S3-CIMA: Supervised spatial single-cell image analysis for identifying disease-associated cell-type compositions in tissue

Article Biochemistry & Molecular Biology

Tumor-associated macrophages trigger MAIT cell dysfunction at the HCC invasive margin

Benjamin Ruf et al.

CELL (2023)

Article Biochemical Research Methods

CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images

Michael Y. Lee et al.

Summary: CellSeg is a powerful cell segmentation software for analyzing highly multiplexed tissue images that is accessible to biology researchers of any programming skill level.

BMC BIOINFORMATICS (2022)

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Article Biotechnology & Applied Microbiology

Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning

Noah F. Greenwald et al.

Summary: In this study, the researchers created the TissueNet dataset and developed the Mesmer segmentation algorithm based on deep learning to address the challenge of cell segmentation. Mesmer showed improved accuracy, generalization to various tissue types and imaging platforms, and achieved human-level performance.

NATURE BIOTECHNOLOGY (2022)

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Review Biotechnology & Applied Microbiology

Spatial components of molecular tissue biology

Giovanni Palla et al.

Summary: Methods for profiling RNA and protein expression in a spatially resolved manner have rapidly advanced, but clear articulation of key biological questions and development of computational tools are crucial. Decisions on molecular features and inclusion of cell shape in analysis need to be made by developers. Optimal ways to compare tissue samples at different length scales are still being sought.

NATURE BIOTECHNOLOGY (2022)

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Article Biochemical Research Methods

Squidpy: a scalable framework for spatial omics analysis

Giovanni Palla et al.

Summary: Squidpy is a Python framework that combines tools from omics and image analysis to efficiently store, manipulate, and visualize spatial omics data. It is extensible and can be interfaced with other libraries for scalable analysis of spatial omics data.

NATURE METHODS (2022)

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Article Multidisciplinary Sciences

Spatially mapped single-cell chromatin accessibility

Casey A. Thornton et al.

Summary: High-throughput single-cell epigenomic assays may lose spatial orientation, but sciMAP-ATAC is introduced to produce spatially resolved single-cell ATAC-seq data with retained positional information for assessing cell types and chromatin states in different tissues.

NATURE COMMUNICATIONS (2021)

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Review Genetics & Heredity

A Shift in Paradigms: Spatial Genomics Approaches to Reveal Single-Cell Principles of Genome Organization

Andres M. Cardozo Gizzi

Summary: The genome tridimensional (3D) organization and its role in regulating key cell processes like transcription is a major question in biology. Recent technological advances have allowed for the resolution of different hierarchical levels of genome organization. Reports increasingly indicate high variability and stochasticity at the single-cell level, with implications for fundamental questions in biology.

FRONTIERS IN GENETICS (2021)

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Article Biochemical Research Methods

CODEX multiplexed tissue imaging with DNA-conjugated antibodies

Sarah Black et al.

Summary: Advances in multiplexed imaging technologies, such as CODEX, using DNA-conjugated antibodies and fluorescently labeled DNA probes, allow visualization of up to 60 markers simultaneously in tissues. This enables a deep view into single-cell spatial relationships and can drive discovery in developmental biology, disease, and therapeutic design.

NATURE PROTOCOLS (2021)

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Article Biotechnology & Applied Microbiology

Giotto: a toolbox for integrative analysis and visualization of spatial expression data

Ruben Dries et al.

Summary: Giotto is a comprehensive open-source toolbox for spatial data analysis and visualization, providing end-to-end analysis with a wide range of algorithms for characterizing tissue composition and cellular interactions, as well as integrating single-cell RNAseq data for cell-type enrichment analysis. The visualization module allows interactive visualization of analysis outputs and imaging features, demonstrating its general applicability across diverse datasets and platforms.

GENOME BIOLOGY (2021)

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Article Biochemistry & Molecular Biology