A novel process for H&E, immunofluorescence, and imaging mass cytometry on a single slide with a concise analytics pipeline

Article Biochemical Research Methods

MIRIAM: A machine and deep learning single-cell segmentation and quantification pipeline for multi-dimensional tissue images

Eliot T. McKinley et al.

Summary: In this study, a new method called MIRIAM is introduced for cell segmentation in tissue sections. It outperforms other widely used segmentation methods and is applicable to different imaging platforms and tissue types, as demonstrated using human colonic adenomas.

CYTOMETRY PART A (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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Article Immunology

Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy

Tobias Hoch et al.

Summary: Intratumoral immune cells play a crucial role in tumor control and antitumor responses during immunotherapy. This study analyzed the chemokine expression and immune infiltration in melanoma using multiplexed mass cytometry-based imaging, and found that tumors lacking immune infiltration had low levels of chemokines, antigen presentation, and markers of inflammation, while infiltrated tumors expressed multiple chemokines.

SCIENCE IMMUNOLOGY (2022)

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Article Computer Science, Software Engineering

ImaCytE: Visual Exploration of Cellular Micro-Environments for Imaging Mass Cytometry Data

Antonios Somarakis et al.

Summary: Imaging Mass Cytometry allows for precise characterization and spatial mapping of cell types in tissues, but the resulting data poses challenges for analysis. An interactive visual analysis tool, ImaCytE, was developed in collaboration with domain experts to help users analyze cell types and microenvironments, aiding in the understanding of tissue architecture and function. The effectiveness of this workflow and tool was demonstrated through a case study conducted by a collaborating specialist.

IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS (2021)

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Review Physiology

Using Imaging Mass Cytometry to Define Cell Identities and Interactions in Human Tissues

Vijayakumar R. Kakade et al.

Summary: This review provides detailed technical details and new insights on the use of imaging mass cytometry (IMC) to study the human kidney, discussing cell types and pathophysiological processes in depth, improving our understanding of human disease pathogenesis through IMC analysis.

FRONTIERS IN PHYSIOLOGY (2021)

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Article Biochemical Research Methods