Enablers and challenges of spatial omics, a melting pot of technologies

T Alexandrov, J Saez‐Rodriguez… - Molecular Systems …, 2023 - embopress.org
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of
publications presenting novel methods for obtaining spatially resolved information for any …

AI analysis of super-resolution microscopy: Biological discovery in the absence of ground truth

IR Nabi, B Cardoen, IM Khater, G Gao, TH Wong… - Journal of Cell …, 2024 - rupress.org
Super-resolution microscopy, or nanoscopy, enables the use of fluorescent-based molecular
localization tools to study molecular structure at the nanoscale level in the intact cell …

A data portal for providing standardized annotations for cryo-electron tomography

U Ermel, A Cheng, JX Ni, J Gadling… - Nature …, 2024 - nature.com
We present the cryoET Data Por-tal (https://cryoetdataportal. czscience. com/), containing
annotated cryoET datasets in standardized formats, as a resource for the cryoET community …

Cell Painting Gallery: an open resource for image-based profiling

E Weisbart, A Kumar, J Arevalo, AE Carpenter… - Nature …, 2024 - nature.com
Image-based or morphological profiling is a rapidly expanding field wherein cells are
'profiled'by extracting hundreds to thousands of unbiased, quantitative features from images …

Image processing tools for petabyte-scale light sheet microscopy data

X Ruan, M Mueller, G Liu, F Görlitz, TM Fu, DE Milkie… - Nature …, 2024 - nature.com
Light sheet microscopy is a powerful technique for high-speed three-dimensional imaging of
subcellular dynamics and large biological specimens. However, it often generates datasets …

WebAtlas pipeline for integrated single-cell and spatial transcriptomic data

T Li, D Horsfall, D Basurto-Lozada, K Roberts… - Nature …, 2024 - nature.com
Single-cell and spatial transcrip-tomics illuminate complementary features of tissues.
Computational integration can synergize these technologies to resolve cell types and …

SpatialData: an open and universal data framework for spatial omics

L Marconato, G Palla, KA Yamauchi, I Virshup… - Nature …, 2024 - nature.com
Spatially resolved omics technologies are transforming our understanding of biological
tissues. However, the handling of uni-and multimodal spatial omics datasets remains a …

Opportunities and challenges for deep learning in cell dynamics research

B Chai, C Efstathiou, H Yue, VM Draviam - Trends in Cell Biology, 2024 - cell.com
The growth of artificial intelligence (AI) has led to an increase in the adoption of computer
vision and deep learning (DL) techniques for the evaluation of microscopy images and …

[HTML][HTML] Thirty years of the DICOM standard

M Larobina - Tomography, 2023 - mdpi.com
Digital Imaging and Communications in Medicine (DICOM) is an international standard that
defines a format for storing medical images and a protocol to enable and facilitate data …

EMBL's European bioinformatics Institute (EMBL-EBI) in 2022

M Thakur, A Bateman, C Brooksbank… - Nucleic acids …, 2023 - academic.oup.com
Abstract The European Molecular Biology Laboratory's European Bioinformatics Institute
(EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the …