flag to False in the proofreading.ini.