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
Read and write Neuroglancer datasets programmatically.
Automated 3D brain registration with support for multiple species and atlases.
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.
Noise Correction Algorithm for sCMOS cameras
Single-cell fluorescence microscopy data analysis
An interactive image processing program for biologists written in Python.
A python package to analyze the matrix fiber orientation and intensity around cells in fiber matrices (as a proxy for cellular forces).