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Dennis (dmichalak)

dmichalak

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Location:Washington, DC, USA

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Dennis's starred repositories

AreTomo2

Language:C++License:BSD-3-ClauseStargazers:41Issues:0Issues:0

DynaMight

Tool for reconstruction and analysis of continuous heterogeneity of a cryo-EM dataset

Language:PythonLicense:NOASSERTIONStargazers:20Issues:0Issues:0

chimerax-trimmings

Useful aliases and startup settings for ChimeraX

Stargazers:24Issues:0Issues:0

pytom-match-pick

GPU-accelerated template matching for cryo-ET

Language:PythonLicense:GPL-2.0Stargazers:25Issues:0Issues:0

colabseg

Jupyter-based tool for membrane segmentation manipulation

Language:Jupyter NotebookLicense:Apache-2.0Stargazers:8Issues:0Issues:0

cryohub

IO hub for Cryo-EM, Cryo-ET and subtomogram averaging data.

Language:PythonLicense:NOASSERTIONStargazers:9Issues:0Issues:0

starfile.vim

VIM syntax for STAR/CIF files.

Language:Vim ScriptLicense:GPL-3.0Stargazers:4Issues:0Issues:0

fourier-guide

An interactive guide to the Fourier-Transform.

Language:MDXLicense:NOASSERTIONStargazers:24Issues:0Issues:0

cryotomosim_CTS

cryo-EM tomogram simulator

Language:MATLABLicense:NOASSERTIONStargazers:18Issues:0Issues:0

abTEM

ab initio Transmission Electron Microscopy

Language:PythonLicense:GPL-3.0Stargazers:190Issues:0Issues:0

imod2relion

A tool reading IMOD points, obtaining particles' info and generating .star file for RELION

Language:PythonLicense:BSD-3-ClauseStargazers:1Issues:0Issues:0

pydev-guide.github.io

Guide to python package development for scientists

Stargazers:14Issues:0Issues:0

dynamo2relion

Converts Dynamo tables to star files for coordinate import into RELION 4.0

Language:PythonLicense:BSD-3-ClauseStargazers:11Issues:0Issues:0

fidder

Detect and erase gold fiducials in cryo-EM images

Language:PythonLicense:NOASSERTIONStargazers:10Issues:0Issues:0

isolde

Interactive molecular dynamics based model building into low-resolution crystallographic and cryo-EM maps

Language:PythonLicense:NOASSERTIONStargazers:31Issues:0Issues:0

membrain-seg

membrane segmentation in 3D for cryo-ET

Language:PythonLicense:NOASSERTIONStargazers:50Issues:0Issues:0

eman2

A scientific image processing software suite with a focus on CryoEM and CryoET

Language:PythonStargazers:145Issues:0Issues:0

Membrane_Associated_Picking

Scripts to pick membrane associated particles

Language:MATLABLicense:MITStargazers:2Issues:0Issues:0

cryodrgn

Neural networks for cryo-EM reconstruction

Language:PythonLicense:GPL-3.0Stargazers:297Issues:0Issues:0

ChimeraX

Source code for molecular graphics program UCSF ChimeraX

Language:PythonLicense:NOASSERTIONStargazers:144Issues:0Issues:0

learn_cryoem_math

Language:Jupyter NotebookStargazers:118Issues:0Issues:0

relion2dynamo

Simple package to convert star files to Dynamo tables.

Language:PythonLicense:BSD-3-ClauseStargazers:3Issues:0Issues:0

subtomo

Language:PythonStargazers:2Issues:0Issues:0

TomoBEAR

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

Language:MATLABLicense:NOASSERTIONStargazers:26Issues:0Issues:0

DeePiCt

Pipeline for the automatic detection and segmentation of particles and cellular structures in 3D Cryo-ET data, based on deep learning (convolutional neural networks).

Language:PythonLicense:Apache-2.0Stargazers:29Issues:0Issues:0

coot

Software for macromolecular model-building

Language:C++License:GPL-3.0Stargazers:118Issues:0Issues:0

tomotwin-cryoet

cryo-ET particle picking by representation and metric learning

Language:PythonLicense:MPL-2.0Stargazers:29Issues:0Issues:0

blik

Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.

Language:PythonLicense:GPL-3.0Stargazers:23Issues:0Issues:0

scipion-em-tomo

Base tomography Scipion plugin with data model definition

Language:PythonLicense:GPL-3.0Stargazers:8Issues:0Issues:0

model-angelo

Automatic atomic model building program for cryo-EM maps

Language:PythonLicense:MITStargazers:114Issues:0Issues:0