CopickLive

CopickLive is a Dash Plotly web server visualizing CZII ML challenge pickathon results with live updates.

CopickLive main page
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Getting Started window
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Visualize pick results for each tomogram (click on the corresponding magnifier in the 3rd column)
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Inspect and modify picked points in a gallery view
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Usage

Python environment setup:
pip install -r requirements.txt

Three configuration files are needed: the copick configuration file, json checkpoint file, and copicklive conifguration file. See explanation below:

The copick configuration json file template
This file is a template for generating a customized copick configuration file for each picker. See copick example.

The json checkpoint file
The file is used to generate a task list for each picker. It contains 3 keywords, ensuring every tomogram sample get 2 people to work on (start += tasks_per_person when repeat >= 2). Below is an example:

{  
    "start": 0,       
    "repeat": 1,    
    "tasks_per_person": 5    
}  

The CopickLive configuration file
The configuration file should be saved as config.ini. This file contains paths for finding the copick configuration template and checkpoint file. It also includes the directory path where copick (overlay) outputs are saved.

[copicklive_config]
COPICKLIVE_CONFIG_PATH = path_to_copicklive_config_file.json

[copick_template]
COPICK_TEMPLATE_PATH = path_to_copick_config_example_file.json

[local_picks]
PICK_FILE_PATH = path_to_copick_overlay_output

[local_cache]
CACHE_ROOT = path_to_copicklive_cache_directory

[counter_checkpoint]
COUNTER_FILE_PATH = path_to_counter_checkpoint_file.json

How to deploy?

1. Run python app.py in the Python environment.
2. You can access the website at http://localhost:8000 in the web browser.