electron-microscopy

There are 3 repositories under electron-microscopy topic.

pycroscopy / pycroscopy
Scientific analysis of nanoscale materials imaging data
microscopy imaging spectroscopy materials-science scanning visualization atom atomic-force-microscopy scanning-probe-microscopy afm stm electron-microscopy stem raman infrared statistics scanning-tunnelling-microscopy machine-learning fft signal-processing
Language:Jupyter Notebook 250
atomai
pycroscopy / atomai
Deep and Machine Learning for Microscopy
microscopy materials machine-learning materials-science deep-learning multivariate-analysis fully-convolutional-networks variational-autoencoders ensemble-learning google-colaboratory jupyter-notebook pytorch semantic-segmentation electron-microscopy scanning-probe-microscopy deep-kernel-learning imaging
Language:Python 179
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
pytorch 3d-cnn convolutional-neural-networks biomedical-image-processing electron-microscopy 3d-convolutional-network semantic-segmentation
Language:Python 161
seung-lab / cloud-volume
Read and write Neuroglancer datasets programmatically.
neuroglancer volumetric-data python cloud numpy connectomics microscopy microscopy-images chunked-image biomedical-image-processing s3 gcs mesh skeletons serverless big-data electron-microscopy tensor matrix large-image
Language:Python 125
awesome-cryoem
kuixu / awesome-cryoem
A collaborative list of awesome CryoEM (Cryo Electron Microscopy) resources.
cryo-em electron-microscopy density-map 3d-reconstruction 3d-denoise model-building protein-structures tomography cryoem
124
LaurentRDC / scikit-ued
Collection of algorithms and routines for (ultrafast) electron diffraction and scattering
diffraction electron-microscopy python science scikit ultrafast-electron
Language:Python 124
axondeepseg / axondeepseg
Axon/Myelin segmentation using Deep Learning
deep-learning machine-learning myelin axon neuropoly spinalcord segmentation electron-microscopy microscopy histology convolutional-neural-networks
Language:Python 112
LiberTEM / LiberTEM
Open pixelated STEM framework
electron-microscopy data-processing image-processing python
Language:Python 105
phonchi / Computational-CryoEM
A curated list of awesome computational cryo-EM methods.
cryo-em electron-microscopy single-particle-analisys computational-biology structural-biology cryoem
Language:Jupyter Notebook 82
I2PC / scipion
Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM)
electron-microscopy cryo-em single-particle-analisys structural-biology workflow reproducible-science usability image-processing python c-plus-plus
Language:Python 75
instamatic-dev / instamatic
Python program for automated electron diffraction data collection
3d-electron-diffraction automation data-collection electron-diffraction electron-microscopy micro-ed serial-crystallography
Language:Python 50
google-research / sofima
Scalable Optical Flow-based Image Montaging and Alignment
connectomics stitching-algorithm alignment-algorithm 2d 3d 4d biomedical-image-processing electron-microscopy microscopy jax python3
Language:Jupyter Notebook 48
katrinleinweber / PhD-thesis
Experimental tech-demo for PhD thesis in Scientific Markdown; official:
latexmk latex-document pandoc zotero citer latex phd-thesis makefile make biology diatom biofilm eds electron-microscopy microscopy biochemistry markdown markdown-template
Language:Shell 42
hyperspy / rosettasciio
Python library for reading and writing scientific data format
python scientific-formats hyperspectral image multi-dimensional electron-microscopy hyperspy raman
Language:Python 41
LBEM-CH / focus
High Throughput Electron Microscopy Image Processing Software
electron-microscopy image-processing qt5 cryo-em
Language:C++ 33
BAMresearch / automatic-sem-image-segmentation
Workflow for Simulation and Automatic Semantic Segmentation of Electron Microscopy Images
cyclegan deep-learning electron-microscopy neural-networks segmentation sem simulation tem unet
Language:Jupyter Notebook 30
FrangakisLab / ArtiaX
ArtiaX is an open-source extension of the molecular visualisation program ChimeraX.
