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Rodgers G, Bikis C, Janz P, Tanner C, Schulz G, Thalmann P, Haas CA, Müller B. 3D X-ray Histology for the Investigation of Temporal Lobe Epilepsy in a Mouse Model. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1730-1745. [PMID: 37584515 DOI: 10.1093/micmic/ozad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/29/2023] [Accepted: 07/28/2023] [Indexed: 08/17/2023]
Abstract
The most common form of epilepsy among adults is mesial temporal lobe epilepsy (mTLE), with seizures often originating in the hippocampus due to abnormal electrical activity. The gold standard for the histopathological analysis of mTLE is histology, which is a two-dimensional technique. To fill this gap, we propose complementary three-dimensional (3D) X-ray histology. Herein, we used synchrotron radiation-based phase-contrast microtomography with 1.6 μm-wide voxels for the post mortem visualization of tissue microstructure in an intrahippocampal-kainate mouse model for mTLE. We demonstrated that the 3D X-ray histology of unstained, unsectioned, paraffin-embedded brain hemispheres can identify hippocampal sclerosis through the loss of pyramidal neurons in the first and third regions of the Cornu ammonis as well as granule cell dispersion within the dentate gyrus. Morphology and density changes during epileptogenesis were quantified by segmentations from a deep convolutional neural network. Compared to control mice, the total dentate gyrus volume doubled and the granular layer volume quadrupled 21 days after injecting kainate. Subsequent sectioning of the same mouse brains allowed for benchmarking 3D X-ray histology against well-established histochemical and immunofluorescence stainings. Thus, 3D X-ray histology is a complementary neuroimaging tool to unlock the third dimension for the cellular-resolution histopathological analysis of mTLE.
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Affiliation(s)
- Griffin Rodgers
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Integrierte Psychiatrie Winterthur-Zürcher Unterland, 8408 Winterthur, Switzerland
| | - Philipp Janz
- Faculty of Medicine, Experimental Epilepsy Research, Department of Neurosurgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79106 Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, 79106 Freiburg, Germany
| | - Christine Tanner
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
- Core Facility Micro- and Nanotomography, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Peter Thalmann
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Carola A Haas
- Faculty of Medicine, Experimental Epilepsy Research, Department of Neurosurgery, Medical Center-University of Freiburg, 79106 Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, 79106 Freiburg, Germany
- Center of Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, 79114 Freiburg, Germany
| | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
- Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
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Hamnett R, Dershowitz LB, Sampathkumar V, Wang Z, Gomez-Frittelli J, De Andrade V, Kasthuri N, Druckmann S, Kaltschmidt JA. Regional cytoarchitecture of the adult and developing mouse enteric nervous system. Curr Biol 2022; 32:4483-4492.e5. [PMID: 36070775 PMCID: PMC9613618 DOI: 10.1016/j.cub.2022.08.030] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 07/19/2022] [Accepted: 08/11/2022] [Indexed: 11/22/2022]
Abstract
The organization and cellular composition of tissues are key determinants of their biological function. In the mammalian gastrointestinal (GI) tract, the enteric nervous system (ENS) intercalates between muscular and epithelial layers of the gut wall and can control GI function independent of central nervous system (CNS) input.1 As in the CNS, distinct regions of the GI tract are highly specialized and support diverse functions, yet the regional and spatial organization of the ENS remains poorly characterized.2 Cellular arrangements,3,4 circuit connectivity patterns,5,6 and diverse cell types7-9 are known to underpin ENS functional complexity and GI function, but enteric neurons are most typically described only as a uniform meshwork of interconnected ganglia. Here, we present a bird's eye view of the mouse ENS, describing its previously underappreciated cytoarchitecture and regional variation. We visually and computationally demonstrate that enteric neurons are organized in circumferential neuronal stripes. This organization emerges gradually during the perinatal period, with neuronal stripe formation in the small intestine (SI) preceding that in the colon. The width of neuronal stripes varies throughout the length of the GI tract, and distinct neuronal subtypes differentially populate specific regions of the GI tract, with stark contrasts between SI and colon as well as within subregions of each. This characterization provides a blueprint for future understanding of region-specific GI function and identifying ENS structural correlates of diverse GI disorders.
