1
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Eraslan IM, Egberts-Brugman M, Read JL, Voglsanger LM, Samarasinghe RM, Hamilton L, Dhar P, Williams RJ, Walker LC, Ch'ng S, Lawrence AJ, Walker AJ, Dean OM, Gundlach AL, Smith CM. Neuroanatomical distribution of fluorophores within adult RXFP3 Cre-tdTomato/YFP mouse brain. Biochem Pharmacol 2024; 225:116265. [PMID: 38714277 DOI: 10.1016/j.bcp.2024.116265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/09/2024]
Abstract
Relaxin-family peptide 3 receptor (RXFP3) is activated by relaxin-3 in the brain to influence arousal and related functions, such as feeding and stress responses. Two transgenic mouse lines have recently been developed that co-express different fluorophores within RXFP3-expressing neurons: either yellow fluorescent protein (YFP; RXFP3-Cre/YFP mice) or tdTomato (RXFP3-Cre/tdTomato mice). To date, the characteristics of neurons that express RXFP3-associated fluorophores in these mice have only been investigated in the bed nucleus of the stria terminalis and the hypothalamic arcuate nucleus. To better determine the utility of these fluorophore-expressing mice for further research, we characterised the neuroanatomical distribution of fluorophores throughout the brain of these mice and compared this to the published distribution of Rxfp3 mRNA (detected by in situ hybridisation) in wildtype mice. Coronal sections of RXFP3-Cre/YFP (n = 8) and RXFP3-Cre/tdTomato (n = 8) mouse brains were imaged, and the density of fluorophore-expressing cells within various brain regions/nuclei was qualitatively assessed. Comparisons with our previously reported RXFP3 mRNA distribution revealed that of 212 brain regions that contained either fluorophore or RXFP3 mRNA, approximately half recorded densities that were within two qualitative measurements of each other (on a 9-point scale), including hippocampal dentate gyrus and amygdala subregions. However, many brain areas with likely non-authentic, false-positive, or false-negative fluorophore expression were also detected, including the cerebellum. Therefore, this study provides a guide to which brain regions should be prioritized for future study of RXFP3 in these mice, to better understand the neuroanatomy and function of this intriguing, neuronal peptide receptor.
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Affiliation(s)
- Izel M Eraslan
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Monique Egberts-Brugman
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Justin L Read
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Lara M Voglsanger
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Rasika M Samarasinghe
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Lee Hamilton
- Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Sciences, Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Poshmaal Dhar
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Richard J Williams
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Leigh C Walker
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Sarah Ch'ng
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Andrew J Lawrence
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Adam J Walker
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Olivia M Dean
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia; The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Andrew L Gundlach
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Craig M Smith
- Faculty of Health, School of Medicine, Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Waurn Ponds, Victoria 3216, Australia.
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2
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Soumier A, Lio G, Demily C. Current and future applications of light-sheet imaging for identifying molecular and developmental processes in autism spectrum disorders. Mol Psychiatry 2024:10.1038/s41380-024-02487-8. [PMID: 38443634 DOI: 10.1038/s41380-024-02487-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 03/07/2024]
Abstract
Autism spectrum disorder (ASD) is identified by a set of neurodevelopmental divergences that typically affect the social communication domain. ASD is also characterized by heterogeneous cognitive impairments and is associated with cooccurring physical and medical conditions. As behaviors emerge as the brain matures, it is particularly essential to identify any gaps in neurodevelopmental trajectories during early perinatal life. Here, we introduce the potential of light-sheet imaging for studying developmental biology and cross-scale interactions among genetic, cellular, molecular and macroscale levels of circuitry and connectivity. We first report the core principles of light-sheet imaging and the recent progress in studying brain development in preclinical animal models and human organoids. We also present studies using light-sheet imaging to understand the development and function of other organs, such as the skin and gastrointestinal tract. We also provide information on the potential of light-sheet imaging in preclinical drug development. Finally, we speculate on the translational benefits of light-sheet imaging for studying individual brain-body interactions in advancing ASD research and creating personalized interventions.
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Affiliation(s)
- Amelie Soumier
- Le Vinatier Hospital Center, 95 boulevard Pinel, 69675, Bron cedex, France.
- iMIND, Center of Excellence for Autism, 95 boulevard Pinel, 69675, Bron cedex, France.
- Institute of Cognitive Science Marc Jeannerod, CNRS, UMR 5229, 67 boulevard Pinel, 69675, Bron cedex, France.
- University Claude Bernard Lyon 1, 43 boulevard du 11 Novembre 1918, 69622, Villeurbanne cedex, France.
| | - Guillaume Lio
- Le Vinatier Hospital Center, 95 boulevard Pinel, 69675, Bron cedex, France
- iMIND, Center of Excellence for Autism, 95 boulevard Pinel, 69675, Bron cedex, France
- Institute of Cognitive Science Marc Jeannerod, CNRS, UMR 5229, 67 boulevard Pinel, 69675, Bron cedex, France
| | - Caroline Demily
- Le Vinatier Hospital Center, 95 boulevard Pinel, 69675, Bron cedex, France
- iMIND, Center of Excellence for Autism, 95 boulevard Pinel, 69675, Bron cedex, France
- Institute of Cognitive Science Marc Jeannerod, CNRS, UMR 5229, 67 boulevard Pinel, 69675, Bron cedex, France
- University Claude Bernard Lyon 1, 43 boulevard du 11 Novembre 1918, 69622, Villeurbanne cedex, France
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3
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Bjerke IE, Yates SC, Carey H, Bjaalie JG, Leergaard TB. Scaling up cell-counting efforts in neuroscience through semi-automated methods. iScience 2023; 26:107562. [PMID: 37636060 PMCID: PMC10457595 DOI: 10.1016/j.isci.2023.107562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023] Open
Abstract
Quantifying how the cellular composition of brain regions vary across development, aging, sex, and disease, is crucial in experimental neuroscience, and the accuracy of different counting methods is continuously debated. Due to the tedious nature of most counting procedures, studies are often restricted to one or a few brain regions. Recently, there have been considerable methodological advances in combining semi-automated feature extraction with brain atlases for cell quantification. Such methods hold great promise for scaling up cell-counting efforts. However, little focus has been paid to how these methods should be implemented and reported to support reproducibility. Here, we provide an overview of practices for conducting and reporting cell counting in mouse and rat brains, showing that critical details for interpretation are typically lacking. We go on to discuss how novel methods may increase efficiency and reproducibility of cell counting studies. Lastly, we provide practical recommendations for researchers planning cell counting.
