A program interfacing Segment Anything with cryoSPARC via cryosparc-tools to efficiently identify vesicle-embedded membrane proteins and complexes in cryo-EM micrographs.

membrane segmentation in 3D for cryo-ET

Tilt Interpolation Generator for Enhanced Reconstruction in cryo electron tomography

Useful aliases and startup settings for ChimeraX

Fast kd-tree implementation in Python

Python scripts for Relion external job type

Automatic atomic model building program for cryo-EM maps

TomoBEAR is a configurable and customizable modular pipeline for streamlined processing of cryo-electron tomographic data for subtomogram averaging.

SUSAN is a sub-tomogram averaging (StA) workflow for CryoET based on sub-stacks of images instead sub-volumes of tomograms. Such an approach substantially lowers computational complexity to speed u…

Miscellaneous scripts for processing cryo-ET data

Rapidly simulate realistic cryo-EM particles

Zotero plugin to automatically move attachments and link them

Official repository for Metric Ion Classification (MIC) code and models

Base tomography Scipion plugin with data model definition

Anisotropic correction of beam induced sample motion for cryo-electron microscopy and tomography

Distributed image processing

Growing Neural Networks Library

This code accompanies "Differentiable probabilistic models of scientific imaging with the Fourier slice theorem", UAI 2019

Algorithms for Single Particle Reconstruction

Fast computation of Gauss transforms in multiple dimensions; enables efficient Kernel Density Estimation (KDE) with Gaussian kernels.

Localized reconstruction of flexible subunits from cryo-EM images

Covariance Estimation and Denoising for Cryo-EM Images (Covariance Wiener Filtering)

SC Fusion

A free and open-source Multidimensional Scaling (MDS) library for Java.