MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification
An open-source tool for characterizing PSF and FWHM measurements from light-microscopic 2D and 3D images of microspheres.
Automated batch processing of cell and tissue microscopy image data in Napari
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".
Interactive point-and-click image counting and landmark placement for scientific images. Built with GLMakie.
Fluidity Calculator – ImageJ/Fiji tool to calculate membrane fluidity from spectral imaging data.
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
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
Consolidation of many useful python image processing tools into an easy-to-use interface.
Online app for playing the coLoc game (https://biop.github.io/coLoc/)
Few-shot Domain Adaptation for Cellular Instance Segmentation
An application for automated high-throughput analysis of cancer and endothelial cell dynamics in hydrogels.
Uses a segmentation NN to count organoids in brightfield images.
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
nnU-Net-based Tumor Spheroids Auto Delineation
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