1
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Planchette AL, Schmidt C, Burri O, Gomez de Agüero M, Radenovic A, Mylonas A, Extermann J. Optical imaging of the small intestine immune compartment across scales. Commun Biol 2023; 6:352. [PMID: 37002381 PMCID: PMC10066397 DOI: 10.1038/s42003-023-04642-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 02/28/2023] [Indexed: 04/03/2023] Open
Abstract
The limitations of 2D microscopy constrain our ability to observe and understand tissue-wide networks that are, by nature, 3-dimensional. Optical projection tomography (OPT) enables the acquisition of large volumes (ranging from micrometres to centimetres) in various tissues. We present a multi-modal workflow for the characterization of both structural and quantitative parameters of the mouse small intestine. As proof of principle, we evidence its applicability for imaging the mouse intestinal immune compartment and surrounding mucosal structures. We quantify the volumetric size and spatial distribution of Isolated Lymphoid Follicles (ILFs) and quantify the density of villi throughout centimetre-long segments of intestine. Furthermore, we exhibit the age and microbiota dependence for ILF development, and leverage a technique that we call reverse-OPT for identifying and homing in on regions of interest. Several quantification capabilities are displayed, including villous density in the autofluorescent channel and the size and spatial distribution of the signal of interest at millimetre-scale volumes. The concatenation of 3D imaging with reverse-OPT and high-resolution 2D imaging allows accurate localisation of ROIs and adds value to interpretations made in 3D. Importantly, OPT may be used to identify sparsely-distributed regions of interest in large volumes whilst retaining compatibility with high-resolution microscopy modalities, including confocal microscopy. We believe this pipeline to be approachable for a wide-range of specialties, and to provide a new method for characterisation of the mouse intestinal immune compartment.
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Affiliation(s)
- Arielle Louise Planchette
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Cédric Schmidt
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202, Geneva, Switzerland
| | - Olivier Burri
- BioImaging & Optics Platform, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Mercedes Gomez de Agüero
- Host-microbial interactions group, Institute of Systems Immunology, Max Planck research group, University of Würzburg, Würzburg, Germany
- Mucosal Immunology Group, Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Aleksandra Radenovic
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.
| | - Alessio Mylonas
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Jérôme Extermann
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202, Geneva, Switzerland
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2
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Darling C, Davis SPX, Kumar S, French PMW, McGinty J. Single-shot optical projection tomography for high-speed volumetric imaging of dynamic biological samples. JOURNAL OF BIOPHOTONICS 2023; 16:e202200232. [PMID: 36087031 DOI: 10.1002/jbio.202200232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
A single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic biological samples is presented. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio, but the sequential acquisition of projection images typically requires samples to be immobilized during the acquisition. A proof-of-principle system capable of single-shot tomography of a ~1 mm3 volume is presented, demonstrating camera-limited rates of up to 62.5 volumes/s, which has been applied to 3D imaging of a freely swimming zebrafish embryo. This is achieved by recording eight projection views simultaneously on four low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under £5000. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including high throughput flow cytometry applied to model organisms and fluid dynamics studies.
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Affiliation(s)
- Connor Darling
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Samuel P X Davis
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
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3
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Durand S, Heller GR, Ramirez TK, Luviano JA, Williford A, Sullivan DT, Cahoon AJ, Farrell C, Groblewski PA, Bennett C, Siegle JH, Olsen SR. Acute head-fixed recordings in awake mice with multiple Neuropixels probes. Nat Protoc 2023; 18:424-457. [PMID: 36477710 DOI: 10.1038/s41596-022-00768-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 08/09/2022] [Indexed: 12/12/2022]
Abstract
Multi-electrode arrays such as Neuropixels probes enable electrophysiological recordings from large populations of single neurons with high temporal resolution. By using such probes, the activity from functionally interacting, yet distinct, brain regions can be measured simultaneously by inserting multiple probes into the same subject. However, the use of multiple probes in small animals such as mice requires the removal of a sizable fraction of the skull, while also minimizing tissue damage and keeping the brain stable during the recordings. Here, we describe a step-by-step process designed to facilitate reliable recordings from up to six Neuropixels probes simultaneously in awake, head-fixed mice. The procedure involves four stages: the implantation of a headframe and a removable glass coverslip, the precise positioning of the Neuropixels probes at targeted points on the brain surface, the placement of a perforated plastic imaging window and the insertion of the probes into the brain of an awake mouse. The approach provides access to multiple brain regions and has been successfully applied across hundreds of mice. The procedure has been optimized for dense recordings from the mouse visual system, but it can be adapted for alternative recording configurations to target multiple probes in other brain areas. The protocol is suitable for users with experience in stereotaxic surgery in mice.
