1
|
Schubert MC, Soyka SJ, Tamimi A, Maus E, Schroers J, Wißmann N, Reyhan E, Tetzlaff SK, Yang Y, Denninger R, Peretzke R, Beretta C, Drumm M, Heuer A, Buchert V, Steffens A, Walshon J, McCortney K, Heiland S, Bendszus M, Neher P, Golebiewska A, Wick W, Winkler F, Breckwoldt MO, Kreshuk A, Kuner T, Horbinski C, Kurz FT, Prevedel R, Venkataramani V. Deep intravital brain tumor imaging enabled by tailored three-photon microscopy and analysis. Nat Commun 2024; 15:7383. [PMID: 39256378 PMCID: PMC11387418 DOI: 10.1038/s41467-024-51432-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 08/07/2024] [Indexed: 09/12/2024] Open
Abstract
Intravital 2P-microscopy enables the longitudinal study of brain tumor biology in superficial mouse cortex layers. Intravital microscopy of the white matter, an important route of glioblastoma invasion and recurrence, has not been feasible, due to low signal-to-noise ratios and insufficient spatiotemporal resolution. Here, we present an intravital microscopy and artificial intelligence-based analysis workflow (Deep3P) that enables longitudinal deep imaging of glioblastoma up to a depth of 1.2 mm. We find that perivascular invasion is the preferred invasion route into the corpus callosum and uncover two vascular mechanisms of glioblastoma migration in the white matter. Furthermore, we observe morphological changes after white matter infiltration, a potential basis of an imaging biomarker during early glioblastoma colonization. Taken together, Deep3P allows for a non-invasive intravital investigation of brain tumor biology and its tumor microenvironment at subcortical depths explored, opening up opportunities for studying the neuroscience of brain tumors and other model systems.
Collapse
Affiliation(s)
- Marc Cicero Schubert
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Stella Judith Soyka
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Amr Tamimi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Emanuel Maus
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Julian Schroers
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- German Cancer Research Center (DKFZ), Division of Radiology, Heidelberg, Germany
| | - Niklas Wißmann
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Ekin Reyhan
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Svenja Kristin Tetzlaff
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Yvonne Yang
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Robert Denninger
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Robin Peretzke
- Division of Medical Image Computing (MIC), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carlo Beretta
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Michael Drumm
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Alina Heuer
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Verena Buchert
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Alicia Steffens
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Jordain Walshon
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Kathleen McCortney
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
| | - Sabine Heiland
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martin Bendszus
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Neher
- Division of Medical Image Computing (MIC), German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health, 1526, Luxembourg, Luxembourg
| | - Wolfgang Wick
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael O Breckwoldt
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Anna Kreshuk
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Thomas Kuner
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Craig Horbinski
- Department of Neurological Surgery, Northwestern University, Chicago, IL, USA
- Department of Pathology, Northwestern University, Chicago, IL, USA
| | - Felix Tobias Kurz
- German Cancer Research Center (DKFZ), Division of Radiology, Heidelberg, Germany
- Department of Neuroradiology, University Hospital Heidelberg, Heidelberg, Germany
- Division of Neuroradiology, Geneva University Hospitals, Geneva, Switzerland
| | - Robert Prevedel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Rome, Italy.
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, Heidelberg, Germany.
- Interdisciplinary Center of Neurosciences, Heidelberg University, Heidelberg, Germany.
| | - Varun Venkataramani
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany.
- Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany.
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| |
Collapse
|
2
|
Diaz-Vegas A, Cooke KC, Cutler HB, Yau B, Masson SWC, Harney D, Fuller OK, Potter M, Madsen S, Craw NR, Zhang Y, Moreno CL, Kebede MA, Neely GG, Stöckli J, Burchfield JG, James DE. Deletion of miPEP in adipocytes protects against obesity and insulin resistance by boosting muscle metabolism. Mol Metab 2024; 86:101983. [PMID: 38960128 PMCID: PMC11292358 DOI: 10.1016/j.molmet.2024.101983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Mitochondria facilitate thousands of biochemical reactions, covering a broad spectrum of anabolic and catabolic processes. Here we demonstrate that the adipocyte mitochondrial proteome is markedly altered across multiple models of insulin resistance and reveal a consistent decrease in the level of the mitochondrial processing peptidase miPEP. OBJECTIVE To determine the role of miPEP in insulin resistance. METHODS To experimentally test this observation, we generated adipocyte-specific miPEP knockout mice to interrogate its role in the aetiology of insulin resistance. RESULTS We observed a strong phenotype characterised by enhanced insulin sensitivity and reduced adiposity, despite normal food intake and physical activity. Strikingly, these phenotypes vanished when mice were housed at thermoneutrality, suggesting that metabolic protection conferred by miPEP deletion hinges upon a thermoregulatory process. Tissue specific analysis of miPEP deficient mice revealed an increment in muscle metabolism, and upregulation of the protein FBP2 that is involved in ATP hydrolysis in the gluconeogenic pathway. CONCLUSION These findings suggest that miPEP deletion initiates a compensatory increase in skeletal muscle metabolism acting as a protective mechanism against diet-induced obesity and insulin resistance.
