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
Automated 3D cell detection in very large images
Deep and Machine Learning for Microscopy
PyTorch Connectomics: segmentation toolbox for EM connectomics
A Python interface to access neuroanatomical atlases
Read and write Neuroglancer datasets programmatically.
Automated 3D brain registration with support for multiple species and atlases.
A collection of tools for painting super-resolution images
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
python functions for simulating optical transfer functions
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.
Noise Correction Algorithm for sCMOS cameras
Single-cell fluorescence microscopy data analysis
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).