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Affiliation(s)
- Ingvild Elise Bjerke
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Sharon Christine Yates
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Harry Carey
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan Gunnar Bjaalie
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve Brauns Leergaard
- Neural Systems Laboratory, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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4
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Perens J, Salinas CG, Roostalu U, Skytte JL, Gundlach C, Hecksher-Sørensen J, Dahl AB, Dyrby TB. Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System. Neuroinformatics 2023; 21:269-286. [PMID: 36809643 DOI: 10.1007/s12021-023-09623-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2023] [Indexed: 02/23/2023]
Abstract
Magnetic resonance imaging (MRI) and light-sheet fluorescence microscopy (LSFM) are technologies that enable non-disruptive 3-dimensional imaging of whole mouse brains. A combination of complementary information from both modalities is desirable for studying neuroscience in general, disease progression and drug efficacy. Although both technologies rely on atlas mapping for quantitative analyses, the translation of LSFM recorded data to MRI templates has been complicated by the morphological changes inflicted by tissue clearing and the enormous size of the raw data sets. Consequently, there is an unmet need for tools that will facilitate fast and accurate translation of LSFM recorded brains to in vivo, non-distorted templates. In this study, we have developed a bidirectional multimodal atlas framework that includes brain templates based on both imaging modalities, region delineations from the Allen's Common Coordinate Framework, and a skull-derived stereotaxic coordinate system. The framework also provides algorithms for bidirectional transformation of results obtained using either MR or LSFM (iDISCO cleared) mouse brain imaging while the coordinate system enables users to easily assign in vivo coordinates across the different brain templates.
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Affiliation(s)
- Johanna Perens
- Gubra ApS, Hørsholm, Denmark.,Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University Denmark, Kongens Lyngby, Denmark.,Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
| | | | | | | | - Carsten Gundlach
- Neutrons and X-rays for Materials Physics, Department of Physics, Technical University Denmark, Kongens Lyngby, Denmark
| | | | - Anders Bjorholm Dahl
- Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University Denmark, Kongens Lyngby, Denmark
| | - Tim B Dyrby
- Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University Denmark, Kongens Lyngby, Denmark.,Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
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5
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Melanthota SK, Gopal D, Chakrabarti S, Kashyap AA, Radhakrishnan R, Mazumder N. Deep learning-based image processing in optical microscopy. Biophys Rev 2022; 14:463-481. [PMID: 35528030 PMCID: PMC9043085 DOI: 10.1007/s12551-022-00949-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 03/14/2022] [Indexed: 12/19/2022] Open
Abstract
Optical microscopy has emerged as a key driver of fundamental research since it provides the ability to probe into imperceptible structures in the biomedical world. For the detailed investigation of samples, a high-resolution image with enhanced contrast and minimal damage is preferred. To achieve this, an automated image analysis method is preferable over manual analysis in terms of both speed of acquisition and reduced error accumulation. In this regard, deep learning (DL)-based image processing can be highly beneficial. The review summarises and critiques the use of DL in image processing for the data collected using various optical microscopic techniques. In tandem with optical microscopy, DL has already found applications in various problems related to image classification and segmentation. It has also performed well in enhancing image resolution in smartphone-based microscopy, which in turn enablse crucial medical assistance in remote places. Graphical abstract
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Affiliation(s)
- Sindhoora Kaniyala Melanthota
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Dharshini Gopal
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Shweta Chakrabarti
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Anirudh Ameya Kashyap
- Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
| | - Raghu Radhakrishnan
- Department of Oral Pathology, Manipal College of Dental Sciences, Manipal, Manipal Academy of Higher Education, Manipal, 576104 India
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104 India
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6
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Delgado-Rodriguez P, Brooks CJ, Vaquero JJ, Muñoz-Barrutia A. Innovations in ex vivo Light Sheet Fluorescence Microscopy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 168:37-51. [PMID: 34293338 DOI: 10.1016/j.pbiomolbio.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Light Sheet Fluorescence Microscopy (LSFM) has revolutionized how optical imaging of biological specimens can be performed as this technique allows to produce 3D fluorescence images of entire samples with a high spatiotemporal resolution. In this manuscript, we aim to provide readers with an overview of the field of LSFM on ex vivo samples. Recent advances in LSFM architectures have made the technique widely accessible and have improved its acquisition speed and resolution, among other features. These developments are strongly supported by quantitative analysis of the huge image volumes produced thanks to the boost in computational capacities, the advent of Deep Learning techniques, and by the combination of LSFM with other imaging modalities. Namely, LSFM allows for the characterization of biological structures, disease manifestations and drug effectivity studies. This information can ultimately serve to develop novel diagnostic procedures, treatments and even to model the organs physiology in healthy and pathological conditions.