Collapse
Affiliation(s)
- Alexis Diaz-Vegas
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia.
| | - Kristen C Cooke
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Harry B Cutler
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Belinda Yau
- School of Medical Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Stewart W C Masson
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Dylan Harney
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Oliver K Fuller
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Meg Potter
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Søren Madsen
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Niamh R Craw
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Yiju Zhang
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Cesar L Moreno
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Melkam A Kebede
- School of Medical Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - G Gregory Neely
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - Jacqueline Stöckli
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - James G Burchfield
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia
| | - David E James
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia; Charles Perkins Centre, University of Sydney, Camperdown, New South Wales, Australia; School of Medical Sciences, University of Sydney, Camperdown, New South Wales, Australia.
| |
Collapse
|
3
|
Sidlipura S, Ayadi A, Lagardère Deléglise M. Assessing Intra-Bundle Impregnation in Partially Impregnated Glass Fiber-Reinforced Polypropylene Composites Using a 2D Extended-Field and Multimodal Imaging Approach. Polymers (Basel) 2024; 16:2171. [PMID: 39125198 PMCID: PMC11315057 DOI: 10.3390/polym16152171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/25/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024] Open
Abstract
This study evaluates multimodal imaging for characterizing microstructures in partially impregnated thermoplastic matrix composites made of woven glass fiber and polypropylene. The research quantifies the impregnation degree of fiber bundles within composite plates manufactured through a simplified compression resin transfer molding process. For comparison, a reference plate was produced using compression molding of film stacks. An original surface polishing procedure was introduced to minimize surface defects while polishing partially impregnated samples. Extended-field 2D imaging techniques, including polarized light, fluorescence, and scanning electron microscopies, were used to generate images of the same microstructure at fiber-scale resolutions throughout the plate. Post-processing workflows at the macro-scale involved stitching, rigid registration, and pixel classification of FM and SEM images. Meso-scale workflows focused on 0°-oriented fiber bundles extracted from extended-field images to conduct quantitative analyses of glass fiber and porosity area fractions. A one-way ANOVA analysis confirmed the reliability of the statistical data within the 95% confidence interval. Porosity quantification based on the conducted multimodal approach indicated the sensitivity of the impregnation degree according to the layer distance from the pool of melted polypropylene in the context of simplified-CRTM. The findings underscore the potential of multimodal imaging for quantitative analysis in composite material production.
Collapse
Affiliation(s)
| | - Abderrahmane Ayadi
- IMT Nord Europe, Institut Mines-Télécom, Univ. Lille, Centre for Materials and Processes, 59000 Lille, France
| | | |
Collapse
|
4
|
Müller A, Schmidt D, Albrecht JP, Rieckert L, Otto M, Galicia Garcia LE, Fabig G, Solimena M, Weigert M. Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets. Nat Protoc 2024; 19:1436-1466. [PMID: 38424188 DOI: 10.1038/s41596-024-00957-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/24/2023] [Indexed: 03/02/2024]
Abstract
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.
Collapse
Affiliation(s)
- Andreas Müller
- 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.
| | - Deborah Schmidt
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany.
