Official implementation of "Self-contrastive learning enables interference-resilient and generalizable fluorescence microscopy signal detection without interference modeling."
Resolution Enhancement Algorithm using Deblurring by Pixel Reassignment. This repository implements cutting-edge techniques for improving image resolution and clarity by reassigning pixels to correct for blur. Ideal for microscopy, photography, image processing, and computational optics researchers.
PSF Generator: a PyTorch-based library to simulate point spread functions for microscopes.
BrightEyes Time-tagging module: open-source hardware, a time to digital converter, multi channels, with a resolution of 30 ps designed for fluorescence scanning laser microscopy.
An open-source tool for characterizing PSF and FWHM measurements from light-microscopic 2D and 3D images of microspheres.
Accurate, generalizable and user-friendly 3D cell segmentation
This repository contains the code for Neural fields for Adaptive Optical Two-photon Fluorescence Microscopy (NeAT).
A MATLAB data analysis toolkit for Fluorescence Lifetime Imaging Microscopy (FLIM) and an Alba v5 time-resolved confocal microscope operations manual
Repository with code for Fluocells Neuronal Cells v2 dataset.
Software for automated analysis of single molecule fluorescence and FRET (smFRET) data
This is an open-source macroscope design based on the Olympus 4x/0.28 objective.
An image analysis pipeline for quantifying the spatial distribution of cell markers in stroma-rich tumors
A PowerShell script that logs the real-time power of a laser line on a CELESTA Light Engine® (and a data visualization/analysis script that estimates the exposure time)
Analysis pipelines for paper Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures
Modular, high-resolution light-sheet microscopes for accessible 3D subcellular imaging.
Semi-automated ImageJ macro for cerebellar lobule segmentation and length quantification. Supports boundary detection, Purkinje cell-based mask refinement, and ROI export for downstream analysis.
Quantitative fluorescence microscopy for biologists who don't code — a single-script pipeline for cell segmentation, puncta detection, and colocalization in 2D or natively in 3D
Single-cell CFTR image-analysis pipeline for the mCherry-YFPCFTR quenching assay. The pipeline includes a custom-made Cellpose model for image segmentation, and per-cell quantification of CFTR membrane proximity and function.
Machine learning tool for analysing single molecule tracking data
A modular web platform for automated fluorescence microscopy image analysis
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