Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
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Tools for computational pathology
Automated 3D cell detection in very large images
PyTorch Connectomics: segmentation toolbox for EM connectomics
Read and write Neuroglancer datasets programmatically.
A collection of tools for painting super-resolution images
Python package for image-based profiling
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
Gaussian processes and Bayesian optimization for images and hyperspectral data
Pure Python library for reading NIS Elements ND2 images and metadata
ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources
Lattice light-sheet post-processing utility.
An interactive image processing program for biologists written in Python.
Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.
A python package to analyze the matrix fiber orientation and intensity around cells in fiber matrices (as a proxy for cellular forces).