Scientific analysis of nanoscale materials imaging data

Deep and Machine Learning for Microscopy

A PyTorch-based library for working with 3D and 2D convolutional neural networks, with focus on semantic segmentation of volumetric biomedical image data

Collection of algorithms and routines for (ultrafast) electron diffraction and scattering

Read and write Neuroglancer datasets programmatically.

A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.

Axon/Myelin segmentation using Deep Learning

Open pixelated STEM framework

A curated list of awesome computational cryo-EM methods.

Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)

Python program for automated electron diffraction data collection

Scalable Optical Flow-based Image Montaging and Alignment

Python library for reading and writing scientific data format

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

Workflow for Simulation and Automatic Semantic Segmentation of Electron Microscopy Images

A curated list of awesome computational cryo-ET methods.

High Throughput Electron Microscopy Image Processing Software

ArtiaX is an open-source extension of the molecular visualisation program ChimeraX.

Utilities for building and using the CEM dataset for unsupervised pre-training and downstream tasks.

Implementation of geometric phase analysis (GPA) in C++