AITom: Open-source AI platform for cryo-electron Tomography data analysis (2019-11-08T00:00:00.000000Z)

TL;DR

AITom is introduced, an open-source artificial intelligence platform for cryo-ET researchers that provides many public as well as in-house algorithms for performing crye-ET data analysis through both the traditional template-based or template-free approach and the deep learning approach.

Abstract

Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution. Tomograms captured by cryo-ET contain heterogeneous structures representing the complex and dynamic subcellular environment. Since the structures are not purified or fluorescently labeled, the spatial organization and interaction between both the known and unknown structures can be studied in their native environment. The rapid advances of cryo-electron tomography (cryo-ET) have generated abundant 3D cellular imaging data. However, the systematic localization, identification, segmentation, and structural recovery of the subcellular components require efficient and accurate large-scale image analysis methods. We introduce AITom, an open-source artificial intelligence platform for cryo-ET researchers. AITom provides many public as well as in-house algorithms for performing cryo-ET data analysis through both the traditional template-based or template-free approach and the deep learning approach. Comprehensive tutorials for each analysis module are provided to guide the user through. We welcome researchers and developers to join this collaborative open-source software development project. Availability: this https URL

Authors

Xiangrui Zeng

1 papers

Min Xu

1 papers

TL;DR

Abstract

Authors

References43 items

Fine-grained alignment of cryo-electron subtomograms based on MPI parallel optimization

Adversarial domain adaptation for cross data source macromolecule in situ structural classification in cellular electron cryo-tomograms

Classification in Cryo-Electron Tomograms

emClarity: Software for High Resolution Cryo-electron Tomography and Sub-tomogram Averaging

An integration of fast alignment and maximum-likelihood methods for electron subtomogram averaging and classification

In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment

Feature Decomposition Based Saliency Detection in Electron Cryo-Tomograms

AuTom: A novel automatic platform for electron tomography reconstruction.

Improved deep learning-based macromolecules structure classification from electron cryo-tomograms

Cellular Electron Cryotomography: Toward Structural Biology In Situ.

A convolutional autoencoder approach for mining features in cellular electron cryo-tomograms and weakly supervised coarse segmentation

TomoMiner and TomoMinerCloud: A Software Platform for Large-Scale Subtomogram Structural Analysis.

Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms

Simulating cryo electron tomograms of crowded cell cytoplasm for assessment of automated particle picking

Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy.

De Novo Structural Pattern Mining in Cellular Electron Cryotomograms.

Deep Residual Learning for Image Recognition

Saliency detection via Cellular Automata

C3D: Generic Features for Video Analysis

Very Deep Convolutional Networks for Large-Scale Image Recognition

Saliency Optimization from Robust Background Detection

Cryo-electron tomography: The challenge of doing structural biology in situ

Structural biology in situ--the potential of subtomogram averaging.

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization

Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.

PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis.

High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching.

Robust principal component analysis?

Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization.

Survey of large protein complexes in D. vulgaris reveals great structural diversity

Classification of cryo-electron sub-tomograms using constrained correlation.

An improved algorithm for anisotropic nonlinear diffusion for denoising cryo-tomograms.

Toward detecting and identifying macromolecules in a cellular context: template matching applied to electron tomograms.

Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State

Open-set Recognition of Unseen Macromolecules in Cellular Electron Cryo-Tomograms by Soft Large Margin Centralized Cosine Loss

Semi-supervised Macromolecule Structural Classification in Cellular Electron Cryo-Tomograms using 3D Autoencoding Classifier

In Situ Structure of Neuronal C 9 orf 72 Poly-GA Aggregates Reveals Proteasome Recruitment Graphical

Alber lab

EMAN2: an extensible image processing suite for electron microscopy.

Computer visualization of three-dimensional image data using IMOD.

Fast Fourier transform and convolution algorithms

Methods details Detailed description for available methods

Field of Study

Journal Information

Name

Volume

Venue Information

Name

Type

URL

Alternate Names