microscopy-image-analysis

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

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

An open-source tool for characterizing PSF and FWHM measurements from light-microscopic 2D and 3D images of microspheres.

Single cell Morphology Quality Control (coSMicQC)

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

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

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

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

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.

Online app for playing the coLoc game (https://biop.github.io/coLoc/)

Interactive point-and-click image counting and landmark placement for scientific images. Built with GLMakie.

MATLAB-based software for cell counting

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

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.

Analysis of Arabidopsis Thaliana roots, FRET-ratio calculation in nuclei compartment. 3D reconstruction of root structure and automatic assignment of tissue layers. Tool developed for the Functional Plant Biology group @ NTNU.

Analysis pipelines for paper Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures

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

3D Nuclear translocation study of YAP in Intestinal Organoids. Tool developed for the Martin-Alonso Regeneration lab.

Batch cell segmentation and size estimation for microscopy images using Cellpose-SAM, with automated good/bad cell classification and an interactive Gradio demo.