The emerging landscape of spatial profiling technologies

JR Moffitt, E Lundberg, H Heyn - Nature Reviews Genetics, 2022 - nature.com
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein
profiling methods as a major pillar for cellular atlas building of complex samples, from …

Spatial profiling technologies illuminate the tumor microenvironment

O Elhanani, R Ben-Uri, L Keren - Cancer cell, 2023 - cell.com
The tumor microenvironment (TME) is composed of many different cellular and acellular
components that together drive tumor growth, invasion, metastasis, and response to …

Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP)

S Jain, L Pei, JM Spraggins, M Angelo, JP Carson… - Nature cell …, 2023 - nature.com
Abstract The Human BioMolecular Atlas Program (HuBMAP) aims to create a multi-scale
spatial atlas of the healthy human body at single-cell resolution by applying advanced …

OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies

J Moore, C Allan, S Besson, JM Burel, E Diel, D Gault… - Nature …, 2021 - nature.com
The rapid pace of innovation in biological imaging and the diversity of its applications have
prevented the establishment of a community-agreed standardized data format. We propose …

Anatomical structures, cell types and biomarkers of the Human Reference Atlas

K Börner, SA Teichmann, EM Quardokus, JC Gee… - Nature cell …, 2021 - nature.com
Abstract The Human Reference Atlas (HRA) aims to map all of the cells of the human body
to advance biomedical research and clinical practice. This Perspective presents …

OME-Zarr: a cloud-optimized bioimaging file format with international community support

J Moore, D Basurto-Lozada, S Besson… - Histochemistry and Cell …, 2023 - Springer
A growing community is constructing a next-generation file format (NGFF) for bioimaging to
overcome problems of scalability and heterogeneity. Organized by the Open Microscopy …

Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs

P Weeratunga, L Denney, JA Bull, E Repapi… - Nature …, 2023 - nature.com
Single cell spatial interrogation of the immune-structural interactions in COVID− 19 lungs is
challenging, mainly because of the marked cellular infiltrate and architecturally distorted …

MITI minimum information guidelines for highly multiplexed tissue images

D Schapiro, C Yapp, A Sokolov, SM Reynolds… - Nature …, 2022 - nature.com
The imminent release of tissue atlases combining multichannel microscopy with single-cell
sequencing and other omics data from normal and diseased specimens creates an urgent …

Bioimage model zoo: a community-driven resource for accessible deep learning in bioimage analysis

W Ouyang, F Beuttenmueller, E Gómez-de-Mariscal… - BioRxiv, 2022 - biorxiv.org
Deep learning-based approaches are revolutionizing imaging-driven scientific research.
However, the accessibility and reproducibility of deep learning-based workflows for imaging …

Data management strategy for a collaborative research center

D Mittal, R Mease, T Kuner, H Flor, R Kuner… - GigaScience, 2023 - academic.oup.com
The importance of effective research data management (RDM) strategies to support the
generation of Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience data …