Open-source volumetric brain vasculature dataset — 12 two-photon microscopy stacks with dense voxel-level segmentation labels
Volumetric vessel segmentation with convolutional networks (Teikari et al., 2016, arXiv:1606.02382). ZNN framework, 3D architecture
MATLAB analysis pipeline for two-photon microscopy vasculature — vessel tracing, diameter measurement, and 3D visualization
This repository contains the code for Neural fields for Adaptive Optical Two-photon Fluorescence Microscopy (NeAT).
Python pipeline to stitch multiple acquisition fields from Bliq Photonics multi-photon microscopes.
Spectral separability analysis for two-photon fluorescence microscopy — fluorophore selection optimization via genetic algorithms
Model-agnostic biomedical segmentation MLOps platform extending the MONAI ecosystem. Preclinical vascular imaging with Docker-per-flow isolation, SkyPilot intercloud compute, and Spec-driven development (?). Companion code to the VASCADIA manuscript.
Decode photodiode pulse markers from a recording and align the played stimulus protocol onto its frame-exact timeline
Browser-based grating stimulus presenter for visual physiology: WebGL gratings, queued protocols, dual-screen operator panel, frame-marked protocol export
Small, self-contained bio-imaging and bioinformatics methods — each tile runs in a minute on its own synthetic example and answers one question, with a before/after figure
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