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
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
Python package for image-based profiling
Axon/Myelin segmentation using Deep Learning
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources
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).
[DEPRECATED] A package for storing morphological profiling data.