OpenNano: A NanoString GeoMx Data Pipeline

A powerful open-source Python package for processing and analyzing NanoString GeoMx DSP data, enabling seamless integration with Scanpy, Squidpy, and other spatial transcriptomics tools.

🚀 Project Overview

Key Features

Automated Data Processing: Converts raw GeoMx data into structured AnnData format.
Seamless Compatibility: Works with Scanpy, Squidpy, and other bioinformatics tools.
Batch Processing: Handles multiple `.dcc` files efficiently.
Flexible Configuration: Provides filtering, normalization, and visualization tools.
Extensive Documentation: Includes a user guide, tutorials, and API reference.

Technologies Used

Python Package Development: Object-Oriented Design for modular functionality.
Data Handling: Pandas, NumPy, AnnData.
Integration: Scanpy, Squidpy, Matplotlib.
Deployment: Hosted on PyPI for easy installation.
Documentation Site: Built with Sphinx and deployed via Cloudflare Pages.

💡 My Contributions

I led the object-oriented programming (OOP) structure of OpenNano, turning it into a fully packaged Python library. I also wrote the documentation and designed the project's official website, hosted via Cloudflare Pages.

⚡ Challenges & Solutions

Handling Large Datasets: Optimized processing time for large spatial transcriptomics data.
Structuring a Package: Ensuring that the package can be used by researchers who want a clear pipeline and those who want a lot of control over experiments
Ensuring Compatibility: Integrated OpenNano with Scanpy and Squidpy.
Documentation & Adoption: Created a Cloudflare-hosted site to onboard users efficiently.

🔗 Project Links

GitHub Repository 📦 PyPI Package 📖 Documentation