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

Axon/Myelin segmentation using Deep Learning

Open pixelated STEM framework

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

Python library for reading and writing scientific data format

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.

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

Python interface for Monte Carlo simulation programs

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

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

Manipulate and mine Relion .star files

Package for analysing particles in electron microscopy data sets.

A single package for analyzing atomic resolution STEM, 4D-STEM and STEM-EELS datasets, along with basic STEM simulation functionality

ImageDataExtractor 2.0 - a Python library for electron microscopy image quantification.

PLEASE: The Python Low-energy Electron Analysis SuitE - Enabling rapid analysis and visualization of LEEM and LEED Data.