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

Scientific analysis of nanoscale materials imaging data

Axon/Myelin segmentation using Deep Learning

TF Implementation of Multiple Instance Learning FCN.

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

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

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.

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

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

Delayed Parallel Image Reading for Microscopy Images in Python

Library for producing and processing on the Adaptive Particle Representation (APR).

Code for my master's thesis. Instance segmentation of fluorescence microscopy images with deep learning.

Methods for Image-Based Cell Profiling

Java (ImageJ/Fiji) software package for 3D deconvolution microscopy

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

python functions for simulating optical transfer functions

Open Delmic Microscope Software

An interactive image processing program for biologists written in Python.

Pure Python library for reading NIS Elements ND2 images and metadata

Fast and Accurate 3D PSF Computation for Fluorescence Microscopy

A convex 3D deconvolution algorithm for low photon count fluorescence imaging

Automated mouse atlas propagation

Python samples for Micro-Manager: image acquisition and microscope control system

Fast and Accurate 3D PSF Computation for Fluorescence Microscopy

🔬🍸 Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ

Noise Correction Algorithm for sCMOS cameras

Microscope control and image acquisition integrated with ImageJ.

A scientific publication, describing a way to improve microscopy. This repository hosts everything you need to reproduce our results. Read the publication here: https://andrewgyork.github.io/remote_refocus/