Electron Microscopy Python Packages

rosettasciio

Python library for reading and writing scientific data format

cloud-volume

Read and write Neuroglancer datasets programmatically.

atomai

Deep and Machine Learning for Microscopy

libertem

Open pixelated STEM framework

axondeepseg

Axon/Myelin segmentation using Deep Learning

scikit-ued

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

please

Software for the analysis of Low Energy Electron Microscopy data

particleanalyzer

SEM Image Analysis Tool

libertem-blobfinder

LiberTEM correlation and refinement library

stemtool

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

libertem-holo

Electron holography reconstruction and preprocessing routines

traceon

Electromagnetic solver and electron tracer

imagedataextractor

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

multimodal-fusion

Fuse multi-modal electron microscopy datasets using inverse problems

stemia

Scripts and Tools for Electron Microscopy Image Analysis.

empanada-napari

Napari plugin of algorithms for Panoptic Segmentation of organelles in EM

sofima

Scalable Optical Flow-based Image Montaging and Alignment

instamatic

Python program for automated electron diffraction data collection

mapfusion

Fuse multi-modal electron microscopy datasets using inverse problems

focustools

Python utilities for the FOCUS package

elektronn3

A PyTorch-based library for working with 3D and 2D convolutional neural networks, with focus on semantic segmentation of volumetric biomedical image data

convert-emd

A tool for exporting data from EMD (Velox) files

particlespy

A package to perform particle segmentation and analysis

empanada-dl

Algorithms for Panoptic Segmentation of organelles in EM