Microscopy
Showing 11 of 47 projects
A napari plugin for reading multiple microscopy and general image file formats directly into the viewer using pure Python.
A foundation model-driven method for semantic cell classification in whole slide images, extending Cellpose with a WSI workflow and QuPath integration.
A Python library for processing lattice light-sheet microscopy data, automating parameter detection and image corrections.
An algorithm that minimizes pixel-dependent noise from sCMOS cameras in microscopy images with arbitrary structures.
An interactive image processing program for biologists written in Python.
Single-cell fluorescence microscopy data analysis
An ImageJ/FIJI plugin that color-codes Z-stack microscopy images by depth using LUTs for enhanced 3D visualization.
Generates synthetic phase contrast or fluorescence microscope images of bacteria for training deep learning segmentation models.
A Python package to quantify fiber alignment and density around cells in 3D fiber matrices as a proxy for cellular contractile forces.
[DEPRECATED] A package for storing morphological profiling data.
A Python package for analyzing high-throughput single-cell imaging data, including protein abundance, endocytosis, and particle tracking.
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