Projects in Awesome Lists tagged with electron-microscopy

https://github.com/pycroscopy/pycroscopy

Scientific analysis of nanoscale materials imaging data

afm atom atomic-force-microscopy electron-microscopy fft imaging infrared machine-learning materials-science microscopy raman scanning scanning-probe-microscopy scanning-tunnelling-microscopy signal-processing spectroscopy statistics stem stm visualization

Last synced: 15 May 2025

https://github.com/pycroscopy/atomai

Deep and Machine Learning for Microscopy

deep-kernel-learning deep-learning electron-microscopy ensemble-learning fully-convolutional-networks google-colaboratory imaging jupyter-notebook machine-learning materials materials-science microscopy multivariate-analysis pytorch scanning-probe-microscopy semantic-segmentation variational-autoencoders

Last synced: 04 Apr 2025

https://github.com/seung-lab/cloud-volume

Read and write Neuroglancer datasets programmatically.

big-data biomedical-image-processing chunked-image cloud connectomics electron-microscopy gcs large-image matrix mesh microscopy microscopy-images neuroglancer numpy python s3 serverless skeletons tensor volumetric-data

Last synced: 15 May 2025

https://github.com/laurentrdc/scikit-ued

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

diffraction electron-microscopy python science scikit ultrafast-electron

Last synced: 12 Apr 2025

https://github.com/libertem/libertem

Open pixelated STEM framework

data-processing electron-microscopy image-processing python

Last synced: 09 Apr 2026

https://github.com/axondeepseg/axondeepseg

Axon/Myelin segmentation using Deep Learning

axon convolutional-neural-networks deep-learning electron-microscopy histology machine-learning microscopy myelin neuropoly segmentation spinalcord

Last synced: 04 Apr 2026

https://github.com/google-research/sofima

Scalable Optical Flow-based Image Montaging and Alignment

2d 3d 4d alignment-algorithm biomedical-image-processing connectomics electron-microscopy jax microscopy python3 stitching-algorithm

Last synced: 05 Apr 2025

https://github.com/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

Last synced: 16 Jan 2026

https://github.com/hyperspy/rosettasciio

Python library for reading and writing scientific data format

electron-microscopy hyperspectral hyperspy image multi-dimensional python raman scientific-formats

Last synced: 16 May 2025

https://github.com/katrinleinweber/phd-thesis

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

biochemistry biofilm biology citer diatom eds electron-microscopy latex latex-document latexmk make makefile markdown markdown-template microscopy pandoc phd-thesis zotero

Last synced: 29 Jul 2025

https://github.com/katrinleinweber/PhD-thesis

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

biochemistry biofilm biology citer diatom eds electron-microscopy latex latex-document latexmk make makefile markdown markdown-template microscopy pandoc phd-thesis zotero

Last synced: 21 Jul 2025

https://github.com/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

Last synced: 05 Jul 2025

https://github.com/sami-chaaban/starparser

Manipulate and mine Relion .star files

cryo-em electron-microscopy relion

Last synced: 27 Jan 2026

https://github.com/pycroscopy/stemtool

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

4d-stem eels electron-microscopy

Last synced: 11 Apr 2025

https://github.com/emx77/ASI_MTF

Imagej macro to calculate the MTF based on a knife edge measurement

electron-microscopy image-analysis imagej imagej-macro imagej-plugins mtf point-spread-function x-ray-imaging

Last synced: 07 May 2025

https://github.com/usnistgov/etspy

A Hyperspy extension package for processing and reconstructing electron tomography data

electron-microscopy tomography

Last synced: 08 Apr 2026

https://github.com/zacharyvarley/ebsdtorch

A PyTorch only Library for Electron Backscatter Diffraction (EBSD) Indexing

ebsd electron-backscatter-diffraction electron-microscopy gpu-acceleration orientations pytorch-implemention spherical-harmonics

Last synced: 15 Apr 2025

https://github.com/lukmuk/em-scalebartools

Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image.

electron-microscopy fiji imagej scalebar

Last synced: 07 May 2025

https://github.com/brisvag/stemia

Scripts and Tools for Electron Microscopy Image Analysis.

electron-microscopy python

Last synced: 15 Mar 2025

https://github.com/leon-vv/traceon

Electromagnetic solver and electron tracer

boundary-element-method electromagnetic-simulation electromagnetism electron electron-microscopy magnetism physics solver tracing

