Automated and autonomous experiments in electron and scanning probe microscopy

SV Kalinin, M Ziatdinov, J Hinkle, S Jesse, A Ghosh… - ACS …, 2021 - ACS Publications
Machine learning and artificial intelligence (ML/AI) are rapidly becoming an indispensable
part of physics research, with domain applications ranging from theory and materials …

Unsupervised deep learning methods for biological image reconstruction and enhancement: An overview from a signal processing perspective

M Akçakaya, B Yaman, H Chung… - IEEE Signal Processing …, 2022 - ieeexplore.ieee.org
Recently, deep learning (DL) approaches have become the main research frontier for
biological image reconstruction and enhancement problems thanks to their high …

CryoDRGN: reconstruction of heterogeneous cryo-EM structures using neural networks

ED Zhong, T Bepler, B Berger, JH Davis - Nature methods, 2021 - nature.com
Cryo-electron microscopy (cryo-EM) single-particle analysis has proven powerful in
determining the structures of rigid macromolecules. However, many imaged protein …

Adversarial generation of continuous images

I Skorokhodov, S Ignatyev… - Proceedings of the …, 2021 - openaccess.thecvf.com
In most existing learning systems, images are typically viewed as 2D pixel arrays. However,
in another paradigm gaining popularity, a 2D image is represented as an implicit neural …

Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN

BM Powell, JH Davis - Nature methods, 2024 - nature.com
Cryo-electron tomography (cryo-ET) enables observation of macromolecular complexes in
their native, spatially contextualized cellular environment. Cryo-ET processing software to …

Improved transformer for high-resolution gans

L Zhao, Z Zhang, T Chen… - Advances in Neural …, 2021 - proceedings.neurips.cc
Attention-based models, exemplified by the Transformer, can effectively model long range
dependency, but suffer from the quadratic complexity of self-attention operation, making …

Amortized inference for heterogeneous reconstruction in cryo-EM

A Levy, G Wetzstein, JNP Martel… - Advances in neural …, 2022 - proceedings.neurips.cc
Cryo-electron microscopy (cryo-EM) is an imaging modality that provides unique insights
into the dynamics of proteins and other building blocks of life. The algorithmic challenge of …

A multi-encoder variational autoencoder controls multiple transformational features in single-cell image analysis

L Ternes, M Dane, S Gross, M Labrie, G Mills… - Communications …, 2022 - nature.com
Image-based cell phenoty** relies on quantitative measurements as encoded
representations of cells; however, defining suitable representations that capture complex …

Orientation-invariant autoencoders learn robust representations for shape profiling of cells and organelles

J Burgess, JJ Nirschl, MC Zanellati, A Lozano… - Nature …, 2024 - nature.com
Cell and organelle shape are driven by diverse genetic and environmental factors and thus
accurate quantification of cellular morphology is essential to experimental cell biology …

Reconstructing continuous distributions of 3D protein structure from cryo-EM images

ED Zhong, T Bepler, JH Davis, B Berger - arxiv preprint arxiv:1909.05215, 2019 - arxiv.org
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of
proteins and other macromolecular complexes at near-atomic resolution. In single particle …