BIA Study Tracker

BIA Study Tracker is a Python tool that analyzes studies from the BioImage Archive (BIA), generates summary and detailed reports, and posts them automatically to Slack on a schedule (via Github actions).

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Features

• Fetch studies from the BioImage Archive (BIA) search API
• Generate reports with:
  • ✅ Summary statistics (studies with/without datasets, images)
  • ✅ Detailed CSV/Excel reports for missing datasets/images and conversion report
• Post reports and files directly to Slack
• CI/CD integration for automated weekly/biweekly runs

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Installation

This project uses Poetry for dependency management.

# Clone the repo
git clone https://github.com/BioImage-Archive/bia-study-tracker.git
cd bia-study-tracker

# Install dependencies
poetry install

Configuration

Configure your environment by either create a .env file from .env_template or set environment variables for the items in .env_template. Set the following environment variables:

Variable	Description	Value
PUBLIC_SEARCH_API	Endpoint for BIA search API	https://alpha.bioimagearchive.org/search
PUBLIC_WEBSITE_URL	Website URL to point at the studies	https://alpha.bioimagearchive.org/bioimage-archive/study
PUBLIC_MONGO_API	Endpoint for BIA MONGO API	URL
VALIDATION_FLAG	Validation flag for validating the ZARR	False
SLACK_BOT_TOKEN	Slack Bot User OAuth Token	xoxb- ....
SLACK_CHANNEL	Slack channel ID	CXXXXXX

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Usage

Run the tracker manually: poetry run track-ingested-studies

Example Slack Output

BIA tracker - Summary stats report

+---------------------------+-------+
| Statistic                 | Value |
+---------------------------+-------+
| Total Studies checked     | 120   |
| Studies With images       | 75    |
| Studies w/ dataset no img | 30    |
| Studies without datasets  | 15    |
+---------------------------+-------+