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Affiliation(s)
| | - Greggory R Heller
- Allen Institute, Seattle, WA, USA.,Department of Brain and Cognitive Sciences, Massachussetts Institute of Technology, Cambridge, MA, USA
| | - Tamina K Ramirez
- Allen Institute, Seattle, WA, USA.,Department of Neurobiology and Behavior, Columbia University, New York, NY, USA
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4
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Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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5
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Liu Y, Dong J, Schmidt C, Boquet-Pujadas A, Extermann J, Unser M. Artifacts in optical projection tomography due to refractive-index mismatch: model and correction. OPTICS LETTERS 2022; 47:2618-2621. [PMID: 35648888 DOI: 10.1364/ol.457144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Optical projection tomography (OPT) is a powerful tool for three-dimensional (3D) imaging of mesoscopic samples. While it is able to achieve resolution of a few tens of microns over a sample volume of several cubic centimeters, the reconstructed images often suffer from artifacts caused by inaccurate calibration. In this work, we focus on the refractive-index mismatch between the sample and the surrounding medium. We derive a 3D cone-beam forward model of OPT that approximates the effect of refractive-index mismatch. We then implement a fast and efficient reconstruction method to correct for the induced seagull-shaped artifacts on experimental images of fluorescent beads.
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6
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Koudounas P, Koniaris E, Manolis I, Asvestas P, Kostopoulos S, Cavouras D, Glotsos D. Three-dimensional tissue volume generation in conventional brightfield microscopy. Microsc Res Tech 2022; 85:2913-2923. [PMID: 35510792 DOI: 10.1002/jemt.24141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 11/07/2022]
Abstract
The purpose of the study is to develop and automate a series of steps for enabling digital 3D tissue volume generation in conventional Brightfield microscopy for histopathology applications. Tissue samples were retrieved from the General Hospital of Athens "Hippocration", Greece. Samples were placed on a microtome that produced consecutive 2 μm sections. Each section was stained using Hematoxylin and Eosin and placed on microscope slides. A histopathologist specified the region of interest (ROI) on each slide. A 2D image was created from each ROI using a LEICA DM2500 microscope with a LEICA DFC 420C camera. Τhe 3D volume was created by stacking consecutive 2D images using a deep learning image interpolation method. The reconstructed 3D tissue volumes were evaluated by an expert histopathologist. Results showed that the 3D volumes might reveal information that is not clearly visible or even undetectable in the conventional 2D Brightfield images. In contrast to other 3D tissue imaging technologies, the proposed method (a) does not depend on the distance of the sample from the objectives producing 3D tissue volumes at any desired magnification, (b) does not require a special instrument, it may be implemented with any conventional Brightfield microscope, and (c) can be used for any given routine application, not only for some specialized clinical studies. The proposed study provides the basis for a feasible, cost-less and time-less upgrade of any standard 2D microscope into a 3D imaging instrument that may enhance the quality of diagnostic assessments in histopathology.