Last synced: 08 Apr 2026

https://github.com/instamatic-dev/pyserialem

Python module to read/write SerialEM navigator files.

electron-microscopy navigator python serialem

Last synced: 25 Dec 2025

https://github.com/elektronn/elektronn2

A highly configurable toolkit for training 3D/2D CNNs and general Neural Networks, based on Theano

3d-cnn 3d-convolutional-network biomedical-image-processing cnn convolutional-neural-networks electron-microscopy theano

Last synced: 21 Feb 2026

https://github.com/kit-data-manager/metadata-schemas-for-materials-science

Metadata Schemas for describing measurement techniques in Materials Science

electron-microscopy json-schema materials-science metadata schema xml

Last synced: 22 Apr 2025

https://github.com/jewettaij/visfd

volumetric image toolkit for simple feature detection in 3D images (segment tomograms)

3d-images cryo-em cryoem electron-microscopy image-processing membrane-detection mrc-format segmentation tensor-voting tomography

Last synced: 18 Jan 2026

https://github.com/libertem/libertem-blobfinder

LiberTEM correlation and refinement library

data-processing electron-microscopy image-processing python

Last synced: 10 Apr 2025

https://github.com/benweare/givemeed

A Digital Micrograph Script to collect three-dimension electron diffraction data.

crystallography data-collection digital-micrograph electron-crystallography electron-diffraction electron-microscopy micro-ed three-dimensional-electron-diffraction transmission-electron-microscopy

Last synced: 07 Apr 2026

https://github.com/jabae/cmito

Mitochondria detection in C. elegans EM images.

convolutional-neural-networks deep-learning electron-microscopy image-processing mitochondria python3 segmentation

Last synced: 18 May 2026

https://github.com/benweare/pyctf

A python package to measure lens aberration from experimental contrast transfer functions (CTFs).

contrast-transfer-function electron-microscopy python transmission-electron-microscope transmission-electron-microscopy

Last synced: 07 Apr 2026

https://github.com/volume-em/empanada

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

deep-learning electron-microscopy instance-segmentation panoptic-segmentation pytorch segmentation semantic-segmentation

Last synced: 21 Oct 2025

https://github.com/jabae/cnapse

Automated synapse detection in C. elegans EM images.

connectomics deep-learning electron-microscopy image-processing python python3 segmentation

Last synced: 18 May 2026

https://github.com/matbryan52/microscopy-images-qem

Presentation for QEM2025: "Digital Images"

electron-microscopy image-processing

Last synced: 16 Feb 2026

https://github.com/benweare/em_scripts

Electron microscopy scripts not associated with any specific publications.

contrast-transfer-function ctf data-analysis digital-micrograph electron-microscopy jupyter-notebook optics python tomography tomography-data-collection transmission-electron-microscopy zemlin-tableau zernike-polynomials

Last synced: 07 Apr 2026

https://github.com/rybakov-ks/particleanalyzer

A Computer Vision-based tool for automatic segmentation and size analysis of particles in Scanning Electron Microscope (SEM) images.

computer-vision data-analysis deep-learning detectron2 electron-microscopy image-segmentation materials-characterization microscopy-images nanotechnology object-detection particle-analysis scanning-electron-microscopy scientific-research sem sem-image-analysis yolo

Last synced: 13 May 2026

https://github.com/acylation/dlsilicaspheres

Using deep learning methods to recognize and measure silica spheres in SEM pictures.

chemistry electron-microscopy electron-microscopy-datasets nanoparticles scanning-electron-microscope

Last synced: 19 Mar 2026

https://github.com/ofir-frd/automatic-size-calculation

In this work an automatic code for collection of the CuS nanoparticles thickness and width is suggested. The code is written in Matlab and uses its advanced image processing tools. Bright field TEM images were produced using Ilse Katz Institute for Nanoscale Science & Technology TEM JEM-1230 (T-12). The images were converted from DigitalMicrograph ‘.dm’ format to ‘.TIF’ files. Graphical and statistical analyze of the ‘.TIF’ files was conducted using Origin and Statistica software.

electron-microscopy histogram-equalization image-processing

Last synced: 13 May 2026