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Affiliation(s)
- Pablo Delgado-Rodriguez
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Claire Jordan Brooks
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain
| | - Juan José Vaquero
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Arrate Muñoz-Barrutia
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
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7
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Lara H, Li Z, Abels E, Aeffner F, Bui MM, ElGabry EA, Kozlowski C, Montalto MC, Parwani AV, Zarella MD, Bowman D, Rimm D, Pantanowitz L. Quantitative Image Analysis for Tissue Biomarker Use: A White Paper From the Digital Pathology Association. Appl Immunohistochem Mol Morphol 2021; 29:479-493. [PMID: 33734106 PMCID: PMC8354563 DOI: 10.1097/pai.0000000000000930] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/12/2021] [Indexed: 01/19/2023]
Abstract
Tissue biomarkers have been of increasing utility for scientific research, diagnosing disease, and treatment response prediction. There has been a steady shift away from qualitative assessment toward providing more quantitative scores for these biomarkers. The application of quantitative image analysis has thus become an indispensable tool for in-depth tissue biomarker interrogation in these contexts. This white paper reviews current technologies being employed for quantitative image analysis, their application and pitfalls, regulatory framework demands, and guidelines established for promoting their safe adoption in clinical practice.
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Affiliation(s)
- Haydee Lara
- GlaxoSmithKline-R&D, Cellular Biomarkers, Collegeville, PA
| | - Zaibo Li
- The Ohio State University, Columbus, OH
| | | | - Famke Aeffner
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Inc
| | | | | | | | | | | | | | | | - David Rimm
- Yale University School of Medicine, New Haven, CT
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8
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Bjerke IE, Yates SC, Laja A, Witter MP, Puchades MA, Bjaalie JG, Leergaard TB. Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain. iScience 2021; 24:101906. [PMID: 33385111 PMCID: PMC7770605 DOI: 10.1016/j.isci.2020.101906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/30/2020] [Accepted: 12/03/2020] [Indexed: 01/12/2023] Open
Abstract
The calcium-binding proteins parvalbumin and calbindin are expressed in neuronal populations regulating brain networks involved in spatial navigation, memory processes, and social interactions. Information about the numbers of these neurons across brain regions is required to understand their functional roles but is scarcely available. Employing semi-automated image analysis, we performed brain-wide analysis of immunohistochemically stained parvalbumin and calbindin sections and show that these neurons distribute in complementary patterns across the mouse brain. Parvalbumin neurons dominate in areas related to sensorimotor processing and navigation, whereas calbindin neurons prevail in regions reflecting behavioral states. We also find that parvalbumin neurons distribute according to similar principles in the hippocampal region of the rat and mouse brain. We validated our results against manual counts and evaluated variability of results among researchers. Comparison of our results to previous reports showed that neuron numbers vary, whereas patterns of relative densities and numbers are consistent. Brain-wide, semi-automatic quantification of parvalbumin and calbindin neurons Largely complementary distribution of calbindin and parvalbumin neurons in mice Comparison with several previous studies shows variable numbers but similar trends Similar distribution of parvalbumin neurons in the rat and mouse hippocampal region
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Affiliation(s)
- Ingvild E Bjerke
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Sharon C Yates
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Arthur Laja
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno P Witter
- Kavli Institute for Systems Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway
| | - Maja A Puchades
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trygve B Leergaard
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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9
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Li Y, Li A, Li J, Zhou H, Cao T, Wang H, Wang K. webTDat: A Web-Based, Real-Time, 3D Visualization Framework for Mesoscopic Whole-Brain Images. Front Neuroinform 2021; 14:542169. [PMID: 33519408 PMCID: PMC7838507 DOI: 10.3389/fninf.2020.542169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
The popularity of mesoscopic whole-brain imaging techniques has increased dramatically, but these techniques generate teravoxel-sized volumetric image data. Visualizing or interacting with these massive data is both necessary and essential in the bioimage analysis pipeline; however, due to their size, researchers have difficulty using typical computers to process them. The existing solutions do not consider applying web visualization and three-dimensional (3D) volume rendering methods simultaneously to reduce the number of data copy operations and provide a better way to visualize 3D structures in bioimage data. Here, we propose webTDat, an open-source, web-based, real-time 3D visualization framework for mesoscopic-scale whole-brain imaging datasets. webTDat uses an advanced rendering visualization method designed with an innovative data storage format and parallel rendering algorithms. webTDat loads the primary information in the image first and then decides whether it needs to load the secondary information in the image. By performing validation on TB-scale whole-brain datasets, webTDat achieves real-time performance during web visualization. The webTDat framework also provides a rich interface for annotation, making it a useful tool for visualizing mesoscopic whole-brain imaging data.
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Affiliation(s)
- Yuxin Li
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Anan Li
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China.,MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China.,HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Junhuai Li
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Hongfang Zhou
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Ting Cao
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Huaijun Wang
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
| | - Kan Wang
- School of Computer Science and Engineering, Xi'an University of Technology, Xi'an, China.,Shaanxi Key Laboratory of Network Computing and Security Technology, Xi'an, China
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10
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Franceschini A, Costantini I, Pavone FS, Silvestri L. Dissecting Neuronal Activation on a Brain-Wide Scale With Immediate Early Genes. Front Neurosci 2020; 14:569517. [PMID: 33192255 PMCID: PMC7645181 DOI: 10.3389/fnins.2020.569517] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
Visualizing neuronal activation on a brain-wide scale yet with cellular resolution is a fundamental technical challenge for neuroscience. This would enable analyzing how different neuronal circuits are disrupted in pathology and how they could be rescued by pharmacological treatments. Although this goal would have appeared visionary a decade ago, recent technological advances make it eventually feasible. Here, we review the latest developments in the fields of genetics, sample preparation, imaging, and image analysis that could be combined to afford whole-brain cell-resolution activation mapping. We show how the different biochemical and optical methods have been coupled to study neuronal circuits at different spatial and temporal scales, and with cell-type specificity. The inventory of techniques presented here could be useful to find the tools best suited for a specific experiment. We envision that in the next years, mapping of neuronal activation could become routine in many laboratories, allowing dissecting the neuronal counterpart of behavior.
