There are 3 repositories under electron-microscopy topic.
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
A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.
Collection of algorithms and routines for (ultrafast) electron diffraction and scattering
Read and write Neuroglancer datasets programmatically.
Axon/Myelin segmentation using Deep Learning
A curated list of awesome computational cryo-EM methods.
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
ArtiaX is an open-source extension of the molecular visualisation program ChimeraX.
A curated list of awesome computational cryo-ET methods.
Utilities for building and using the CEM dataset for unsupervised pre-training and downstream tasks.
Python interface for Monte Carlo simulation programs
Package for analysing particles in electron microscopy data sets.
pyCHIP is a tool for segmentation and feature classification in transmission electron microscopy (TEM) images based on a small support set of user-provided examples.
Quantitative Data Analysis for spectroscopic LEEM
A single package for analyzing atomic resolution STEM, 4D-STEM and STEM-EELS datasets, along with basic STEM simulation functionality
Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari
Deep neural network for low-dose electron micrograph denoising
Felix: Bloch wave method diffraction pattern simulation software
ImageDataExtractor 2.0 - a Python library for electron microscopy image quantification.