CV Zebrafish — a modular software tool to track and analyze zebrafish movements from high-speed imaging. It integrates with DeepLabCut outputs to compute metrics like fin angles, movement timing, speed, and behavior classification

Napari plugin for spatial RNA quantification

Automated 3D morphometric pipeline to quantify nuclear hypertrophy in Cdh2-deficient zebrafish embryos using Python and Streamlit.

A vocabulary for describing Zebrafish Phenotypes

Capstone Project for my Data Scientist Certification based on data from my PhD thesis: "High-content screening for cardiovascular modulators in zebrafish (Danio rerio)"

Code for 3D reconstruction and anatomical annotation of lipid mass spectrometry imaging (MSI) data from zebrafish embryos (Nature Methods, 2025).

Fourier analysis of neuron activity data. Identify neuron associated with periodic perturbation.

Zebrafish project for Champalimaud Research

Multimodal project: MuSiC used to process gene expression data using a signature matrix built from single-cell RNA-seq data that defines gene profiles for each cell type. The goal of this project is to use multimodal to quantify how environmental exposures alter gene expression in zebrafish.

Zebrafish embryo fluorescence quantification

Early life GC exposed time-series mRNA-seq analysis and DNA methylome

RNA-seq analysis for zebrafish with muscle injury

Behavioral and Transcriptomic Analyses of mecp2 Function in Zebrafish

A simple tool for zebrafish brain visualization.

#GliaMorph - Toolkit to Process and Analyse Müller Glia Morphology

A 2D-3D histological brain slice registration application for mouse, rat, zebrafish brains.

Software for analyis of zebrafish embryo sponaneous tail contractions and photomotor response

Code used for analysis in the publication: Disentangling the link between zebrafish diet, gut microbiome succession, and Mycobacterium chelonae infection. Don't hesitate to reach out with any questions.

Analysis of 16S rRNA and in vitro data from larval zebrafish with loperamide treatment