Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets.

Autor: Müller A; Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany. andreas.mueller1@tu-dresden.de.; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany. andreas.mueller1@tu-dresden.de.; German Center for Diabetes Research, Neuherberg, Germany. andreas.mueller1@tu-dresden.de., Schmidt D; HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany. deborah.schmidt@mdc-berlin.de., Albrecht JP; HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.; Humboldt-Universität zu Berlin, Faculty of Mathematics and Natural Sciences, Berlin, Germany., Rieckert L; HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany., Otto M; HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany., Galicia Garcia LE; Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany.; German Center for Diabetes Research, Neuherberg, Germany.; DFG Cluster of Excellence 'Physics of Life', TU Dresden, Dresden, Germany., Fabig G; Experimental Center, Faculty of Medicine Carl Gustav Carus, Dresden, Dresden, Germany., Solimena M; Molecular Diabetology, University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany.; Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Faculty of Medicine of the TU Dresden, Dresden, Germany.; German Center for Diabetes Research, Neuherberg, Germany.; DFG Cluster of Excellence 'Physics of Life', TU Dresden, Dresden, Germany., Weigert M; Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. martin.weigert@epfl.ch.
Jazyk: angličtina
Zdroj: Nature protocols [Nat Protoc] 2024 May; Vol. 19 (5), pp. 1436-1466. Date of Electronic Publication: 2024 Feb 29.
DOI: 10.1038/s41596-024-00957-5
Abstrakt: Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and spatial analysis is necessary. Here we describe a practical and annotation-efficient pipeline for organelle-specific segmentation, spatial analysis and visualization of large volume electron microscopy datasets using freely available, user-friendly software tools that can be run on a single standard workstation. The procedures are aimed at researchers in the life sciences with modest computational expertise, who use volume electron microscopy and need to generate three-dimensional (3D) segmentation labels for different types of cell organelles while minimizing manual annotation efforts, to analyze the spatial interactions between organelle instances and to visualize the 3D segmentation results. We provide detailed guidelines for choosing well-suited segmentation tools for specific cell organelles, and to bridge compatibility issues between freely available open-source tools, we distribute the critical steps as easily installable Album solutions for deep learning segmentation, spatial analysis and 3D rendering. Our detailed description can serve as a reference for similar projects requiring particular strategies for single- or multiple-organelle analysis, which can be achieved with computational resources commonly available to single-user setups.
(© 2024. Springer Nature Limited.)
Databáze: MEDLINE
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