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Affiliation(s)
| | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy (LENS), Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council (INO-CNR), Sesto Fiorentino, Italy
| | - Francesco S Pavone
- European Laboratory for Non-linear Spectroscopy (LENS), Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council (INO-CNR), Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy (LENS), Sesto Fiorentino, Italy.,National Institute of Optics, National Research Council (INO-CNR), Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Florence, Italy
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11
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Corain L, Grisan E, Graïc JM, Carvajal-Schiaffino R, Cozzi B, Peruffo A. Multi-aspect testing and ranking inference to quantify dimorphism in the cytoarchitecture of cerebellum of male, female and intersex individuals: a model applied to bovine brains. Brain Struct Funct 2020; 225:2669-2688. [PMID: 32989472 PMCID: PMC7674367 DOI: 10.1007/s00429-020-02147-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/08/2020] [Indexed: 11/28/2022]
Abstract
The dimorphism among male, female and freemartin intersex bovines, focusing on the vermal lobules VIII and IX, was analyzed using a novel data analytics approach to quantify morphometric differences in the cytoarchitecture of digitalized sections of the cerebellum. This methodology consists of multivariate and multi-aspect testing for cytoarchitecture-ranking, based on neuronal cell complexity among populations defined by factors, such as sex, age or pathology. In this context, we computed a set of shape descriptors of the neural cell morphology, categorized them into three domains named size, regularity and density, respectively. The output and results of our methodology are multivariate in nature, allowing an in-depth analysis of the cytoarchitectonic organization and morphology of cells. Interestingly, the Purkinje neurons and the underlying granule cells revealed the same morphological pattern: female possessed larger, denser and more irregular neurons than males. In the Freemartin, Purkinje neurons showed an intermediate setting between males and females, while the granule cells were the largest, most regular and dense. This methodology could be a powerful instrument to carry out morphometric analysis providing robust bases for objective tissue screening, especially in the field of neurodegenerative pathologies.
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Affiliation(s)
- L Corain
- Department of Management and Engineering, University of Padova, 36100, Vicenza, VI, Italy
| | - E Grisan
- Department of Information Engineering, University of Padova, 35131, Padua, PD, Italy
- School of Engineering, London South Bank University, London, SE1 0AA, UK
| | - J-M Graïc
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, PD, Italy.
| | - R Carvajal-Schiaffino
- Department of Mathematics and Computer Science, University of Santiago de Chile, Santiago, Chile
| | - B Cozzi
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, PD, Italy
| | - A Peruffo
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università 16, 35020, Legnaro, PD, Italy
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12
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Radiomics-Based Prediction of Overall Survival in Lung Cancer Using Different Volumes-Of-Interest. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10186425] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lung cancer accounts for the largest amount of deaths worldwide with respect to the other oncological pathologies. To guarantee the most effective cure to patients for such aggressive tumours, radiomics is increasing as a novel and promising research field that aims at extracting knowledge from data in terms of quantitative measures that are computed from diagnostic images, with prognostic and predictive ends. This knowledge could be used to optimize current treatments and to maximize their efficacy. To this end, we hereby study the use of such quantitative biomarkers computed from CT images of patients affected by Non-Small Cell Lung Cancer to predict Overall Survival. The main contributions of this work are two: first, we consider different volumes of interest for the same patient to find out whether the volume surrounding the visible lesions can provide useful information; second, we introduce 3D Local Binary Patterns, which are texture measures scarcely explored in radiomics. As further validation, we show that the proposed signature outperforms not only the features automatically computed by a deep learning-based approach, but also another signature at the state-of-the-art using other handcrafted features.
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13
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Slomianka L. Basic quantitative morphological methods applied to the central nervous system. J Comp Neurol 2020; 529:694-756. [PMID: 32639600 PMCID: PMC7818269 DOI: 10.1002/cne.24976] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022]
Abstract
Generating numbers has become an almost inevitable task associated with studies of the morphology of the nervous system. Numbers serve a desire for clarity and objectivity in the presentation of results and are a prerequisite for the statistical evaluation of experimental outcomes. Clarity, objectivity, and statistics make demands on the quality of the numbers that are not met by many methods. This review provides a refresher of problems associated with generating numbers that describe the nervous system in terms of the volumes, surfaces, lengths, and numbers of its components. An important aim is to provide comprehensible descriptions of the methods that address these problems. Collectively known as design‐based stereology, these methods share two features critical to their application. First, they are firmly based in mathematics and its proofs. Second and critically underemphasized, an understanding of their mathematical background is not necessary for their informed and productive application. Understanding and applying estimators of volume, surface, length or number does not require more of an organizational mastermind than an immunohistochemical protocol. And when it comes to calculations, square roots are the gravest challenges to overcome. Sampling strategies that are combined with stereological probes are efficient and allow a rational assessment if the numbers that have been generated are “good enough.” Much may be unfamiliar, but very little is difficult. These methods can no longer be scapegoats for discrepant results but faithfully produce numbers on the material that is assessed. They also faithfully reflect problems that associated with the histological material and the anatomically informed decisions needed to generate numbers that are not only valid in theory. It is within reach to generate practically useful numbers that must integrate with qualitative knowledge to understand the function of neural systems.
