title	Bioimage Analysis Triage Bot
emoji	🔬
colorFrom	blue
colorTo	indigo
sdk	gradio
sdk_version	6.19.0
python_version	3.14.6
app_file	app.py
pinned	false

BIA BOT

A conversational chatbot for triaging bioimage analysis requests for the Image Analysis Team at the Francis Crick Institute.

Overview

BIA BOT is an AI-powered triage system that interviews users about their bioimage analysis projects and automatically generates:

• Triage Reports — comprehensive summaries of user requirements and project details
• Python Scripts — executable analysis scripts tailored to the specific analysis task

The chatbot uses a structured 20-question framework to gather information efficiently while minimizing user fatigue.

Live Demo

Try it here: https://huggingface.co/spaces/djpbarry/bia-bot

Features

• 🤖 Conversational Interview — Natural language dialogue guided by a 20-question framework
• 📋 Automated Report Generation — Comprehensive markdown reports summarizing the triage
• 🐍 Script Generation — Clean, commented Python code for the proposed analysis
• 📧 Email Delivery — Reports and scripts zipped and sent to the facility team
• 💾 Interaction Logging — Full conversation transcripts saved for reference
• ♿ User-Friendly UI — Clean Gradio interface with progress feedback

How It Works

1. User starts a conversation with the chatbot
2. AI asks targeted questions about their bioimage analysis project
3. User provides information about images, objectives, constraints, and requirements
4. When complete, the bot automatically:
   • Saves the interaction transcript
   • Generates a comprehensive triage report
   • Creates a Python analysis script
   • Sends both as a zip file to the facility team
5. Facility team reviews and follows up with detailed recommendations

Technical Stack

• LLM: Claude Haiku (Anthropic API)
• Interface: Gradio
• Backend: Python
• Deployment: Hugging Face Spaces
• Email: Gmail SMTP

Local Setup

Requirements

• Python 3.14+
• pixi (or pip for manual installation)
• Anthropic API key
• Gmail app password (for email functionality)

Installation

# Clone the repo
git clone https://github.com/djpbarry/biabot.git
cd biabot

# Install dependencies with pixi
pixi install

# Or with pip
pip install -r requirements.txt

Configuration

Create a .env file in the project root:

ANTHROPIC_API_KEY=your-anthropic-key
GMAIL_ADDRESS=your-email@gmail.com
GMAIL_APP_PASSWORD=your-app-password

Running Locally

python app.py

The app will launch at http://127.0.0.1:7860

File Structure

.
├── app.py                      # Main Gradio application
├── papers/Twenty_Questions.pdf # Triage framework document
├── requirements.txt            # Python dependencies
├── interactions/               # Saved conversation logs (JSON)
├── reports/                    # Generated triage reports (markdown)
├── scripts/                    # Generated analysis scripts (Python)
└── README.md                   # This file

Notes

• The chatbot will ask for your email address so the facility team can contact you with recommendations
• Reports and scripts are sent as a single zip file to bypass email client filters
• All conversations are logged locally for quality assurance
• The framework is based on the "Twenty Questions" standard for bioimage analysis