Electron Microscopy Python Packages

rosettasciio

Python library for reading and writing scientific data format

cloud-volume

Read and write Neuroglancer datasets programmatically.

axondeepseg

Axon/Myelin segmentation using Deep Learning

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

atomai

Deep and Machine Learning for Microscopy

stemtool

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

traceon

Solver and tracer for electrostatic problems

libertem-blobfinder

LiberTEM correlation and refinement library

multimodal-fusion

Multi-Modal Electron Microscopy Data Fusion

stemia

Scripts and Tools for Electron Microscopy Image Analysis.

mapfusion

Fuse multi-modal electron microscopy datasets using inverse problems

instamatic

Python program for automated electron diffraction data collection

empanada-napari

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

imagedataextractor

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

particlespy

A package to perform particle segmentation and analysis

etspy

Suite of tools for processing and reconstruction of electron tomography data

elektronn3

Utilities for 3D CNNs in PyTorch

focustools

Python utilities for the FOCUS package

libertem-holo

Electron holography reconstruction and preprocessing routines

sofima

Scalable Optical Flow-based Image Montaging and Alignment

tempo4d

High-throughput analysis of Bragg discs from 4D-STEM datasets using ML object detection.