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Affiliation(s)
- Panteleimon Koudounas
- Medical Image and Signal Processing Laboratory, Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | | | - Ioannis Manolis
- Department of Biomedical Sciences, University of West Attica, Athens, Greece
| | - Panteleimon Asvestas
- Medical Image and Signal Processing Laboratory, Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Spiros Kostopoulos
- Medical Image and Signal Processing Laboratory, Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Dionisis Cavouras
- Medical Image and Signal Processing Laboratory, Department of Biomedical Engineering, University of West Attica, Athens, Greece
| | - Dimitris Glotsos
- Medical Image and Signal Processing Laboratory, Department of Biomedical Engineering, University of West Attica, Athens, Greece
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7
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Pomarico E, Schmidt C, Chays F, Nguyen D, Planchette A, Tissot A, Roux A, Pagès S, Batti L, Clausen C, Lasser T, Radenovic A, Sanguinetti B, Extermann J. Statistical distortion of supervised learning predictions in optical microscopy induced by image compression. Sci Rep 2022; 12:3464. [PMID: 35236913 PMCID: PMC8891276 DOI: 10.1038/s41598-022-07445-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 02/10/2022] [Indexed: 11/23/2022] Open
Abstract
The growth of data throughput in optical microscopy has triggered the extensive use of supervised learning (SL) models on compressed datasets for automated analysis. Investigating the effects of image compression on SL predictions is therefore pivotal to assess their reliability, especially for clinical use. We quantify the statistical distortions induced by compression through the comparison of predictions on compressed data to the raw predictive uncertainty, numerically estimated from the raw noise statistics measured via sensor calibration. Predictions on cell segmentation parameters are altered by up to 15% and more than 10 standard deviations after 16-to-8 bits pixel depth reduction and 10:1 JPEG compression. JPEG formats with higher compression ratios show significantly larger distortions. Interestingly, a recent metrologically accurate algorithm, offering up to 10:1 compression ratio, provides a prediction spread equivalent to that stemming from raw noise. The method described here allows to set a lower bound to the predictive uncertainty of a SL task and can be generalized to determine the statistical distortions originated from a variety of processing pipelines in AI-assisted fields.
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Affiliation(s)
- Enrico Pomarico
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Rue de la Prairie 4, 1202, Geneva, Switzerland.
| | - Cédric Schmidt
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Rue de la Prairie 4, 1202, Geneva, Switzerland
| | - Florian Chays
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Rue de la Prairie 4, 1202, Geneva, Switzerland
| | - David Nguyen
- Laboratory of Nanoscale Biology, School of Engineering, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Arielle Planchette
- Laboratory of Nanoscale Biology, School of Engineering, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | - Audrey Tissot
- Wyss Center for Bio- and Neuroengineering, Geneva, Switzerland
| | - Adrien Roux
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Rue de la Prairie 4, 1202, Geneva, Switzerland
| | - Stéphane Pagès
- Wyss Center for Bio- and Neuroengineering, Geneva, Switzerland.,Department of Basic Neurosciences, Geneva Neuroscience Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Laura Batti
- Wyss Center for Bio- and Neuroengineering, Geneva, Switzerland
| | | | - Theo Lasser
- Max-Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, School of Engineering, École Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
| | | | - Jérôme Extermann
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Rue de la Prairie 4, 1202, Geneva, Switzerland
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8
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Chourrout M, Roux M, Boisvert C, Gislard C, Legland D, Arganda-Carreras I, Olivier C, Peyrin F, Boutin H, Rama N, Baron T, Meyronet D, Brun E, Rositi H, Wiart M, Chauveau F. Brain virtual histology with X-ray phase-contrast tomography Part II:3D morphologies of amyloid- β plaques in Alzheimer's disease models. BIOMEDICAL OPTICS EXPRESS 2022; 13:1640-1653. [PMID: 35414980 PMCID: PMC8973161 DOI: 10.1364/boe.438890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 05/15/2023]
Abstract
While numerous transgenic mouse strains have been produced to model the formation of amyloid-β (Aβ) plaques in the brain, efficient methods for whole-brain 3D analysis of Aβ deposits have to be validated and standardized. Moreover, routine immunohistochemistry performed on brain slices precludes any shape analysis of Aβ plaques, or require complex procedures for serial acquisition and reconstruction. The present study shows how in-line (propagation-based) X-ray phase-contrast tomography (XPCT) combined with ethanol-induced brain sample dehydration enables hippocampus-wide detection and morphometric analysis of Aβ plaques. Performed in three distinct Alzheimer mouse strains, the proposed workflow identified differences in signal intensity and 3D shape parameters: 3xTg displayed a different type of Aβ plaques, with a larger volume and area, greater elongation, flatness and mean breadth, and more intense average signal than J20 and APP/PS1. As a label-free non-destructive technique, XPCT can be combined with standard immunohistochemistry. XPCT virtual histology could thus become instrumental in quantifying the 3D spreading and the morphological impact of seeding when studying prion-like properties of Aβ aggregates in animal models of Alzheimer's disease. This is Part II of a series of two articles reporting the value of in-line XPCT for virtual histology of the brain; Part I shows how in-line XPCT enables 3D myelin mapping in the whole rodent brain and in human autopsy brain tissue.
