Stamatios C. Nicolis

  • Unit of Biological and Artificial Self-organised Systems
  • Center for Nonlinear Phenomena and Complex Systems (CENOLI)
  • Service de Chimie-Physique et Biologie Théorique
  • Faculté des Sciences
  • Université Libre de Bruxelles

Current projects

  • BioDiMoBot (European Commission, since 2025): data analysis, AI detection in images and audio, and mathematical modelling for biodiversity monitoring
  • CubanWaterLab (ARES, since 2023): in situ monitoring of water quality in Cuban bays, with the University of Havana; co-manager, data analysis and visualisation
Email / Scholar / GitLab
Stamatios C. Nicolis

Research Interests

Biocomplexity and Collective Behaviour

Emergent phenomena in biological and artificial systems, focusing on self-organization, group dynamics and decision-making in social and group-living organisms.

Nonlinear Dynamics and Mathematical Modelling

Nonlinear dynamical systems, pattern formation, stochastic simulations and mathematical models of biological phenomena.

Image Analysis, AI Detection and Tracking

Computer vision and deep learning methods for automated detection, classification and tracking of individuals in video recordings of behavioral experiments.

Data Analysis and Statistics

Statistical methods and data-driven approaches for the analysis of experimental and observational data in biological systems.

Daphnia daphnia
Tuna tuna
Shadowgraph shadowgraph
Woodlice woodlice

Publications

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Teaching

Course description (BIOL-F446, Université Libre de Bruxelles)

Binary-choice experiments: modelling and simulation, with notebooks in R and Python that run in the browser (in French).

Practicals

Course description

Lectures

Projects

Materials

Course description

Lectures

Apps & Codes

Annotation & Tracking Tools

Shadowgraph annotation interface: a cluster of zooplankton detections, one of them selected and shown on its frame in the inspector

Shadowgraph Annotation

Review and correct the particle detections of the shadowgraph pipeline; export them as YOLO, CSV or Darwin Core. Runs in the browser, files stay on your computer.

Launch
Fish Annotator with a lake clip open: labelled boxes on the frame, the selected fish with its species and notes, and the list of fish found in the clip

Fish Annotator

Annotate fish in ZED stereo lake footage and export ready-to-train YOLO datasets, with optional AI detection. No Python, ZED SDK or GPU needed.

Mac with Apple Silicon · version 0.9.0 beta 3.3 · 82 MB

Download
jTracker following individuals in the wells of a six-well plate filmed under red light, each with its ID and trail

jTracker

Measure and track objects in video, by colour or a background model, in up to four regions; export detections and trajectories.

Mac with Apple Silicon, macOS 13 or later · 19 MB · MIT licence

Download

The Mac apps are not notarized: the first time, macOS refuses to open them; then open System Settings → Privacy & Security and click Open Anyway.

Event Marker

Log timestamped events while watching videos using customizable keyboard shortcuts

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Pre-labelling

Automatic labelling for YOLO object detection

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Data Platforms

Biodimobot GBIF Database

Collect, check and publish species occurrence records on GBIF (Global Biodiversity Information Facility) in the Darwin Core standard. Imports the workbooks exported by Shadowgraph Annotation.

Visit

SmartWater Weather Station

Real-time data from Brussels ponds

Visit

SmartWater Data Dashboard

Interactive visualization and analysis of the SmartWater data

Visit

Calculators & Simulators

Binomial Calculator

Interactive probability calculator for binomial distributions

Launch

Aggregation Model

Monte Carlo simulation of collective aggregation behavior

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Binary Choice Model

Simulation of decision-making in collective systems

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Pólya Urn

Reinforcement, path dependence and the Beta/Dirichlet limit, one ball at a time

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Co-occurrence Permutation Test

C-score and pairwise tests of species co-occurrence against null models

Launch

Hardware

Experimental Setups for Behavioral Research

3D models (STL and OpenSCAD)

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