| | - Jan Philipp Albrecht
- 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
| | - Lucas Rieckert
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Maximilian Otto
- HELMHOLTZ IMAGING, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Berlin, Germany
| | - Leticia Elizabeth Galicia Garcia
- 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
| | - Gunar Fabig
- Experimental Center, Faculty of Medicine Carl Gustav Carus, Dresden, Dresden, Germany
| | - Michele Solimena
- 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
| | - Martin Weigert
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| |
Collapse
|
5
|
Vásquez CE, Knak Guerra KT, Renner J, Rasia-Filho AA. Morphological heterogeneity of neurons in the human central amygdaloid nucleus. J Neurosci Res 2024; 102:e25319. [PMID: 38629777 DOI: 10.1002/jnr.25319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/23/2024] [Accepted: 03/03/2024] [Indexed: 04/19/2024]
Abstract
The central amygdaloid nucleus (CeA) has an ancient phylogenetic development and functions relevant for animal survival. Local cells receive intrinsic amygdaloidal information that codes emotional stimuli of fear, integrate them, and send cortical and subcortical output projections that prompt rapid visceral and social behavior responses. We aimed to describe the morphology of the neurons that compose the human CeA (N = 8 adult men). Cells within CeA coronal borders were identified using the thionine staining and were further analyzed using the "single-section" Golgi method followed by open-source software procedures for two-dimensional and three-dimensional image reconstructions. Our results evidenced varied neuronal cell body features, number and thickness of primary shafts, dendritic branching patterns, and density and shape of dendritic spines. Based on these criteria, we propose the existence of 12 morphologically different spiny neurons in the human CeA and discuss the variability in the dendritic architecture within cellular types, including likely interneurons. Some dendritic shafts were long and straight, displayed few collaterals, and had planar radiation within the coronal neuropil volume. Most of the sampled neurons showed a few to moderate density of small stubby/wide spines. Long spines (thin and mushroom) were observed occasionally. These novel data address the synaptic processing and plasticity in the human CeA. Our morphological description can be combined with further transcriptomic, immunohistochemical, and electrophysiological/connectional approaches. It serves also to investigate how neurons are altered in neurological and psychiatric disorders with hindered emotional perception, in anxiety, following atrophy in schizophrenia, and along different stages of Alzheimer's disease.
Collapse
Affiliation(s)
- Carlos E Vásquez
- Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Kétlyn T Knak Guerra
- Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Josué Renner
- Department of Basic Sciences/Physiology and Graduate Program in Biosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| | - Alberto A Rasia-Filho
- Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Department of Basic Sciences/Physiology and Graduate Program in Biosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil
| |
Collapse
|
6
|
Weng S, Devitt CC, Nyaoga BM, Havnen AE, Alvarado J, Wallingford JB. New tools reveal PCP-dependent polarized mechanics in the cortex and cytoplasm of single cells during convergent extension. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.07.566066. [PMID: 37986924 PMCID: PMC10659385 DOI: 10.1101/2023.11.07.566066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Understanding biomechanics of biological systems is crucial for unraveling complex processes like tissue morphogenesis. However, current methods for studying cellular mechanics in vivo are limited by the need for specialized equipment and often provide limited spatiotemporal resolution. Here we introduce two new techniques, Tension by Transverse Fluctuation (TFlux) and in vivo microrheology, that overcome these limitations. They both offer time-resolved, subcellular biomechanical analysis using only fluorescent reporters and widely available microscopes. Employing these two techniques, we have revealed a planar cell polarity (PCP)-dependent mechanical gradient both in the cell cortex and the cytoplasm of individual cells engaged in convergent extension. Importantly, the non-invasive nature of these methods holds great promise for its application for uncovering subcellular mechanical variations across a wide array of biological contexts. Summary Non-invasive imaging-based techniques providing time-resolved biomechanical analysis at subcellular scales in developing vertebrate embryos.
Collapse
|
7
|
Guerra KTK, Renner J, Vásquez CE, Rasia‐Filho AA. Human cortical amygdala dendrites and spines morphology under open‐source three‐dimensional reconstruction procedures. J Comp Neurol 2022; 531:344-365. [PMID: 36355397 DOI: 10.1002/cne.25430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/05/2022] [Accepted: 10/14/2022] [Indexed: 11/12/2022]
Abstract
Visualizing nerve cells has been fundamental for the systematic description of brain structure and function in humans and other species. Different approaches aimed to unravel the morphological features of neuron types and diversity. The inherent complexity of the human nervous tissue and the need for proper histological processing have made studying human dendrites and spines challenging in postmortem samples. In this study, we used Golgi data and open-source software for 3D image reconstruction of human neurons from the cortical amygdaloid nucleus to show different dendrites and pleomorphic spines at different angles. Procedures required minimal equipment and generated high-quality images for differently shaped cells. We used the "single-section" Golgi method adapted for the human brain to engender 3D reconstructed images of the neuronal cell body and the dendritic ramification by adopting a neuronal tracing procedure. In addition, we elaborated 3D reconstructions to visualize heterogeneous dendritic spines using a supervised machine learning-based algorithm for image segmentation. These tools provided an additional upgrade and enhanced visual display of information related to the spatial orientation of dendritic branches and for dendritic spines of varied sizes and shapes in these human subcortical neurons. This same approach can be adapted for other techniques, areas of the central or peripheral nervous system, and comparative analysis between species.