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Affiliation(s)
- Matthieu Chourrout
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
| | - Margaux Roux
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
| | - Carlie Boisvert
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
- Current affiliation: Faculty of Medicine, The Ottawa Hospital and University of Ottawa, Ottawa, Ontario, Canada
| | - Coralie Gislard
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Ignacio Arganda-Carreras
- University of the Basque Country (UPV/EHU), San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Donostia International Physics Center (DIPC), San Sebastian, Spain
| | - Cécile Olivier
- Univ. Lyon, CREATIS; CNRS UMR5220; INSERM U1044; INSA-Lyon; Univ. Lyon 1, Lyon, France
| | - Françoise Peyrin
- Univ. Lyon, CREATIS; CNRS UMR5220; INSERM U1044; INSA-Lyon; Univ. Lyon 1, Lyon, France
| | - Hervé Boutin
- Univ. Manchester, Faculty of Biology Medicine and Health, Wolfson Molecular Imaging Centre, Manchester, UK
| | - Nicolas Rama
- Univ. Lyon, CRCL; INSERM U1052; CNRS UMR5286; Univ. Lyon 1; Centre Léon Bérard, Lyon, France
| | | | | | - Emmanuel Brun
- Univ. Grenoble Alpes, Inserm UA07 Strobe Grenoble, France
| | - Hugo Rositi
- Univ. Clermont Auvergne, Institut Pascal; CNRS UMR 6602; SIGMA Clermont, Clermont-Ferrand, France
| | - Marlène Wiart
- Univ. Lyon, CarMeN Laboratory; INSERM U1060; INRA U1397; Hospices Civils de Lyon, Lyon, France
- CNRS, Lyon, France
- These authors contributed equally to this work
| | - Fabien Chauveau
- Univ. Lyon, Lyon Neuroscience Research Center, CNRS UMR5292, Inserm U1028, Université Claude Bernard Lyon 1, Lyon, France
- CNRS, Lyon, France
- These authors contributed equally to this work
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9
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Schmidt C, Planchette AL, Nguyen D, Giardina G, Neuenschwander Y, Franco MD, Mylonas A, Descloux AC, Pomarico E, Radenovic A, Extermann J. High resolution optical projection tomography platform for multispectral imaging of the mouse gut. BIOMEDICAL OPTICS EXPRESS 2021; 12:3619-3629. [PMID: 34221683 PMCID: PMC8221953 DOI: 10.1364/boe.423284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 05/06/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Optical projection tomography (OPT) is a powerful tool for three-dimensional imaging of mesoscopic biological samples with great use for biomedical phenotyping studies. We present a fluorescent OPT platform that enables direct visualization of biological specimens and processes at a centimeter scale with high spatial resolution, as well as fast data throughput and reconstruction. We demonstrate nearly isotropic sub-28 µm resolution over more than 60 mm3 after reconstruction of a single acquisition. Our setup is optimized for imaging the mouse gut at multiple wavelengths. Thanks to a new sample preparation protocol specifically developed for gut specimens, we can observe the spatial arrangement of the intestinal villi and the vasculature network of a 3-cm long healthy mouse gut. Besides the blood vessel network surrounding the gastrointestinal tract, we observe traces of vasculature at the villi ends close to the lumen. The combination of rapid acquisition and a large field of view with high spatial resolution in 3D mesoscopic imaging holds an invaluable potential for gastrointestinal pathology research.
