electron-microscopy
There are 106 repositories under electron-microscopy topic.
pycroscopy/pycroscopy
Scientific analysis of nanoscale materials imaging data
pycroscopy/atomai
Deep and Machine Learning for Microscopy
ELEKTRONN/elektronn3
A PyTorch-based library for working with 3D and 2D convolutional neural networks, with focus on semantic segmentation of volumetric biomedical image data
kuixu/awesome-cryoem
A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.
seung-lab/cloud-volume
Read and write Neuroglancer datasets programmatically.
LaurentRDC/scikit-ued
Collection of algorithms and routines for (ultrafast) electron diffraction and scattering
axondeepseg/axondeepseg
Axon/Myelin segmentation using Deep Learning
LiberTEM/LiberTEM
Open pixelated STEM framework
phonchi/Computational-CryoEM
A curated list of awesome computational cryo-EM methods.
I2PC/scipion
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
instamatic-dev/instamatic
Python program for automated electron diffraction data collection
google-research/sofima
Scalable Optical Flow-based Image Montaging and Alignment
hyperspy/rosettasciio
Python library for reading and writing scientific data format
katrinleinweber/PhD-thesis
Experimental tech-demo for PhD thesis in Scientific Markdown; official:
BAMresearch/automatic-sem-image-segmentation
Workflow for Simulation and Automatic Semantic Segmentation of Electron Microscopy Images
LBEM-CH/focus
High Throughput Electron Microscopy Image Processing Software
FrangakisLab/ArtiaX
ArtiaX is an open-source extension of the molecular visualisation program ChimeraX.
JJPPeters/Strainpp
Implementation of geometric phase analysis (GPA) in C++
phonchi/Computational-CryoET
A curated list of awesome computational cryo-ET methods.
volume-em/cem-dataset
Utilities for building and using the CEM dataset for unsupervised pre-training and downstream tasks.
TAdeJong/pyGPA
A python package collecting an assortment of geometric phase analysis algorithms and tools to analyse regular (moiré) lattices.
pymontecarlo/pymontecarlo
Python interface for Monte Carlo simulation programs
by256/bpartis
Bayesian Particle Instance Segmentation for Electron Microscopy Image Quantification (JCIM 2021).
ePSIC-DLS/particlespy
Package for analysing particles in electron microscopy data sets.
pnnl/pychip_gui
pyCHIP is a tool for segmentation and feature classification in transmission electron microscopy (TEM) images based on a small support set of user-provided examples.
by256/emps
Electron Microscopy Particle Segmentation Dataset
sami-chaaban/starparser
Manipulate and mine Relion .star files
TAdeJong/LEEM-analysis
Quantitative Data Analysis for spectroscopic LEEM
mgrady3/PLEASE
PLEASE: The Python Low-energy Electron Analysis SuitE - Enabling rapid analysis and visualization of LEEM and LEED Data.
pycroscopy/stemtool
A single package for analyzing atomic resolution STEM, 4D-STEM and STEM-EELS datasets, along with basic STEM simulation functionality
volume-em/empanada-napari
Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari
WarwickMicroscopy/Felix
Felix: Bloch wave method diffraction pattern simulation software
Jeffrey-Ede/Electron-Micrograph-Denoiser
Deep neural network for low-dose electron micrograph denoising
emx77/ASI_MTF
Imagej macro to calculate the MTF based on a knife edge measurement
JJPPeters/clTEM
OpenCL accelerated multislice simulation for electron microscopy.
by256/imagedataextractor
ImageDataExtractor 2.0 - a Python library for electron microscopy image quantification.