https://github.com/copick/copick_live
A Dash Plotly server visualizing CZII ML Challenge Pickathon with live updates and analyses
https://github.com/copick/copick_live
copick visualization web
Last synced: 4 months ago
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A Dash Plotly server visualizing CZII ML Challenge Pickathon with live updates and analyses
- Host: GitHub
- URL: https://github.com/copick/copick_live
- Owner: copick
- License: mit
- Created: 2024-04-19T18:16:23.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-07-25T15:36:22.000Z (almost 2 years ago)
- Last Synced: 2025-04-12T03:54:28.149Z (about 1 year ago)
- Topics: copick, visualization, web
- Language: Python
- Homepage:
- Size: 1.87 MB
- Stars: 3
- Watchers: 2
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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](https://github.com/uermel/copick).
**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.