zebrafish

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

A vocabulary for describing Zebrafish Phenotypes

Software for performing offline tracking of zebrafish larvae.

Code for "Convergent Temperature Representations in Artificial and Biological Neural Networks"

Napari plugin for spatial RNA quantification

Zebrafish embryo fluorescence quantification

A simple tool for zebrafish brain visualization.

Desktop platform (Python/Tkinter) for multi-animal tracking and behavioral analysis of zebrafish (*Danio rerio*): YOLO/OpenVINO detection with NPU support, pre-recorded video or live camera input, parallel multi-tank analysis, scientific metrics (ROIs/zones, geotaxis, cm calibration), Arduino triggers, and Excel/Word reports.

Zebrafish project for Champalimaud Research

Open-source desktop application for OECD TG 236 zebrafish embryo toxicity (FET) assays — experimental design, daily well scoring, LC50/NOEC/LOEC and sublethal endpoint analysis, OECD validity checks, and automated Word report generation. Developed by Henrique Tamanini S. Moschen, University of Brasilia.

Larval zebrafish virtual lab and 3D live WebSocket viewer for active inference simulations in MuJoCo

Kaggle entry for Biohub – Cell Tracking During Development: 3D+time cell tracking in zebrafish embryo microscopy via U-Net + transformer + ILP with graph repair. Public LB 0.817.

Segmentation software for muscle, from Mendieta-Serrano 2022

Finomena a is zebrafish time-series behavioral analysis tool that uses Generative Additive Mixed Models and unsupervised machine learning to explore the similarities and differences in movement between zebrafish in experimental settings.

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

Two-pass Scanpy analysis of zebrafish whole-head scRNA-seq: QC, doublet handling, compartment assignment and marker-led annotation. Consumes the ambient-corrected matrices from cellranger-cellbender-workflow.

Toolkit for providing visual stimuli to zebrafish larvae and mice.

Johnson-SU vs z-score normalization on ZAPBench neural activity traces: reliable gains at small neuron subsets, unstable by 10,000 neurons. Multi-seed and reproducible.

Browser-based normalization and QC for zebrafish embryo DCF fluorescence CSV experiments.

Zebrafish analysis — Gradio webapp + 3D Slicer extension