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

Read and write Neuroglancer datasets programmatically.

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

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

Workflow for Simulation and Automatic Semantic Segmentation of Electron Microscopy Images

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

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.

A python package collecting an assortment of geometric phase analysis algorithms and tools to analyse regular (moiré) lattices.

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