Collapse
Affiliation(s)
- Kétlyn T. Knak Guerra
- Graduate Program in Neuroscience Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Josué Renner
- Department of Basic Sciences/Physiology Universidade Federal de Ciências da Saúde de Porto Alegre Porto Alegre Brazil
- Graduate Program in Biosciences Universidade Federal de Ciências da Saúde de Porto Alegre Porto Alegre Brazil
| | - Carlos E. Vásquez
- Graduate Program in Neuroscience Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Alberto A. Rasia‐Filho
- Graduate Program in Neuroscience Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
- Department of Basic Sciences/Physiology Universidade Federal de Ciências da Saúde de Porto Alegre Porto Alegre Brazil
- Graduate Program in Biosciences Universidade Federal de Ciências da Saúde de Porto Alegre Porto Alegre Brazil
| |
Collapse
|
8
|
Automated detection and classification of tumor histotypes on dynamic PET imaging data through machine-learning driven voxel classification. Comput Biol Med 2022; 145:105423. [DOI: 10.1016/j.compbiomed.2022.105423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/11/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022]
|
9
|
Laliberte AM, Farah C, Steiner KR, Tariq O, Bui TV. Changes in Sensorimotor Connectivity to dI3 Interneurons in Relation to the Postnatal Maturation of Grasping. Front Neural Circuits 2022; 15:768235. [PMID: 35153680 PMCID: PMC8828486 DOI: 10.3389/fncir.2021.768235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/31/2021] [Indexed: 11/23/2022] Open
Abstract
Primitive reflexes are evident shortly after birth. Many of these reflexes disappear during postnatal development as part of the maturation of motor control. This study investigates the changes of connectivity related to sensory integration by spinal dI3 interneurons during the time in which the palmar grasp reflex gradually disappears in postnatal mice pups. Our results reveal an increase in GAD65/67-labeled terminals to perisomatic Vglut1-labeled sensory inputs contacting cervical and lumbar dI3 interneurons between postnatal day 3 and day 25. In contrast, there were no changes in the number of perisomatic Vglut1-labeled sensory inputs to lumbar and cervical dI3 interneurons other than a decrease between postnatal day 15 and day 25. Changes in postsynaptic GAD65/67-labeled inputs to dI3 interneurons were inconsistent with a role in the sustained loss of the grasp reflex. These results suggest a possible link between the maturation of hand grasp during postnatal development and increased presynaptic inhibition of sensory inputs to dI3 interneurons.
Collapse
Affiliation(s)
- Alex M. Laliberte
- Brain and Mind Research Institute, Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Carl Farah
- Brain and Mind Research Institute, Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Kyra R. Steiner
- Brain and Mind Research Institute, Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Omar Tariq
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Tuan V. Bui
- Brain and Mind Research Institute, Department of Biology, University of Ottawa, Ottawa, ON, Canada
- *Correspondence: Tuan V. Bui
| |
Collapse
|
10
|
Newmaster KT, Kronman FA, Wu YT, Kim Y. Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain. Front Neuroanat 2022; 15:787601. [PMID: 35095432 PMCID: PMC8794814 DOI: 10.3389/fnana.2021.787601] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/02/2021] [Indexed: 12/14/2022] Open
Abstract
The brain is composed of diverse neuronal and non-neuronal cell types with complex regional connectivity patterns that create the anatomical infrastructure underlying cognition. Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists to examine microscopic details in macroscopic brain circuits. Nevertheless, implementing these tools is fraught with many technical and analytical challenges with a need for high-level data analysis. Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system. Specifically, we provide practical details for choosing methods including cell type specific labeling, sample preparation (e.g., tissue clearing), microscopy modalities, image processing, and data analysis (e.g., image registration to standard atlases). We also highlight the need to develop better 3D atlases with standardized anatomical labels and nomenclature across species and developmental time points to extend the mapping to other species including humans and to facilitate data sharing, confederation, and integrative analysis. In summary, this review provides key elements and currently available resources to consider while developing and implementing high-resolution mapping methods.
