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.

Image-processing software for cryo-electron microscopy

Tools for computational pathology

Scientific analysis of nanoscale materials imaging data

Automated 3D cell detection and registration of whole-brain images

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

PyTorch Connectomics: segmentation toolbox for EM connectomics

Axon/Myelin segmentation using Deep Learning

Read and write Neuroglancer datasets programmatically.

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

TF Implementation of Multiple Instance Learning FCN.

Deep and Machine Learning for Microscopy

A fully cloud- and browser-based 3D annotation tool for distributed large-scale data analysis in light- and electron-microscopy based Connectomics

A collection of tools for painting super-resolution images

Open Source Cross-Platform C++ library to read CZI image files

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

A lightweight python module to interact with atlases for systems neuroscience

This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)

Manual, source-code and binaries for the NanoJ-Fluidics project