Nature Search

Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows

This study presents a comprehensive evaluation of Xenium In Situ datasets and provides recommendations on analysis workflows.

Sergio Marco Salas
Louis B. Kuemmerle
Mats Nilsson
ResearchOpen Access13 Mar 2025
Nature Methods

Volume: 22, P: 813-823
Comprehensive in situ mapping of human cortical transcriptomic cell types

Langseth et al. present cell type maps of human cortical tissue sections and show an efficient and robust workflow to accurately resolve anatomical organization of human brain tissue.

Christoffer Mattsson Langseth
Daniel Gyllborg
Mats Nilsson
ResearchOpen Access24 Aug 2021
Communications Biology

Volume: 4, P: 1-7
Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images

Deconwolf is a computationally efficient and user-friendly software tool for fluorescence microscopy image deconvolution that improves the analysis of diverse fluorescence in situ hybridization methods and can handle large datasets.

Erik Wernersson
Eleni Gelali
Magda Bienko
ResearchOpen Access06 Jun 2024
Nature Methods

Volume: 21, P: 1245-1256
A community effort to track commercial single-cell and spatial ’omic technologies and business trends

There is an ever-growing choice of single-cell and spatial ’omics platforms for industry and academia. The scTrends Consortium provides a brief historical overview of the established platforms and companies, revealing market trends and presenting possible angles for how technologies may differentiate themselves.

Joachim De Jonghe
James W. Opzoomer
Jake P. Taylor-King
Comments & Opinion17 Jul 2024
Nature Biotechnology

Volume: 42, P: 1017-1023
Molecular architecture of the developing mouse brain

A comprehensive single-cell transcriptomic atlas of the mouse brain between gastrulation and birth identifies hundreds of cellular states and reveals the spatiotemporal organization of brain development.

Gioele La Manno
Kimberly Siletti
Sten Linnarsson
Research28 Jul 2021
Nature

Volume: 596, P: 92-96
Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin

The authors created a comprehensive developmental cell atlas for spatiotemporal gene expression of the human spinal cord, revealed species-specific regulation during development and used the atlas to infer novel markers for pediatric ependymomas.

Xiaofei Li
Zaneta Andrusivova
Erik Sundström
ResearchOpen Access24 Apr 2023
Nature Neuroscience

Volume: 26, P: 891-901
Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

Yun Zhang
Jeremy A. Miller
Richard H. Scheuermann
ResearchOpen Access13 Jun 2023
Scientific Reports

Volume: 13, P: 1-17

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Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows

Comprehensive in situ mapping of human cortical transcriptomic cell types

Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images

A community effort to track commercial single-cell and spatial ’omic technologies and business trends

Molecular architecture of the developing mouse brain

Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin

Reference-based cell type matching of in situ image-based spatial transcriptomics data on primary visual cortex of mouse brain

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