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 …

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 …

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 …

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 …

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 …

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 …

A comparison of neuroelectrophysiology databases

P Subash, A Gray, M Boswell, SL Cohen, R Garner… - Scientific Data, 2023 - nature.com
As data sharing has become more prevalent, three pillars-archives, standards, and analysis
tools-have emerged as critical components in facilitating effective data sharing and …

Building a FAIR image data ecosystem for microscopy communities

I Kemmer, A Keppler, B Serrano-Solano… - Histochemistry and Cell …, 2023 - Springer
Bioimaging has now entered the era of big data with faster-than-ever development of
complex microscopy technologies leading to increasingly complex datasets. This enormous …

Connecting theory and experiment in cell and tissue mechanics

C Schwayer, DB Brückner - Journal of Cell Science, 2023 - journals.biologists.com
Understanding complex living systems, which are fundamentally constrained by physical
phenomena, requires combining experimental data with theoretical physical and …

Moving beyond the desktop: prospects for practical bioimage analysis via the web

W Ouyang, KW Eliceiri, BA Cimini - Frontiers in Bioinformatics, 2023 - frontiersin.org
As biological imaging continues to rapidly advance, it results in increasingly complex image
data, necessitating a reevaluation of conventional bioimage analysis methods and their …