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.

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

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

Axon/Myelin segmentation using Deep Learning

A curated list of awesome computational cryo-EM methods.

Open pixelated STEM framework

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

Scalable Optical Flow-based Image Montaging and Alignment

Python program for automated electron diffraction data collection

Python library for reading and writing scientific data format

A curated list of awesome computational cryo-ET methods.

Workflow for Simulation and Automatic Semantic Segmentation of Electron Microscopy Images

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

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.

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