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Affiliation(s)
- Lutz Slomianka
- University of Zürich, Institute of Anatomy, Zürich, Switzerland
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14
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Matsumoto K, Mitani TT, Horiguchi SA, Kaneshiro J, Murakami TC, Mano T, Fujishima H, Konno A, Watanabe TM, Hirai H, Ueda HR. Advanced CUBIC tissue clearing for whole-organ cell profiling. Nat Protoc 2019; 14:3506-3537. [DOI: 10.1038/s41596-019-0240-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/28/2019] [Indexed: 11/09/2022]
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15
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Hildebrand S, Schueth A, Herrler A, Galuske R, Roebroeck A. Scalable Labeling for Cytoarchitectonic Characterization of Large Optically Cleared Human Neocortex Samples. Sci Rep 2019; 9:10880. [PMID: 31350519 PMCID: PMC6659684 DOI: 10.1038/s41598-019-47336-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 07/12/2019] [Indexed: 01/27/2023] Open
Abstract
Optical clearing techniques and light sheet microscopy have transformed fluorescent imaging of rodent brains, and have provided a crucial alternative to traditional confocal or bright field techniques for thin sections. However, clearing and labeling human brain tissue through all cortical layers and significant portions of a cortical area, has so far remained extremely challenging, especially for formalin fixed adult cortical tissue. Here, we present MASH (Multiscale Architectonic Staining of Human cortex): a simple, fast and low-cost cytoarchitectonic labeling approach for optically cleared human cortex samples, which can be applied to large (up to 5 mm thick) formalin fixed adult brain samples. A suite of small-molecule fluorescent nuclear and cytoplasmic dye protocols in combination with new refractive index matching solutions allows deep volume imaging. This greatly reduces time and cost of imaging cytoarchitecture in thick samples and enables classification of cytoarchitectonic layers over the full cortical depth. We demonstrate application of MASH to large archival samples of human visual areas, characterizing cortical architecture in 3D from the scale of cortical areas to that of single cells. In combination with scalable light sheet imaging and data analysis, MASH could open the door to investigation of large human cortical systems at cellular resolution and in the context of their complex 3-dimensional geometry.
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Affiliation(s)
- Sven Hildebrand
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht, The Netherlands
| | - Anna Schueth
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht, The Netherlands
| | - Andreas Herrler
- Department of Anatomy & Embryology, Faculty of Health, Medicine & Life Science, Maastricht University, Maastricht, The Netherlands
| | - Ralf Galuske
- Systems Neurophysiology, Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Alard Roebroeck
- Department of Cognitive Neuroscience, Faculty of Psychology & Neuroscience, Maastricht, The Netherlands.
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16
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Caspers S, Axer M. Decoding the microstructural correlate of diffusion MRI. NMR IN BIOMEDICINE 2019; 32:e3779. [PMID: 28858413 DOI: 10.1002/nbm.3779] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 06/28/2017] [Accepted: 07/05/2017] [Indexed: 06/07/2023]
Abstract
Diffusion imaging has evolved considerably over the past decade. While it provides valuable information about the structural connectivity at the macro- and mesoscopic scale, bridging the gap to the microstructure at the level of single nerve fibers poses an enormous challenge. This is particularly true for the human brain with its large size, its large white-matter volume and availability of histological techniques for studying human whole-brain sections and subsequent 3D reconstruction. Classic post-mortem techniques for studying the fiber architecture of the brain, such as myeloarchitectonic staining or dye tracing, are complemented by novel histological approaches, such as 3D polarized light imaging or optical coherence tomography, enabling unique insight into the fiber architecture from large fiber bundles within deep white matter to single nerve fibers in the cortex. The present review discusses the benefits and challenges of these latest developments in comparison with the classic techniques, with particular focus on the mutual exchange between in vivo and post-mortem diffusion imaging and post-mortem microstructural approaches for understanding the wiring of the brain across different scales.
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Affiliation(s)
- Svenja Caspers
- C. and O. Vogt Institute for Brain Research, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- JARA-BRAIN, Jülich-Aachen Research Alliance, Jülich, Germany
| | - Markus Axer
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
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17
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Vandenberghe ME, Souedet N, Hérard AS, Ayral AM, Letronne F, Balbastre Y, Sadouni E, Hantraye P, Dhenain M, Frouin F, Lambert JC, Delzescaux T. Voxel-Based Statistical Analysis of 3D Immunostained Tissue Imaging. Front Neurosci 2018; 12:754. [PMID: 30498427 PMCID: PMC6250035 DOI: 10.3389/fnins.2018.00754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 10/01/2018] [Indexed: 12/23/2022] Open
Abstract
Recently developed techniques to visualize immunostained tissues in 3D and in large samples have expanded the scope of microscopic investigations at the level of the whole brain. Here, we propose to adapt voxel-based statistical analysis to 3D high-resolution images of the immunostained rodent brain. The proposed approach was first validated with a simulation dataset with known cluster locations. Then, it was applied to characterize the effect of ADAM30, a gene involved in the metabolism of the amyloid precursor protein, in a mouse model of Alzheimer's disease. This work introduces voxel-based analysis of 3D immunostained microscopic brain images and, therefore, opens the door to localized whole-brain exploratory investigation of pathological markers and cellular alterations.
