Image-processing software for cryo-electron microscopy

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

cuCIM - RAPIDS GPU-accelerated image processing library

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

Scientific analysis of nanoscale materials imaging data

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

DeepTrack2 is a modular Python library for generating, manipulating, and analyzing image data pipelines for machine learning and experimental imaging.

Automated 3D cell detection in very large images

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

Deep and Machine Learning for Microscopy

PyTorch Connectomics: segmentation toolbox for EM connectomics

Read and write Neuroglancer datasets programmatically.

A Python interface to access neuroanatomical atlases

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

Visualize, share and annotate your large 3D images online

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

Loading and handling microscopy data in blender

Automated 3D brain registration with support for multiple species and atlases.

A collection of tools for painting super-resolution images