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Affiliation(s)
- Cédric Schmidt
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202 Geneva, Switzerland
| | - Arielle L. Planchette
- Laboratoire de Biologie à l’Échelle Nanométrique, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - David Nguyen
- Zlatic Lab, Neurobiology, MRC-Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Gabriel Giardina
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202 Geneva, Switzerland
| | - Yoan Neuenschwander
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202 Geneva, Switzerland
| | - Mathieu Di Franco
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202 Geneva, Switzerland
| | - Alessio Mylonas
- Laboratoire de Biologie à l’Échelle Nanométrique, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Adrien C. Descloux
- Laboratoire de Biologie à l’Échelle Nanométrique, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Enrico Pomarico
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202 Geneva, Switzerland
| | - Aleksandra Radenovic
- Laboratoire de Biologie à l’Échelle Nanométrique, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jérôme Extermann
- HEPIA/HES-SO, University of Applied Sciences of Western Switzerland, Rue de la Prairie 4, 1202 Geneva, Switzerland
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10
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Kong C, Bobe S, Pilger C, Lachetta M, Øie CI, Kirschnick N, Mönkemöller V, Hübner W, Förster C, Schüttpelz M, Kiefer F, Huser T, Schulte Am Esch J. Multiscale and Multimodal Optical Imaging of the Ultrastructure of Human Liver Biopsies. Front Physiol 2021; 12:637136. [PMID: 33679449 PMCID: PMC7925637 DOI: 10.3389/fphys.2021.637136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/27/2021] [Indexed: 12/30/2022] Open
Abstract
The liver as the largest organ in the human body is composed of a complex macroscopic and microscopic architecture that supports its indispensable function to maintain physiological homeostasis. Optical imaging of the human liver is particularly challenging because of the need to cover length scales across 7 orders of magnitude (from the centimeter scale to the nanometer scale) in order to fully assess the ultrastructure of the entire organ down to the subcellular scale and probe its physiological function. This task becomes even more challenging the deeper within the organ one hopes to image, because of the strong absorption and scattering of visible light by the liver. Here, we demonstrate how optical imaging methods utilizing highly specific fluorescent labels, as well as label-free optical methods can seamlessly cover this entire size range in excised, fixed human liver tissue and we exemplify this by reconstructing the biliary tree in three-dimensional space. Imaging of tissue beyond approximately 0.5 mm length requires optical clearing of the human liver. We present the successful use of optical projection tomography and light-sheet fluorescence microscopy to derive information about the liver architecture on the millimeter scale. The intermediate size range is covered using label-free structural and chemically sensitive methods, such as second harmonic generation and coherent anti-Stokes Raman scattering microscopy. Laser-scanning confocal microscopy extends the resolution to the nanoscale, allowing us to ultimately image individual liver sinusoidal endothelial cells and their fenestrations by super-resolution structured illumination microscopy. This allowed us to visualize the human hepatobiliary system in 3D down to the cellular level, which indicates that reticular biliary networks communicate with portal bile ducts via single or a few ductuli. Non-linear optical microscopy enabled us to identify fibrotic regions extending from the portal field to the parenchyma, along with microvesicular steatosis in liver biopsies from an older patient. Lastly, super-resolution microscopy allowed us to visualize and determine the size distribution of fenestrations in human liver sinusoidal endothelial cells for the first time under aqueous conditions. Thus, this proof-of-concept study allows us to demonstrate, how, in combination, these techniques open up a new chapter in liver biopsy analysis.
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Affiliation(s)
- Cihang Kong
- Department of Physics, Bielefeld University, Bielefeld, Germany
| | - Stefanie Bobe
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
| | | | - Mario Lachetta
- Department of Physics, Bielefeld University, Bielefeld, Germany
| | - Cristina Ionica Øie
- Vascular Biology Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Nils Kirschnick
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
| | | | - Wolfgang Hübner
- Department of Physics, Bielefeld University, Bielefeld, Germany.,Forschungsverbund BioMedizin Bielefeld (FBMB), Bielefeld, Germany
| | | | - Mark Schüttpelz
- Department of Physics, Bielefeld University, Bielefeld, Germany
| | - Friedemann Kiefer
- European Institute for Molecular Imaging, University of Münster, Münster, Germany
| | - Thomas Huser
- Department of Physics, Bielefeld University, Bielefeld, Germany.,Forschungsverbund BioMedizin Bielefeld (FBMB), Bielefeld, Germany
| | - Jan Schulte Am Esch
- Forschungsverbund BioMedizin Bielefeld (FBMB), Bielefeld, Germany.,Department of General and Visceral Surgery, Evangelisches Klinikum Bethel gGmbH, University Hospital OWL of the University of Bielefeld, Bielefeld, Germany
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11