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Affiliation(s)
- Michel E. Vandenberghe
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Nicolas Souedet
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Anne-Sophie Hérard
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Anne-Marie Ayral
- INSERM U1167, Institut Pasteur de LilleUniversité Lille-Nord de France, Lille, France
| | - Florent Letronne
- INSERM U1167, Institut Pasteur de LilleUniversité Lille-Nord de France, Lille, France
| | - Yaël Balbastre
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Elmahdi Sadouni
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Philippe Hantraye
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Marc Dhenain
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
| | - Frédérique Frouin
- Laboratoire Imagerie Moléculaire in vivo (IMIV UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS)Orsay, France
| | - Jean-Charles Lambert
- INSERM U1167, Institut Pasteur de LilleUniversité Lille-Nord de France, Lille, France
| | - Thierry Delzescaux
- CEA, DRF, Institut François JacobMolecular Imaging Research Center, Fontenay-aux-Roses, France
- Neurodegenerative Diseases Laboratory, CNRS, CEA, Paris-Sud University, Paris-Saclay UniversityUMR9199, Fontenay-aux-Roses, France
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18
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Chatterjee K, Pratiwi FW, Wu FCM, Chen P, Chen BC. Recent Progress in Light Sheet Microscopy for Biological Applications. APPLIED SPECTROSCOPY 2018; 72:1137-1169. [PMID: 29926744 DOI: 10.1177/0003702818778851] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The introduction of light sheet fluorescence microscopy (LSFM) has overcome the challenges in conventional optical microscopy. Among the recent breakthroughs in fluorescence microscopy, LSFM had been proven to provide a high three-dimensional spatial resolution, high signal-to-noise ratio, fast imaging acquisition rate, and minuscule levels of phototoxic and photodamage effects. The aforementioned auspicious properties are crucial in the biomedical and clinical research fields, covering a broad range of applications: from the super-resolution imaging of intracellular dynamics in a single cell to the high spatiotemporal resolution imaging of developmental dynamics in an entirely large organism. In this review, we provided a systematic outline of the historical development of LSFM, detailed discussion on the variants and improvements of LSFM, and delineation on the most recent technological advancements of LSFM and its potential applications in single molecule/particle detection, single-molecule super-resolution imaging, imaging intracellular dynamics of a single cell, multicellular imaging: cell-cell and cell-matrix interactions, plant developmental biology, and brain imaging and developmental biology.
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Affiliation(s)
- Krishnendu Chatterjee
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 3 Department of Engineering and System Science, National Tsing-Hua University, Hsinchu, Taiwan
| | - Feby Wijaya Pratiwi
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 4 Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | | | - Peilin Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
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19
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Bjerke IE, Øvsthus M, Papp EA, Yates SC, Silvestri L, Fiorilli J, Pennartz CMA, Pavone FS, Puchades MA, Leergaard TB, Bjaalie JG. Data integration through brain atlasing: Human Brain Project tools and strategies. Eur Psychiatry 2018. [PMID: 29519589 DOI: 10.1016/j.eurpsy.2018.02.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The Human Brain Project (HBP), an EU Flagship Initiative, is currently building an infrastructure that will allow integration of large amounts of heterogeneous neuroscience data. The ultimate goal of the project is to develop a unified multi-level understanding of the brain and its diseases, and beyond this to emulate the computational capabilities of the brain. Reference atlases of the brain are one of the key components in this infrastructure. Based on a new generation of three-dimensional (3D) reference atlases, new solutions for analyzing and integrating brain data are being developed. HBP will build services for spatial query and analysis of brain data comparable to current online services for geospatial data. The services will provide interactive access to a wide range of data types that have information about anatomical location tied to them. The 3D volumetric nature of the brain, however, introduces a new level of complexity that requires a range of tools for making use of and interacting with the atlases. With such new tools, neuroscience research groups will be able to connect their data to atlas space, share their data through online data systems, and search and find other relevant data through the same systems. This new approach partly replaces earlier attempts to organize research data based only on a set of semantic terminologies describing the brain and its subdivisions.
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Affiliation(s)
- Ingvild E Bjerke
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Martin Øvsthus
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Eszter A Papp
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Sharon C Yates
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy
| | - Julien Fiorilli
- Cognitive and Systems Neuroscience Group, SILS Center for Neuroscience, University of Amsterdam, The Netherlands
| | - Cyriel M A Pennartz
- Cognitive and Systems Neuroscience Group, SILS Center for Neuroscience, University of Amsterdam, The Netherlands
| | - Francesco S Pavone
- European Laboratory for Non-linear Spectroscopy, Sesto Fiorentino, Italy
| | - Maja A Puchades
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Trygve B Leergaard
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Norway.
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20
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Abstract
Egocentric (self-centered) and allocentric (viewpoint independent) representations of space are essential for spatial navigation and wayfinding. Deficits in spatial memory come with age-related cognitive decline, are marked in mild cognitive impairment (MCI) and Alzheimer’s disease (AD), and are associated with cognitive deficits in autism. In most of these disorders, a change in the brain areas engaged in the spatial reference system processing has been documented. However, the spatial memory deficits observed during physiological and pathological aging are quite different. While patients with AD and MCI have a general spatial navigation impairment in both allocentric and egocentric strategies, healthy older adults are particularly limited in the allocentric navigation, but they can still count on egocentric navigation strategy to solve spatial tasks. Therefore, specific navigational tests should be considered for differential diagnosis between healthy and pathological aging conditions. Finally, more research is still needed to better understand the spatial abilities of autistic individuals.