Collapse
Affiliation(s)
- Kyra T Newmaster
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| | - Fae A Kronman
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| | - Yuan-Ting Wu
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| |
Collapse
|
11
|
Emerging technologies and infection models in cellular microbiology. Nat Commun 2021; 12:6764. [PMID: 34799563 PMCID: PMC8604907 DOI: 10.1038/s41467-021-26641-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 10/18/2021] [Indexed: 01/09/2023] Open
Abstract
The field of cellular microbiology, rooted in the co-evolution of microbes and their hosts, studies intracellular pathogens and their manipulation of host cell machinery. In this review, we highlight emerging technologies and infection models that recently promoted opportunities in cellular microbiology. We overview the explosion of microscopy techniques and how they reveal unprecedented detail at the host-pathogen interface. We discuss the incorporation of robotics and artificial intelligence to image-based screening modalities, biochemical mapping approaches, as well as dual RNA-sequencing techniques. Finally, we describe chips, organoids and animal models used to dissect biophysical and in vivo aspects of the infection process. As our knowledge of the infected cell improves, cellular microbiology holds great promise for development of anti-infective strategies with translational applications in human health.
Collapse
|
12
|
Universal autofocus for quantitative volumetric microscopy of whole mouse brains. Nat Methods 2021; 18:953-958. [PMID: 34312564 DOI: 10.1038/s41592-021-01208-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
Unbiased quantitative analysis of macroscopic biological samples demands fast imaging systems capable of maintaining high resolution across large volumes. Here we introduce RAPID (rapid autofocusing via pupil-split image phase detection), a real-time autofocus method applicable in every widefield-based microscope. RAPID-enabled light-sheet microscopy reliably reconstructs intact, cleared mouse brains with subcellular resolution, and allowed us to characterize the three-dimensional (3D) spatial clustering of somatostatin-positive neurons in the whole encephalon, including densely labeled areas. Furthermore, it enabled 3D morphological analysis of microglia across the entire brain. Beyond light-sheet microscopy, we demonstrate that RAPID maintains high image quality in various settings, from in vivo fluorescence imaging to 3D tracking of fast-moving organisms. RAPID thus provides a flexible autofocus solution that is suitable for traditional automated microscopy tasks as well as for quantitative analysis of large biological specimens.
Collapse
|
13
|
Cellular correlates of gray matter volume changes in magnetic resonance morphometry identified by two-photon microscopy. Sci Rep 2021; 11:4234. [PMID: 33608622 PMCID: PMC7895945 DOI: 10.1038/s41598-021-83491-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Magnetic resonance imaging (MRI) of the brain combined with voxel-based morphometry (VBM) revealed changes in gray matter volume (GMV) in various disorders. However, the cellular basis of GMV changes has remained largely unclear. We correlated changes in GMV with cellular metrics by imaging mice with MRI and two-photon in vivo microscopy at three time points within 12 weeks, taking advantage of age-dependent changes in brain structure. Imaging fluorescent cell nuclei allowed inferences on (i) physical tissue volume as determined from reference spaces outlined by nuclei, (ii) cell density, (iii) the extent of cell clustering, and (iv) the volume of cell nuclei. Our data indicate that physical tissue volume alterations only account for 13.0% of the variance in GMV change. However, when including comprehensive measurements of nucleus volume and cell density, 35.6% of the GMV variance could be explained, highlighting the influence of distinct cellular mechanisms on VBM results.
Collapse
|
14
|
Fischer CA, Besora-Casals L, Rolland SG, Haeussler S, Singh K, Duchen M, Conradt B, Marr C. MitoSegNet: Easy-to-use Deep Learning Segmentation for Analyzing Mitochondrial Morphology. iScience 2020; 23:101601. [PMID: 33083756 PMCID: PMC7554024 DOI: 10.1016/j.isci.2020.101601] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 08/18/2020] [Accepted: 09/17/2020] [Indexed: 12/29/2022] Open
Abstract
While the analysis of mitochondrial morphology has emerged as a key tool in the study of mitochondrial function, efficient quantification of mitochondrial microscopy images presents a challenging task and bottleneck for statistically robust conclusions. Here, we present Mitochondrial Segmentation Network (MitoSegNet), a pretrained deep learning segmentation model that enables researchers to easily exploit the power of deep learning for the quantification of mitochondrial morphology. We tested the performance of MitoSegNet against three feature-based segmentation algorithms and the machine-learning segmentation tool Ilastik. MitoSegNet outperformed all other methods in both pixelwise and morphological segmentation accuracy. We successfully applied MitoSegNet to unseen fluorescence microscopy images of mitoGFP expressing mitochondria in wild-type and catp-6 ATP13A2 mutant C. elegans adults. Additionally, MitoSegNet was capable of accurately segmenting mitochondria in HeLa cells treated with fragmentation inducing reagents. We provide MitoSegNet in a toolbox for Windows and Linux operating systems that combines segmentation with morphological analysis.
