Théo Fabien

Ecological data processing / Server admin

My work as an engineer at UMR IGEPP (INRAE) focuses on developing and maintaining data processing pipelines and computational tools for ecological research. I currently build pielines that automate image-based analysis of ecological systems. In parallel, I design and manage a local server infrastructure used to store, process and share large-scale datasets, turning experimental pipelines into usable tools.

Here are the main components of my ecosystem:

In my spare time, I like building some side-projects such as my homelab. I also love climbing and hiking, and I have a very cute cat named Harold.

Work

Software Engineer - INRAE, UMR IGEPP

[February 2025 - now]

  • Automation of insects tracking through image sequences
  • CVAT server administration, deployment of fine-tuned models (using the Nuclio platform) for semi-automated annotations

Engineer - INRAE, UMR IGEPP

[May - July 2024]

  • Modelling the spatio-temporal diffusion of spores using public geographic databases
  • Data exploration using visualization tools and statistics
  • Streamlit web interface

Doctoral student - INRAE, UMR LISAH

[September - December 2023]

  • Worked on the Pl@ntNet project

MSc Internship - INRAE, UMR IGEPP

[January - July 2023]

  • Spatio-temporal Fisher-KPP growth model
  • Image segmentation neural networks
  • Work on computing servers and cloud platforms

Supervising

Océane Gourdin (now PhD student at UMR IGEPP)
Deep learning algorithms for detecting small insects in high density scenes.

Teaching

Online Collaborative Resources at University of Rennes (Fall 2025)
Introduction to virtual machines and containers for data science.

Pinned projects

My Outdoor Archive

A self-hosted web service designed to archive and explore hiking routes and outdoor places. It combines an interactive map interface with a spatial database to store GPX tracks, places or areas I visited. The backend is built with FastAPI and connects to a PostgreSQL database extended with PostGIS to handle geographic data. GPX files can be imported and parsed automatically to extract route geometry and elevation statistics. The Vue.js frontend uses Leaflet to build the interactive map.

Home Server Infrastructure

A collection of self-hosted services that I use daily. The initial goal of this project was to get better experience with system and network administration, but it quickly escalated into a fascinating pool of experimentation. Here are some of my deployed services:

This infrastructure is designed to be energy-efficient for both economical and ecological reasons. This was a primary criterion when picking hardware for building my servers. On the software side, I almost exclusively use containerized services (Docker, LXC), and limit my use of virtual machines (which I still occasionally use for testing new things) to save even more power.

Msc Internship project : late blight growth model

A model built to describe the growth of late blight lesions on potatoes. This project was supervised by Melen Leclerc (IGEPP, INRAE). It leverages efficient image registration techniques, as well as deep image segmentation algorithms, before building the reaction-diffusion model itself.