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Affiliation(s)
- Ryan Hamnett
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Lori B Dershowitz
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA
| | - Vandana Sampathkumar
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Ziyue Wang
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Neurobiology, Stanford University, Stanford, CA 94305, USA
| | - Julieta Gomez-Frittelli
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Vincent De Andrade
- Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Narayanan Kasthuri
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA; Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Shaul Druckmann
- Department of Neurobiology, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Julia A Kaltschmidt
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA.
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Quesada J, Sathidevi L, Liu R, Ahad N, Jackson JM, Azabou M, Xiao J, Liding C, Jin M, Urzay C, Gray-Roncal W, Johnson EC, Dyer EL. MTNeuro: A Benchmark for Evaluating Representations of Brain Structure Across Multiple Levels of Abstraction. ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 2022; 35:5299-5314. [PMID: 38414814 PMCID: PMC10898440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
There are multiple scales of abstraction from which we can describe the same image, depending on whether we are focusing on fine-grained details or a more global attribute of the image. In brain mapping, learning to automatically parse images to build representations of both small-scale features (e.g., the presence of cells or blood vessels) and global properties of an image (e.g., which brain region the image comes from) is a crucial and open challenge. However, most existing datasets and benchmarks for neuroanatomy consider only a single downstream task at a time. To bridge this gap, we introduce a new dataset, annotations, and multiple downstream tasks that provide diverse ways to readout information about brain structure and architecture from the same image. Our multi-task neuroimaging benchmark (MTNeuro) is built on volumetric, micrometer-resolution X-ray microtomography images spanning a large thalamocortical section of mouse brain, encompassing multiple cortical and subcortical regions. We generated a number of different prediction challenges and evaluated several supervised and self-supervised models for brain-region prediction and pixel-level semantic segmentation of microstructures. Our experiments not only highlight the rich heterogeneity of this dataset, but also provide insights into how self-supervised approaches can be used to learn representations that capture multiple attributes of a single image and perform well on a variety of downstream tasks. Datasets, code, and pre-trained baseline models are provided at: https://mtneuro.github.io/.
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Affiliation(s)
| | | | - Ran Liu
- Georgia Institute of Technology
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Álvaro-Espinosa L, de Pablos-Aragoneses A, Valiente M, Priego N. Brain Microenvironment Heterogeneity: Potential Value for Brain Tumors. Front Oncol 2021; 11:714428. [PMID: 34540682 PMCID: PMC8440906 DOI: 10.3389/fonc.2021.714428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/16/2021] [Indexed: 11/13/2022] Open
Abstract
Uncovering the complexity of the microenvironment that emerges in brain disorders is key to identify potential vulnerabilities that might help challenging diseases affecting this organ. Recently, genomic and proteomic analyses, especially at the single cell level, have reported previously unrecognized diversity within brain cell types. The complexity of the brain microenvironment increases during disease partly due to the immune infiltration from the periphery that contributes to redefine the brain connectome by establishing a new crosstalk with resident brain cell types. Within the rewired brain ecosystem, glial cell subpopulations are emerging hubs modulating the dialogue between the Immune System and the Central Nervous System with important consequences in the progression of brain tumors and other disorders. Single cell technologies are crucial not only to define and track the origin of disease-associated cell types, but also to identify their molecular similarities and differences that might be linked to specific brain injuries. These altered molecular patterns derived from reprogramming the healthy brain into an injured organ, might provide a new generation of therapeutic targets to challenge highly prevalent and lethal brain disorders that remain incurable with unprecedented specificity and limited toxicities. In this perspective, we present the most relevant clinical and pre-clinical work regarding the characterization of the heterogeneity within different components of the microenvironment in the healthy and injured brain with a special interest on single cell analysis. Finally, we discuss how understanding the diversity of the brain microenvironment could be exploited for translational purposes, particularly in primary and secondary tumors affecting the brain.