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Siegle JH, Jia X, Durand S, Gale S, Bennett C, Graddis N, Heller G, Ramirez TK, Choi H, Luviano JA, Groblewski PA, Ahmed R, Arkhipov A, Bernard A, Billeh YN, Brown D, Buice MA, Cain N, Caldejon S, Casal L, Cho A, Chvilicek M, Cox TC, Dai K, Denman DJ, de Vries SEJ, Dietzman R, Esposito L, Farrell C, Feng D, Galbraith J, Garrett M, Gelfand EC, Hancock N, Harris JA, Howard R, Hu B, Hytnen R, Iyer R, Jessett E, Johnson K, Kato I, Kiggins J, Lambert S, Lecoq J, Ledochowitsch P, Lee JH, Leon A, Li Y, Liang E, Long F, Mace K, Melchior J, Millman D, Mollenkopf T, Nayan C, Ng L, Ngo K, Nguyen T, Nicovich PR, North K, Ocker GK, Ollerenshaw D, Oliver M, Pachitariu M, Perkins J, Reding M, Reid D, Robertson M, Ronellenfitch K, Seid S, Slaughterbeck C, Stoecklin M, Sullivan D, Sutton B, Swapp J, Thompson C, Turner K, Wakeman W, Whitesell JD, Williams D, Williford A, Young R, Zeng H, Naylor S, Phillips JW, Reid RC, Mihalas S, Olsen SR, Koch C. Survey of spiking in the mouse visual system reveals functional hierarchy. Nature 2021; 592:86-92. [PMID: 33473216 PMCID: PMC10399640 DOI: 10.1038/s41586-020-03171-x] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically1. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset-part of the Allen Brain Observatory2-that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli. Using cross-correlation analysis, we reveal that the organization of inter-area functional connectivity during visual stimulation mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas3. We find that four classical hierarchical measures-response latency, receptive-field size, phase-locking to drifting gratings and response decay timescale-are all correlated with the hierarchy. Moreover, recordings obtained during a visual task reveal that the correlation between neural activity and behavioural choice also increases along the hierarchy. Our study provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.
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Affiliation(s)
| | - Xiaoxuan Jia
- Allen Institute for Brain Science, Seattle, WA, USA.
| | | | - Sam Gale
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Nile Graddis
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Hannah Choi
- Allen Institute for Brain Science, Seattle, WA, USA.,Department of Applied Mathematics, University of Washington, Seattle, WA, USA
| | | | | | | | | | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Dillan Brown
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Nicolas Cain
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Linzy Casal
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Andrew Cho
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Timothy C Cox
- University of Missouri-Kansas City School of Dentistry, Kansas City, MO, USA
| | - Kael Dai
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Daniel J Denman
- Allen Institute for Brain Science, Seattle, WA, USA.,The University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | | | | | | | | | - David Feng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Brian Hu
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Ross Hytnen
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - India Kato
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Jerome Lecoq
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Yang Li
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Fuhui Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kyla Mace
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Kat North
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Jed Perkins
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - David Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Sam Seid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Ben Sutton
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jackie Swapp
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Rob Young
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Sarah Naylor
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - R Clay Reid
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Shawn R Olsen
- Allen Institute for Brain Science, Seattle, WA, USA.
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12
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Soliton microcomb based spectral domain optical coherence tomography. Nat Commun 2021; 12:427. [PMID: 33462200 PMCID: PMC7813855 DOI: 10.1038/s41467-020-20404-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 11/05/2020] [Indexed: 12/22/2022] Open
Abstract
Spectral domain optical coherence tomography (OCT) is a widely employed, minimally invasive bio-medical imaging technique, which requires a broadband light source, typically implemented by super-luminescent diodes. Recent advances in soliton based photonic integrated frequency combs (soliton microcombs) have enabled the development of low-noise, broadband chipscale frequency comb sources, whose potential for OCT imaging has not yet been unexplored. Here, we explore the use of dissipative Kerr soliton microcombs in spectral domain OCT and show that, by using photonic chipscale Si3N4 resonators in conjunction with 1300 nm pump lasers, spectral bandwidths exceeding those of commercial OCT sources are possible. We characterized the exceptional noise properties of our source (in comparison to conventional OCT sources) and demonstrate that the soliton states in microresonators exhibit a residual intensity noise floor at high offset frequencies that is ca. 3 dB lower than a traditional OCT source at identical power, and can exhibit significantly lower noise performance for powers at the milli-Watt level. Moreover, we demonstrate that classical amplitude noise of all soliton comb teeth are correlated, i.e., common mode, in contrast to superluminescent diodes or incoherent microcomb states, which opens a new avenue to improve imaging speed and performance beyond the thermal noise limit. Superluminescent diodes, that provide a broadband spectrum are typically used in spectral domain coherence tomography. Here, the authors use chipscale silicon nitride resonators to generate soliton microcombs with a lower noise flor that could substitute the diode sources.