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Affiliation(s)
- Maria Concetta Miniaci
- Department of Pharmacy , School of Medicine, University of Naples Federico II, Naples, Italy
| | - Elvira De Leonibus
- Institute of Genetics and Biophysics (IGB) , National Research Council, Naples, Italy.,Telethon Institute of Genetics and Medicine, Telethon Foundation, Pozzuoli, Italy
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21
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Konno A, Okazaki S. Aqueous-based tissue clearing in crustaceans. ZOOLOGICAL LETTERS 2018; 4:13. [PMID: 29930867 PMCID: PMC5991465 DOI: 10.1186/s40851-018-0099-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/11/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Investigation of the internal tissues and organs of a macroscopic organism usually requires destructive processes, such as dissection or sectioning. These processes are inevitably associated with the loss of some spatial information. Recently, aqueous-based tissue clearing techniques, which allow whole-organ or even whole-body clearing of small rodents, have been developed and opened a new method of three-dimensional histology. It is expected that these techniques will be useful tools in the field of zoology, in which organisms with highly diverse morphology are investigated and compared. However, most of these new methods are optimized for soft, non-pigmented organs in small rodents, especially the brain, and their applicability to non-model organisms with hard exoskeletons and stronger pigmentation has not been tested. RESULTS We explored the possible application of an aqueous-based tissue clearing technique, advanced CUBIC, on small crustaceans. The original CUBIC procedure did not clear the terrestrial isopod, Armadillidium vulgare. Therefore, to apply the whole-mount clearing method to isopods with strong pigmentation and calcified exoskeletons, we introduced several pretreatment steps, including decalcification and bleaching. Thereafter, the clearing capacity of the procedure was dramatically improved, and A. vulgare became transparent. The internal organs, such as the digestive tract and male reproductive organs, were visible through sclerites using an ordinary stereomicroscope. We also found that fluorescent nuclear staining using propidium iodide (PI) helped to visualize the internal organs of cleared specimens. Our procedure was also effective on the marine crab, Philyra sp. CONCLUSIONS In this study, we developed a method to clear whole tissues of crustaceans. To the best of our knowledge, this is the first report of whole-mount clearing applied to crustaceans using an aqueous-based technique. This technique could facilitate morphological studies of crustaceans and other organisms with calcified exoskeletons and pigmentation.
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Affiliation(s)
- Alu Konno
- Department of Medical Spectroscopy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu-City, Shizuoka-Pref 431-3192 Japan
| | - Shigetoshi Okazaki
- Department of Medical Spectroscopy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu-City, Shizuoka-Pref 431-3192 Japan
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22
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Zhang C, Yan C, Ren M, Li A, Quan T, Gong H, Yuan J. A platform for stereological quantitative analysis of the brain-wide distribution of type-specific neurons. Sci Rep 2017; 7:14334. [PMID: 29085023 PMCID: PMC5662727 DOI: 10.1038/s41598-017-14699-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 10/16/2017] [Indexed: 01/15/2023] Open
Abstract
Quantifying the distribution of specific neurons throughout the whole brain is crucial for understanding physiological actions, pathological alterations and pharmacological treatments. However, the precise cell number and density of specific neurons in the entire brain remain unknown because of a lack of suitable research tools. Here, we propose a pipeline to automatically acquire and analyse the brain-wide distribution of type-specific neurons in a mouse brain. We employed a Brain-wide Positioning System to collect high-throughput anatomical information with the co-localized cytoarchitecture of the whole brain at subcellular resolution and utilized the NeuroGPS algorithm to locate and count cells in the whole brain. We evaluated the data continuity of the 3D dataset and the accuracy of stereological cell counting in 3D. To apply this pipeline, we acquired and quantified the brain-wide distributions and somatic morphology of somatostatin-expressing neurons in transgenic mouse brains. The results indicated that this whole-brain cell counting pipeline has the potential to become a routine tool for cell type neuroscience studies.
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Affiliation(s)
- Chen Zhang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Cheng Yan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Miao Ren
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Tingwei Quan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China. .,MoE Key Laboratory for Biomedical Photonics, Collaborative Innovation Center for Biomedical Engineering, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.
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23
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Buzin AR, Macedo ND, De Araujo IBBA, Nogueira BV, de Andrade TU, Endringer DC, Lenz D. Automatic detection of hypoxia in renal tissue stained with HIF-1alpha. J Immunol Methods 2017; 444:47-50. [PMID: 28212880 DOI: 10.1016/j.jim.2017.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 02/12/2017] [Indexed: 11/29/2022]
Abstract
OBJECTIVE The objective of this study was the identification of the stain HIF-alpha using the Image Cytometry, and to help to count the positive cells (with HIF-alpha) and the negative cells (without HIF-alpha) from the same sample. METHOD 17 images of renal tissues from male rats of Winstar lineage; overall, there were 12.587 objects (cells) in the images for analysis. The acquired images were then analyzed through the free softwares CellProfiler (version 2.1.1) and CellProfiler Analyst (version 2.0). In the software CellProfiler Anlyst, there was a separation with the classes of the object, using a classifier, and the classes were: 1) class with HIF-alpha and 2) class without HIF-alpha. RESULTS With the data obtained through Score All, it was possible to calculate the percentage of cells that had HIF-alpha; out of 12.587 objects of the sample, 6.773 (54%) had HIF-alpha and 5.814 (46%) did not have HIF-alpha. Data of sensibility 0.90, specificity 0.84 and standard deviation 0.10 and 0.12. CONCLUSION The research shows that the free software CellProfiler, through the light microscope, was able to identify the stains, perform the machine's learning, and subsequently count and separate cells from distinct classes (with and without the stain of HIF-alpha).
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Affiliation(s)
| | | | - Isabela Bastos Binotti Abreu De Araujo
- Department of Morphology, Federal University of Espirito Santo, Brazil; Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden (TUD), Dresden, Germany
| | | | | | | | - Dominik Lenz
- Pharmaceutical Sciences, University of Vila Velha, Brazil.
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24
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Peter S, De Zeeuw CI, Boeckers TM, Schmeisser MJ. Cerebellar and Striatal Pathologies in Mouse Models of Autism Spectrum Disorder. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2017; 224:103-119. [PMID: 28551753 DOI: 10.1007/978-3-319-52498-6_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component. To date, several hundred different genetic mutations have been identified to play a role in its aetiology. The heterogeneity of genetic abnormalities combined with the different brain regions where aberrations are found makes the search for causative mechanisms a daunting task. Even within a limited number of brain regions, a myriad of different neural circuit dysfunctions may lead to ASD. Here, we review mouse models that incorporate mutations of ASD risk genes causing pathologies in the cerebellum and striatum and highlight the vulnerability of related circuit dysfunctions within these brain regions in ASD pathophysiology.
