MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification
Single cell Morphology Quality Control (coSMicQC)
🔬Python package for high-throughput single-cell imaging analysis.
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.
Fluidity Calculator – ImageJ/Fiji tool to calculate membrane fluidity from spectral imaging data.
A Napari plugin for automated cell nuclei detection, cell proliferation & population growth analysis, and single-cell tracking in brightfield and fluorescence microscopy images
MATLAB-based software for cell counting
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.
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
Single-Molecule Localization Microscopy scripts used in my report "Computational Methods in Single-Molecule Localization Microscopy"
count lipid droplets in tetrahymena thermophila with Python
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.
An application for automated high-throughput analysis of cancer and endothelial cell dynamics in hydrogels.
Pipeline to assist in understanding sub-cellular events in large 4-D, 3-channel lattice light sheet
Repository for the Crucible application, the Lawrence Berkeley National Laboratory microscopy sharing and analyzing software
this repository access all my work about building a digital annalyser (Digital Microscope ) that can analyse blood to detect particle ,and do Hematologia Exam , it build with opencv qt itk vtk
Streamline fluorescent microscopy workflows with these scripts. This collection provides automated cell segmentation & tracking using TrackMate, featuring two-step segmentation, flexible temporal/spatial tracking, and efficient analysis of large datasets. Ideal for researchers automating imaging analysis.
Jupyter Notebook for analyzing microscopy libraries for use with my python backend Microscopy App
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