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Affiliation(s)
| | | | | | - Neibla Priego
- Brain Metastasis Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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Matelsky JK, Reilly EP, Johnson EC, Stiso J, Bassett DS, Wester BA, Gray-Roncal W. DotMotif: an open-source tool for connectome subgraph isomorphism search and graph queries. Sci Rep 2021; 11:13045. [PMID: 34158519 PMCID: PMC8219732 DOI: 10.1038/s41598-021-91025-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/29/2021] [Indexed: 01/02/2023] Open
Abstract
Recent advances in neuroscience have enabled the exploration of brain structure at the level of individual synaptic connections. These connectomics datasets continue to grow in size and complexity; methods to search for and identify interesting graph patterns offer a promising approach to quickly reduce data dimensionality and enable discovery. These graphs are often too large to be analyzed manually, presenting significant barriers to searching for structure and testing hypotheses. We combine graph database and analysis libraries with an easy-to-use neuroscience grammar suitable for rapidly constructing queries and searching for subgraphs and patterns of interest. Our approach abstracts many of the computer science and graph theory challenges associated with nanoscale brain network analysis and allows scientists to quickly conduct research at scale. We demonstrate the utility of these tools by searching for motifs on simulated data and real public connectomics datasets, and we share simple and complex structures relevant to the neuroscience community. We contextualize our findings and provide case studies and software to motivate future neuroscience exploration.
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Affiliation(s)
- Jordan K. Matelsky
- The Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723 USA
| | - Elizabeth P. Reilly
- The Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723 USA
| | - Erik C. Johnson
- The Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723 USA
| | - Jennifer Stiso
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104 USA
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Danielle S. Bassett
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Electrical and Systems Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Physics and Astronomy, College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Santa Fe Institute, Santa Fe, NM 87501 USA
| | - Brock A. Wester
- The Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723 USA
| | - William Gray-Roncal
- The Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723 USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218 USA
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6
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Johnson EC, Wilt M, Rodriguez LM, Norman-Tenazas R, Rivera C, Drenkow N, Kleissas D, LaGrow TJ, Cowley HP, Downs J, K. Matelsky J, J. Hughes M, P. Reilly E, A. Wester B, L. Dyer E, P. Kording K, R. Gray-Roncal W. Toward a scalable framework for reproducible processing of volumetric, nanoscale neuroimaging datasets. Gigascience 2020; 9:giaa147. [PMID: 33347572 PMCID: PMC7751400 DOI: 10.1093/gigascience/giaa147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/19/2020] [Accepted: 12/18/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Emerging neuroimaging datasets (collected with imaging techniques such as electron microscopy, optical microscopy, or X-ray microtomography) describe the location and properties of neurons and their connections at unprecedented scale, promising new ways of understanding the brain. These modern imaging techniques used to interrogate the brain can quickly accumulate gigabytes to petabytes of structural brain imaging data. Unfortunately, many neuroscience laboratories lack the computational resources to work with datasets of this size: computer vision tools are often not portable or scalable, and there is considerable difficulty in reproducing results or extending methods. RESULTS We developed an ecosystem of neuroimaging data analysis pipelines that use open-source algorithms to create standardized modules and end-to-end optimized approaches. As exemplars we apply our tools to estimate synapse-level connectomes from electron microscopy data and cell distributions from X-ray microtomography data. To facilitate scientific discovery, we propose a generalized processing framework, which connects and extends existing open-source projects to provide large-scale data storage, reproducible algorithms, and workflow execution engines. CONCLUSIONS Our accessible methods and pipelines demonstrate that approaches across multiple neuroimaging experiments can be standardized and applied to diverse datasets. The techniques developed are demonstrated on neuroimaging datasets but may be applied to similar problems in other domains.
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Affiliation(s)
- Erik C Johnson
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Miller Wilt
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Luis M Rodriguez
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Raphael Norman-Tenazas
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Corban Rivera
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Nathan Drenkow
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Dean Kleissas
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Theodore J LaGrow
- School of Electrical & Computer Engineering, Georgia Institute of Technology, 777 Atlantic Dr. NW, Atlanta, GA, 30332 USA
| | - Hannah P Cowley
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Joseph Downs
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Jordan K. Matelsky
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Marisa J. Hughes
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Elizabeth P. Reilly
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Brock A. Wester
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
| | - Eva L. Dyer
- School of Electrical & Computer Engineering, Georgia Institute of Technology, 777 Atlantic Dr. NW, Atlanta, GA, 30332 USA
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology, 313 Ferst Dr., Atlanta, GA, 30332 USA
| | - Konrad P. Kording
- Department of Biomedical Engineering, University of Pennsylvania, 210 South 33rd St., Philadelphia, PA, 19104 USA
| | - William R. Gray-Roncal
- Research And Exploratory Development Department, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Rd., Laurel, MD, 20723 USA
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