https://github.com/divital-coder/cryoet-tomogram-search-agent

Ai agents that navigate to the CryoET datasets url by czi and search for the relevant tomograms based on user query.
https://github.com/divital-coder/cryoet-tomogram-search-agent

Last synced: about 1 month ago
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Ai agents that navigate to the CryoET datasets url by czi and search for the relevant tomograms based on user query.

• Host: GitHub
• URL: https://github.com/divital-coder/cryoet-tomogram-search-agent
• Owner: divital-coder
• Created: 2025-04-03T12:29:27.000Z (about 2 months ago)
• Default Branch: main
• Last Pushed: 2025-04-03T13:24:13.000Z (about 2 months ago)
• Last Synced: 2025-04-09T16:59:47.827Z (about 1 month ago)
• Language: Python
• Size: 546 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Cryo ET Tomogram Dataset Search with Camel's OWL framework.

Searching a Cryogenic Electron tomogram dataset of cellular proteins and other organisms, with the help of thecamel-ai's OWL (Optimized Workforce Learning) framework, with native browser interaction.

## General Introduction Video

[![CryoET Tomogram Dataset Search Walkthrough with CamelAI's OWL Framework.](http://img.youtube.com/vi/81arCK0RHwo/0.jpg)](https://youtu.be/81arCK0RHwo)

https://youtu.be/81arCK0RHwo

## CryoET Tomogram Search

An AI-powered tool for searching and analyzing protein tomograms from the CZI CryoET Data Portal using CAMEL-AI's OWL framework.

--- Browsing Images

![Cryo ET Data portal by CZI being Navigated](./tmp/datasets_0403174754.png)

![Cryo ET Data portal being searched for a specific tomogram](./tmp/datasets_0403174814.png)

## Sample Testing

Running a sample script is relatively straightforward : 

## Activating Environment 

Set up your virtual environment with the conda-forge channels using a package manager such as mamba.

```bash

mamba create -n owl_env python=3.12

mamba activate owl_env

```

## Setting up Environment Variables

Currently only Gemini and Groq platforms are only supported.

```bash

export GEMINI_API_KEY={your_key}

export GROQ_API_KEY={your_key}

export OPENAI_API_BASE_URL={https://api.groq.com/openai/v1}

```

## Installation

```bash

pip install -r requirements.txt

playwright install

```

## Usage : 

```python

python run.py "salmonella"

```

Features

--  Web-based search of CryoET Data Portal

--  Automated tomogram analysis

--  Data export capabilities