[HTML][HTML] Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

JG Chen, JC Chávez-Fuentes, M O'Brien, J Xu, E Ruiz… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Emerging spatial omics technologies continue to advance the molecular mapping of tissue
architecture and the investigation of gene regulation and cellular crosstalk, which in turn …

emObject: domain specific data abstraction for spatial omics

EAG Baker, MY Huang, A Lam, MK Rahim… - bioRxiv, 2023 - biorxiv.org
Recent advances in high-parameter spatial biology have yielded a rapidly growing new
class of biological data, allowing researchers to more comprehensively characterize cellular …

Sopa: a technology-invariant pipeline for analyses of image-based spatial omics

Q Blampey, K Mulder, M Gardet… - Nature …, 2024 - nature.com
Spatial omics data allow in-depth analysis of tissue architectures, opening new opportunities
for biological discovery. In particular, imaging techniques offer single-cell resolutions …

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 …

VoltRon: A Spatial Omics Analysis Platform for Multi-Resolution and Multi-omics Integration using Image Registration

A Manukyan, E Bahry, E Wyler, E Becher… - bioRxiv, 2023 - biorxiv.org
The growing number of spatial omic technologies have created a demand for computational
tools capable of managing, storing, and analyzing spatial datasets with multiple modalities …

Spatial omics technologies at multimodal and single cell/subcellular level

J Park, J Kim, T Lewy, CM Rice, O Elemento… - Genome Biology, 2022 - Springer
Spatial omics technologies enable a deeper understanding of cellular organizations and
interactions within a tissue of interest. These assays can identify specific compartments or …

Spatially Resolved Single-Cell Omics: Methods, Challenges, and Future Perspectives

FS Dezem, NS Morosini, W Arjumand… - Annual Review of …, 2024 - annualreviews.org
Overlaying omics data onto spatial biological dimensions has been a promising technology
to provide high-resolution insights into the interactome and cellular heterogeneity relative to …

SODB facilitates comprehensive exploration of spatial omics data

Z Yuan, W Pan, X Zhao, F Zhao, Z Xu, X Li, Y Zhao… - Nature …, 2023 - nature.com
Spatial omics technologies generate wealthy but highly complex datasets. Here we present
Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources …

[PDF][PDF] Squidpy: a scalable framework for spatial single cell 2 analysis

G Palla, H Spitzer, M Klein, D Fischer, A Christina… - BioRxiv, 2021 - scholar.archive.org
16 Abstract 17 Spatial omics data are advancing the study of tissue organization and cellular
18 communication at an unprecedented scale. Here, we present Squidpy, a Python …

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 …