Electron Microscopy Python Packages

rosettasciio

Python library for reading and writing scientific data format

102K 72 54

cloud-volume

Read and write Neuroglancer datasets programmatically.

35K 174 52

sofima

Scalable Optical Flow-based Image Montaging and Alignment

18K 96 22

libertem

Open pixelated STEM framework

10K 129 73

scikit-ued

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

3K 156 21

axondeepseg

Axon/Myelin segmentation using Deep Learning

3K 127 33

libertem-blobfinder

LiberTEM correlation and refinement library

2K 5 3

atomai

Deep and Machine Learning for Microscopy

2K 228 42

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

2K 25 4

please

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

1K 17 4

libertem-holo

Electron holography reconstruction and preprocessing routines

1K 5 9

empanada-napari

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

1K 33 16

etspy

A Hyperspy extension package for processing and reconstructing electron tomography data

1K 16 6

stemtool

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

1K 19 2

multimodal-fusion

Fuse multi-modal electron microscopy datasets using inverse problems

979 5 3

traceon

Electromagnetic solver and electron tracer

874 12 7

imagedataextractor

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

792 22 2

instamatic

Python program for automated electron diffraction data collection

779 62 30

mapfusion

Multi-Modal Electron Microscopy Data Fusion for Spectral Maps

580 5 3

stemia

A personal collection of (sometimes...) useful scripts and tools for cryoem/cryoet.

480 11 1

focustools

Python utilities for the FOCUS package

478 6 1

empanada-dl

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

452 2 1

particlespy

Package for analysing particles in electron microscopy data sets.

433 21 11

convert-emd

A tool for exporting data from EMD (Velox) files

400 1 0