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Affiliation(s)
- Saša Peter
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands. .,Department of Neuroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Chris I De Zeeuw
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.,Department of Neuroscience, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tobias M Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - Michael J Schmeisser
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany. .,Division of Neuroanatomy, Institute of Anatomy, Otto-von-Guericke University, Magdeburg, Germany. .,Leibniz Institute for Neurobiology, Magdeburg, Germany.
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Rockland KS. Lighting up Neuroanatomy. Front Neurosci 2016; 10:293. [PMID: 27444725 PMCID: PMC4917544 DOI: 10.3389/fnins.2016.00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 06/10/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Kathleen S Rockland
- Department of Anatomy & Neurobiology, Boston University School Medicine Boston, MA, USA
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26
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Stefaniuk M, Gualda EJ, Pawlowska M, Legutko D, Matryba P, Koza P, Konopka W, Owczarek D, Wawrzyniak M, Loza-Alvarez P, Kaczmarek L. Light-sheet microscopy imaging of a whole cleared rat brain with Thy1-GFP transgene. Sci Rep 2016; 6:28209. [PMID: 27312902 PMCID: PMC4911560 DOI: 10.1038/srep28209] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/31/2016] [Indexed: 12/03/2022] Open
Abstract
Whole-brain imaging with light-sheet fluorescence microscopy and optically cleared tissue is a new, rapidly developing research field. Whereas successful attempts to clear and image mouse brain have been reported, a similar result for rats has proven difficult to achieve. Herein, we report on creating novel transgenic rat harboring fluorescent reporter GFP under control of neuronal gene promoter. We then present data on clearing the rat brain, showing that FluoClearBABB was found superior over passive CLARITY and CUBIC methods. Finally, we demonstrate efficient imaging of the rat brain using light-sheet fluorescence microscopy.
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Affiliation(s)
| | - Emilio J. Gualda
- Institut de Ciencies Fotoniques (ICFO), Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain
| | | | | | | | - Paulina Koza
- Nencki Institute, Pasteura 3, 02-093 Warsaw, Poland
| | | | | | | | - Pablo Loza-Alvarez
- Institut de Ciencies Fotoniques (ICFO), Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain
| | - Leszek Kaczmarek
- Nencki Institute, Pasteura 3, 02-093 Warsaw, Poland
- Institut de Ciencies Fotoniques (ICFO), Barcelona Institute of Science and Technology, 08860, Castelldefels (Barcelona), Spain
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27
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Axer M, Strohmer S, Gräßel D, Bücker O, Dohmen M, Reckfort J, Zilles K, Amunts K. Estimating Fiber Orientation Distribution Functions in 3D-Polarized Light Imaging. Front Neuroanat 2016; 10:40. [PMID: 27147981 PMCID: PMC4835454 DOI: 10.3389/fnana.2016.00040] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/29/2016] [Indexed: 11/13/2022] Open
Abstract
Research of the human brain connectome requires multiscale approaches derived from independent imaging methods ideally applied to the same object. Hence, comprehensible strategies for data integration across modalities and across scales are essential. We have successfully established a concept to bridge the spatial scales from microscopic fiber orientation measurements based on 3D-Polarized Light Imaging (3D-PLI) to meso- or macroscopic dimensions. By creating orientation distribution functions (pliODFs) from high-resolution vector data via series expansion with spherical harmonics utilizing high performance computing and supercomputing technologies, data fusion with Diffusion Magnetic Resonance Imaging has become feasible, even for a large-scale dataset such as the human brain. Validation of our approach was done effectively by means of two types of datasets that were transferred from fiber orientation maps into pliODFs: simulated 3D-PLI data showing artificial, but clearly defined fiber patterns and real 3D-PLI data derived from sections through the human brain and the brain of a hooded seal.
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Affiliation(s)
- Markus Axer
- Research Centre Jülich, Institute of Neuroscience and Medicine Jülich, Germany
| | - Sven Strohmer
- Jülich Supercomputing Centre, Institute for Advanced Simulation, Research Centre JülichJülich, Germany; Research Centre Jülich, Simulation Lab Neuroscience, Bernstein Facility for Simulation and Database Technology, Institute for Advanced SimulationJülich, Germany
| | - David Gräßel
- Research Centre Jülich, Institute of Neuroscience and Medicine Jülich, Germany
| | - Oliver Bücker
- Jülich Supercomputing Centre, Institute for Advanced Simulation, Research Centre Jülich Jülich, Germany
| | - Melanie Dohmen
- Research Centre Jülich, Institute of Neuroscience and Medicine Jülich, Germany
| | - Julia Reckfort
- Research Centre Jülich, Institute of Neuroscience and Medicine Jülich, Germany
| | - Karl Zilles
- Research Centre Jülich, Institute of Neuroscience and MedicineJülich, Germany; Department of Psychiatry, Psychotherapy, and Psychosomatics, RWTH Aachen UniversityAachen, Germany; JARA Jülich-Aachen Research Alliance, Translational Brain MedicineAachen, Germany
| | - Katrin Amunts
- Research Centre Jülich, Institute of Neuroscience and MedicineJülich, Germany; C. and O. Vogt Institute for Brain Research, Heinrich-Heine-University DüsseldorfDüsseldorf, Germany
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28
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TeraFly: real-time three-dimensional visualization and annotation of terabytes of multidimensional volumetric images. Nat Methods 2016; 13:192-4. [DOI: 10.1038/nmeth.3767] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Susaki E, Ueda H. Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals. Cell Chem Biol 2016; 23:137-157. [DOI: 10.1016/j.chembiol.2015.11.009] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 11/20/2015] [Accepted: 11/20/2015] [Indexed: 12/29/2022]
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