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13
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Zhang H, Waldmann L, Manuel R, Boije H, Haitina T, Allalou A. zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging. BIOMEDICAL OPTICS EXPRESS 2020; 11:4290-4305. [PMID: 32923043 PMCID: PMC7449731 DOI: 10.1364/boe.393519] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Optical projection tomography (OPT) is a 3D imaging alternative to conventional microscopy which allows imaging of millimeter-sized object with isotropic micrometer resolution. The zebrafish is an established model organism and an important tool used in genetic and chemical screening. The size and optical transparency of the embryo and larva makes them well suited for imaging using OPT. Here, we present an open-source implementation of an OPT platform, built around a customized sample stage, 3D-printed parts and open source algorithms optimized for the system. We developed a versatile automated workflow including a two-step image processing approach for correcting the center of rotation and generating accurate 3D reconstructions. Our results demonstrate high-quality 3D reconstruction using synthetic data as well as real data of live and fixed zebrafish. The presented 3D-printable OPT platform represents a fully open design, low-cost and rapid loading and unloading of samples. Our system offers the opportunity for researchers with different backgrounds to setup and run OPT for large scale experiments, particularly in studies using zebrafish larvae as their key model organism.
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Affiliation(s)
- Hanqing Zhang
- Division of Visual Information and
Interaction, Department of Information Technology, Uppsala University,
S-75105 Uppsala, Sweden
- BioImage Informatics Facility at
SciLifeLab, S-75105 Uppsala, Sweden
| | - Laura Waldmann
- Department of Organismal Biology, Uppsala
University, S-75236 Uppsala, Sweden
| | - Remy Manuel
- Department of Neuroscience, Uppsala
University, S-75124 Uppsala, Sweden
| | - Henrik Boije
- Department of Neuroscience, Uppsala
University, S-75124 Uppsala, Sweden
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala
University, S-75236 Uppsala, Sweden
| | - Amin Allalou
- Division of Visual Information and
Interaction, Department of Information Technology, Uppsala University,
S-75105 Uppsala, Sweden
- BioImage Informatics Facility at
SciLifeLab, S-75105 Uppsala, Sweden
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14
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Davis SPX, Kumar S, Alexandrov Y, Bhargava A, da Silva Xavier G, Rutter GA, Frankel P, Sahai E, Flaxman S, French PMW, McGinty J. Convolutional neural networks for reconstruction of undersampled optical projection tomography data applied to in vivo imaging of zebrafish. JOURNAL OF BIOPHOTONICS 2019; 12:e201900128. [PMID: 31386281 PMCID: PMC7065643 DOI: 10.1002/jbio.201900128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/27/2019] [Accepted: 08/04/2019] [Indexed: 06/10/2023]
Abstract
Optical projection tomography (OPT) is a 3D mesoscopic imaging modality that can utilize absorption or fluorescence contrast. 3D images can be rapidly reconstructed from tomographic data sets sampled with sufficient numbers of projection angles using the Radon transform, as is typically implemented with optically cleared samples of the mm-to-cm scale. For in vivo imaging, considerations of phototoxicity and the need to maintain animals under anesthesia typically preclude the acquisition of OPT data at a sufficient number of angles to avoid artifacts in the reconstructed images. For sparse samples, this can be addressed with iterative algorithms to reconstruct 3D images from undersampled OPT data, but the data processing times present a significant challenge for studies imaging multiple animals. We show here that convolutional neural networks (CNN) can be used in place of iterative algorithms to remove artifacts-reducing processing time for an undersampled in vivo zebrafish dataset from 77 to 15 minutes. We also show that using CNN produces reconstructions of equivalent quality to compressed sensing with 40% fewer projections. We further show that diverse training data classes, for example, ex vivo mouse tissue data, can be used for CNN-based reconstructions of OPT data of other species including live zebrafish.