3d-graphics cryo-em cryo-et electron-microscopy subtomogram virtual-reality
Language:Python 26
JJPPeters / Strainpp
Implementation of geometric phase analysis (GPA) in C++
gpa strain geometric-phase-analysis electron-microscopy
Language:C++ 26
volume-em / cem-dataset
Utilities for building and using the CEM dataset for unsupervised pre-training and downstream tasks.
deep-learning unsupervised-learning pytorch pretrained-models electron-microscopy semantic-segmentation benchmarking weights
Language:Jupyter Notebook 24
phonchi / Computational-CryoET
A curated list of awesome computational cryo-ET methods.
computational-biology cryo-et cryoet electron-microscopy structural-biology
23
pymontecarlo / pymontecarlo
Python interface for Monte Carlo simulation programs
electron-microscopy microanalysis microscopy monte-carlo-simulation x-ray x-ray-spectroscopy
Language:Python 20
TAdeJong / pyGPA
A python package collecting an assortment of geometric phase analysis algorithms and tools to analyse regular (moiré) lattices.
electron-microscopy image-analysis image-processing physics
Language:Python 20
by256 / bpartis
Bayesian Particle Instance Segmentation for Electron Microscopy Image Quantification (JCIM 2021).
deep-learning electron-microscopy electron-microscopy-datasets segmentation
Language:Python 19
ePSIC-DLS / particlespy
Package for analysing particles in electron microscopy data sets.
electron-microscopy analysing-particles
Language:Python 18
pychip_gui
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.
electron-microscopy gui machine-learning python
Language:HTML 18
LEEM-analysis
TAdeJong / LEEM-analysis
Quantitative Data Analysis for spectroscopic LEEM
leem data-visualization data-analysis electron-microscopy physics surface-science parallel-programming low-energy-electron-microscopy image-registration
Language:Jupyter Notebook 17
mgrady3 / PLEASE
PLEASE: The Python Low-energy Electron Analysis SuitE - Enabling rapid analysis and visualization of LEEM and LEED Data.
leed leem electron-microscopy surface-science
Language:Python 16
pycroscopy / stemtool
A single package for analyzing atomic resolution STEM, 4D-STEM and STEM-EELS datasets, along with basic STEM simulation functionality
4d-stem electron-microscopy eels
Language:Python 15
sami-chaaban / starparser
Manipulate and mine Relion .star files
relion cryo-em electron-microscopy
Language:Python 15
volume-em / empanada-napari
Panoptic segmentation algorithms for 2D and 3D electron microscopy in napari
deep-learning electron-microscopy mitochondria panoptic-segmentation instance-segmentation 3d 2d napari-plugin
Language:Python 15
Jeffrey-Ede / Electron-Micrograph-Denoiser
Deep neural network for low-dose electron micrograph denoising
neural-network electron-microscopy noise-removal low-dose tensorflow
Language:Python 14
WarwickMicroscopy / Felix
Felix: Bloch wave method diffraction pattern simulation software
electron-microscopy physical-modeling fortran optimisation
Language:Fortran 14
emx77 / ASI_MTF
Imagej macro to calculate the MTF based on a knife edge measurement
imagej-macro electron-microscopy image-analysis x-ray-imaging point-spread-function mtf imagej imagej-plugins
Language:ImageJ Macro 13
JJPPeters / clTEM
OpenCL accelerated multislice simulation for electron microscopy.
opencl multislice electron-microscopy simulation
Language:C++ 13
oinanoanalysis / h5oina
Oxford Instruments NanoAnalysis HDF5 File Specification
hdf5 microanalysis electron-microscopy fileformat electron-backscatter-diffraction ebsd
12
lukmuk / em-scalebartools
Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image.
imagej fiji electron-microscopy scalebar
Language:ImageJ Macro 11