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
Python package for image-based profiling
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
Lattice light-sheet post-processing utility.