MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification

Single cell Morphology Quality Control (coSMicQC)

Automated batch processing of cell and tissue microscopy image data in Napari

🔬Python package for high-throughput single-cell imaging analysis.

An open-source tool for characterizing PSF and FWHM measurements from light-microscopic 3D images of microspheres.

Official implementation of "PanopMamba: Vision State Space Modeling for Nuclei Panoptic Segmentation".

CellLocator: Automated live-cell image analysis for Incucyte®. Streamlined cell segmentation, fluorescence quantification, and kinetic analysis. Open-source and freely available under the MIT License.

A Napari plugin for automated cell nuclei detection, cell proliferation & population growth analysis, and single-cell tracking in brightfield and fluorescence microscopy images

Fluidity Calculator – ImageJ/Fiji tool to calculate membrane fluidity from spectral imaging data.

This repository summarizes our group's previous work on cellular image analysis in parasite microbiology.

MATLAB codes developed in Courtemanche lab at University of Minnesota for automating analysis of actin filament properties from single molecule microscopy images.

MATLAB-based software for cell counting

Few-shot Domain Adaptation for Cellular Instance Segmentation

nnU-Net-based Tumor Spheroids Auto Delineation

Computer vision tool using Tensorflow and Keras to train U-Net and U-Net++ with the optional use of EfficientNetB7 as a pretrained backbone for binary segmentation of microscopy images

An application for automated high-throughput analysis of cancer and endothelial cell dynamics in hydrogels.

Consolidation of many useful python image processing libraries into an easy-to-use interface.

Single-Molecule Localization Microscopy scripts used in my report "Computational Methods in Single-Molecule Localization Microscopy"

Multi-Orientation MAXWELL: A novel approach to three-dimensional super resolution mapping of X-ray excited, visible light emitting fluorophores using the X-ray Light Sheet Microscopy technique MAXWELL.

A sophisticated all-in-one FRET Tool developed by SONLab Team