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

A curated list of awesome computational cryo-EM methods.

Axon/Myelin segmentation using Deep Learning

Open pixelated STEM framework

Scalable Optical Flow-based Image Montaging and Alignment

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

Workflow for Simulation and Automatic Semantic Segmentation of Electron Microscopy Images

Python library for reading and writing scientific data format

A curated list of awesome computational cryo-ET methods.

Python program for automated electron diffraction data collection

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

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

High Throughput Electron Microscopy Image Processing Software

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++

Python interface for Monte Carlo simulation programs

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

Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari

[TMI 2024.10] GobletNet: Wavelet-Based High Frequency Fusion Network for Semantic Segmentation of Electron Microscopy Images

S/TEM Automated Nanoparticle Analysis

Electron Microscopy Particle Segmentation Dataset

Bayesian Particle Instance Segmentation for Electron Microscopy Image Quantification (JCIM 2021).

Finite-Element Assisted Brain Assembly System for stitching & alignment of connectomics data

Functions for analysis of high resolution electron microscopy and spectroscopy data.

Oxford Instruments NanoAnalysis HDF5 File Specification