Electron Microscopy Python Packages

rosettasciio

Python library for reading and writing scientific data format

cloud-volume

Read and write Neuroglancer datasets programmatically.

sofima

Scalable Optical Flow-based Image Montaging and Alignment

em-database

Database for easily downloading electron microscopy datasets and model weights

axondeepseg

Axon/Myelin segmentation using Deep Learning

atomai

Deep and Machine Learning for Microscopy

scikit-ued

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

libertem

Open pixelated STEM framework

please

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

particleanalyzer

A Computer Vision-Based Tool for Automatic Segmentation and Size Analysis of Nanoparticles in Scanning Electron Microscope (SEM) and Transmission Electron Microscope (TEM) Images

stemtool

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

empanada-napari

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

multimodal-fusion

Fuse multi-modal electron microscopy datasets using inverse problems

instamatic

Python program for automated electron diffraction data collection

stemia

Scripts and Tools for Electron Microscopy Image Analysis.

traceon

Electromagnetic solver and electron tracer

libertem-blobfinder

LiberTEM correlation and refinement library

mapfusion

Fuse multi-modal electron microscopy datasets using inverse problems

particlespy

Package for analysing particles in electron microscopy data sets.

empanada-dl

Panoptic segmentation algorithms for 2D and 3D electron microscopy images

focustools

Python utilities for the FOCUS package

etspy

A Hyperspy extension package for processing and reconstructing electron tomography data

convert-emd

A tool for exporting data from EMD (Velox) files

imagedataextractor

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