Collapse
Affiliation(s)
- Christian A. Fischer
- Fakultät für Biologie, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Munich, 82152 Bavaria, Germany
- Centre for Integrated Protein Science, Ludwig-Maximilians-University, Planegg-Martinsried, Munich, 82152 Bavaria, Germany
- Institute of Computational Biology, Helmholtz Zentrum München – German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Laura Besora-Casals
- Fakultät für Biologie, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Munich, 82152 Bavaria, Germany
| | - Stéphane G. Rolland
- Fakultät für Biologie, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Munich, 82152 Bavaria, Germany
| | - Simon Haeussler
- Fakultät für Biologie, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Munich, 82152 Bavaria, Germany
| | - Kritarth Singh
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6AP, UK
| | - Michael Duchen
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6AP, UK
| | - Barbara Conradt
- Fakultät für Biologie, Ludwig-Maximilians-Universität Munich, Planegg-Martinsried, Munich, 82152 Bavaria, Germany
- Centre for Integrated Protein Science, Ludwig-Maximilians-University, Planegg-Martinsried, Munich, 82152 Bavaria, Germany
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6AP, UK
| | - Carsten Marr
- Institute of Computational Biology, Helmholtz Zentrum München – German Research Center for Environmental Health, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| |
Collapse
|
15
|
Rasse TM, Hollandi R, Horvath P. OpSeF: Open Source Python Framework for Collaborative Instance Segmentation of Bioimages. Front Bioeng Biotechnol 2020; 8:558880. [PMID: 33117778 PMCID: PMC7576117 DOI: 10.3389/fbioe.2020.558880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/15/2020] [Indexed: 11/13/2022] Open
Abstract
Various pre-trained deep learning models for the segmentation of bioimages have been made available as developer-to-end-user solutions. They are optimized for ease of use and usually require neither knowledge of machine learning nor coding skills. However, individually testing these tools is tedious and success is uncertain. Here, we present the Open Segmentation Framework (OpSeF), a Python framework for deep learning-based instance segmentation. OpSeF aims at facilitating the collaboration of biomedical users with experienced image analysts. It builds on the analysts' knowledge in Python, machine learning, and workflow design to solve complex analysis tasks at any scale in a reproducible, well-documented way. OpSeF defines standard inputs and outputs, thereby facilitating modular workflow design and interoperability with other software. Users play an important role in problem definition, quality control, and manual refinement of results. OpSeF semi-automates preprocessing, convolutional neural network (CNN)-based segmentation in 2D or 3D, and postprocessing. It facilitates benchmarking of multiple models in parallel. OpSeF streamlines the optimization of parameters for pre- and postprocessing such, that an available model may frequently be used without retraining. Even if sufficiently good results are not achievable with this approach, intermediate results can inform the analysts in the selection of the most promising CNN-architecture in which the biomedical user might invest the effort of manually labeling training data. We provide Jupyter notebooks that document sample workflows based on various image collections. Analysts may find these notebooks useful to illustrate common segmentation challenges, as they prepare the advanced user for gradually taking over some of their tasks and completing their projects independently. The notebooks may also be used to explore the analysis options available within OpSeF in an interactive way and to document and share final workflows. Currently, three mechanistically distinct CNN-based segmentation methods, the U-Net implementation used in Cellprofiler 3.0, StarDist, and Cellpose have been integrated within OpSeF. The addition of new networks requires little; the addition of new models requires no coding skills. Thus, OpSeF might soon become both an interactive model repository, in which pre-trained models might be shared, evaluated, and reused with ease.
Collapse
Affiliation(s)
- Tobias M. Rasse
- Scientific Service Group Microscopy, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Réka Hollandi
- Synthetic and Systems Biology Unit, Biological Research Center (BRC), Szeged, Hungary
| | - Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Center (BRC), Szeged, Hungary
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| |
Collapse
|