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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.
Tools for computational pathology
Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.
Image restoration for fluorescence microscopy
Automated 3D cell detection in very large images
PyTorch Connectomics: segmentation toolbox for EM connectomics
A Python interface to access neuroanatomical atlases
Interoperable web-based DICOM slide microscopy viewer and annotation tool
Automated 3D brain registration with support for multiple species and atlases.
Axon/Myelin segmentation using Deep Learning
Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources