Topic: "cryo-et"
IsoNet-cryoET/IsoNet
Self-supervised learning for isotropic cryoET reconstruction
Language: Python - Size: 116 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 75 - Forks: 13
MLI-lab/DeepDeWedge
Self-supervised deep learning for denoising and missing wedge reconstruction of cryo-ET tomograms
Language: Jupyter Notebook - Size: 8.66 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 39 - Forks: 11
alncat/opusDSD
deep structural disentanglement
Language: Python - Size: 21.5 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 37 - Forks: 5
MPI-Dortmund/tomotwin-cryoet
cryo-ET particle picking by representation and metric learning
Language: Python - Size: 64.3 MB - Last synced at: 4 days ago - Pushed at: 20 days ago - Stars: 36 - Forks: 7
phonchi/Computational-CryoET
A curated list of awesome computational cryo-ET methods.
Size: 174 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 36 - Forks: 1
FrangakisLab/ArtiaX
ArtiaX is an open-source extension of the molecular visualisation program ChimeraX.
Language: Python - Size: 3.62 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 33 - Forks: 4
KudryashevLab/TomoBEAR
TomoBEAR is a configurable and customizable modular pipeline for streamlined processing of cryo-electron tomographic data for subtomogram averaging.
Language: MATLAB - Size: 2.97 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 27 - Forks: 7
brisvag/blik
Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
Language: Python - Size: 2.49 MB - Last synced at: 4 days ago - Pushed at: 2 months ago - Stars: 26 - Forks: 8
ZauggGroup/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: Python - Size: 7.23 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 25 - Forks: 8
logicvay2010/TomoNet
TomoNet is a GUI based pipeline package focusing on cryoET and STA data processing
Language: Python - Size: 38.1 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 17 - Forks: 2
nextpyp/next
Web-interface for nextPYP
Language: Kotlin - Size: 3.5 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 1
nextpyp/pyp
Cryo-EM/ET image analysis
Language: Python - Size: 3.31 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 9 - Forks: 0
alncat/opusTomo
structural heterogeneity analysis for cryo-ET subtomogram
Language: Python - Size: 15.4 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 8 - Forks: 0
nextpyp/cet_pick
Cellular content mining and particle localization
Language: Python - Size: 8.4 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 8 - Forks: 1
Lucaslab-Berkeley/Leopard-EM
Two-Dimensional Template Matching implemented in Python
Language: Python - Size: 25.2 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 7 - Forks: 5
Chlanda-Lab/cryoCLEM
Toolbox for post-correlation cryo-CLEM workflow developed at Chlanda Lab, Heidelberg University.
Language: Java - Size: 103 KB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 0
chanzuckerberg/octopi
Search for Protein 3D Coordinates in CryoET Tomograms
Language: Jupyter Notebook - Size: 27.2 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 4 - Forks: 1
deep-finder/napari-deepfinder
A napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.
Language: Python - Size: 5.5 MB - Last synced at: 13 days ago - Pushed at: 4 months ago - Stars: 3 - Forks: 1
homurachan/GisSPA Fork of Autumn1998/GisSPA
fork of GPU version of isSPA
Language: C++ - Size: 186 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0
bwmr/napari-segselect
Napari Plugin to clean membrain-seg segmentations
Language: Python - Size: 678 KB - Last synced at: 4 days ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0
Fickincool/master-thesis
Denoising and segmentation networks for cryoET based on U-net architecture implemented in Pytorch
Language: Jupyter Notebook - Size: 972 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1
hmrishavbandy/SoftLMCCL
PyTorch implementation of "Open-set Recognition of Unseen Macromolecules in Cellular Electron Cryo-Tomograms by Soft Large Margin Centralized Cosine Loss"
Language: Python - Size: 60.5 KB - Last synced at: over 2 years ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 1
elemeng/mrc2movie
Convert mrc image from cryoEM and cryo-ET (tomo) into a movie or pngs for quickly checking and presentation.
Language: Python - Size: 111 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0
builab/DomainFit
A pipeline to detect domains in cryo-EM density map by parsing domains from AlphaFold databases and fitting into the map for the best hits.
Language: Python - Size: 21.8 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 1
nextpyp/spr_pick
2D NN-based particle picking from sparse labels
Language: Python - Size: 111 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
ZhenHuangLab/imod2relion
A tool reading IMOD points, obtaining particles' info and generating .star file for RELION
Language: Python - Size: 13.7 KB - Last synced at: about 1 month ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
ZhenHuangLab/tbl2star
A tool converting DYNAMO table files(.tbl) to RELION star files(.star)
Language: Python - Size: 22.5 KB - Last synced at: 1 day ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
bwmr/microbiome_morphology
Code and Data related to Wimmer and Morais et al (2023)
Language: R - Size: 1.48 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 0
anmartinezs/poly-GA
Python scritps for rendering and distance analysis of proteins (proteasome) and segmentations (poly-GA aggregates) in Cryo-ET
Language: Python - Size: 9.77 KB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0
anmartinezs/pyseg-poly-GA
Python package for segmentation and analysis of Cryo-ET
Language: Python - Size: 102 KB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0
scipion-em/scipion-em-membrain
Plugin to run MemBrain software within Scipion
Language: Python - Size: 118 KB - Last synced at: 5 days ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
tomotools/subtomotools
Some scripts to facilitate subtomogram-averaging workflows.
Language: Python - Size: 56.6 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
bwmr/sizepicker
Pick blobs in cryo-ET data.
Language: Python - Size: 17.6 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
TomCrey/CryoCARE_with_GUI Fork of juglab/cryoCARE_pip
CryoCARE : denoising tomograms for cryo-ET (by @juglab)
Language: Python - Size: 183 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
TomCrey/MemBrain_with_GUI Fork of teamtomo/membrain-seg
MemBrain : Membrane segmentation in 3D for cryo-ET (by @TeamTomo)
Language: Python - Size: 141 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
wan-lab-vanderbilt/subtomo-tutorials
Subtomogram averaging tutorials
Size: 518 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
anmartinezs/arp23
Python scripts to quantiatively describe Arp2/3 complex organization on travelling Actin Waves
Language: Python - Size: 665 KB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0