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Affiliation(s)
| | - Sunil Kumar
- Department of PhysicsImperial College LondonLondonUK
- The Francis Crick InstituteLondonUK
| | - Yuriy Alexandrov
- Department of PhysicsImperial College LondonLondonUK
- The Francis Crick InstituteLondonUK
| | | | - Gabriela da Silva Xavier
- Department of MedicineImperial College LondonLondonUK
- Institute of Metabolism and Systems ResearchUniversity of BirminghamBirminghamUK
| | - Guy A. Rutter
- Department of MedicineImperial College LondonLondonUK
| | - Paul Frankel
- Division of MedicineUniversity College LondonLondonUK
| | | | - Seth Flaxman
- Department of Mathematics and Data Science InstituteImperial College LondonLondonUK
| | - Paul M. W. French
- Department of PhysicsImperial College LondonLondonUK
- The Francis Crick InstituteLondonUK
| | - James McGinty
- Department of PhysicsImperial College LondonLondonUK
- The Francis Crick InstituteLondonUK
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15
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Koskela O, Montonen T, Belay B, Figueiras E, Pursiainen S, Hyttinen J. Gaussian Light Model in Brightfield Optical Projection Tomography. Sci Rep 2019; 9:13934. [PMID: 31558755 PMCID: PMC6763473 DOI: 10.1038/s41598-019-50469-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 01/27/2023] Open
Abstract
This study focuses on improving the reconstruction process of the brightfield optical projection tomography (OPT). OPT is often described as the optical equivalent of X-ray computed tomography, but based on visible light. The detection optics used to collect light in OPT focus on a certain distance and induce blurring in those features out of focus. However, the conventionally used inverse Radon transform assumes an absolute focus throughout the propagation axis. In this study, we model the focusing properties of the detection by coupling Gaussian beam model (GBM) with the Radon transform. The GBM enables the construction of a projection operator that includes modeling of the blurring caused by the light beam. We also introduce the concept of a stretched GBM (SGBM) in which the Gaussian beam is scaled in order to avoid the modeling errors related to the determination of the focal plane. Furthermore, a thresholding approach is used to compress memory usage. We tested the GBM and SGBM approaches using simulated and experimental data in mono- and multifocal modes. When compared with the traditionally used filtered backprojection algorithm, the iteratively computed reconstructions, including the Gaussian models GBM and SGBM, provided smoother images with higher contrast.
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Affiliation(s)
- Olli Koskela
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland.
- HAMK Smart Research Unit, Häme University of Applied Sciences, Hämeenlinna, 13100, Finland.
| | - Toni Montonen
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
| | - Birhanu Belay
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
| | - Edite Figueiras
- Champalimaud Research, Champalimaud Foundation, Lisbon, 1400-038, Portugal
| | - Sampsa Pursiainen
- Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, 33014, Finland
| | - Jari Hyttinen
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
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16
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Abstract
When neuroscience’s focus moves from molecular and cellular level to systems level, information technology mixes in and cultivates a new branch neuroinformatics. Especially under the investments of brain initiatives all around the world, brain atlases and connectomics are identified as the substructure to understand the brain. We think it is time to call for a potential interdisciplinary subject, brainsmatics, referring to brain-wide spatial informatics science and emphasizing on precise positioning information affiliated to brain-wide connectome, genome, proteome, transcriptome, metabolome, etc. Brainsmatics methodology includes tracing, surveying, visualizing, and analyzing brain-wide spatial information. Among all imaging techniques, optical imaging is the most appropriate solution to achieve whole-brain connectome in consistent single-neuron resolution. This review aims to introduce contributions of optical imaging to brainsmatics studies, especially the major strategies applied in tracing and surveying processes. After discussions on the state-of-the-art technology, the development objectives of optical imaging in brainsmatics field are suggested. We call for a global contribution to the brainsmatics field from all related communities such as neuroscientists, biologists, engineers, programmers, chemists, mathematicians, physicists, clinicians, pharmacists, etc. As the leading approach, optical imaging will, in turn, benefit from the prosperous development of brainsmatics.
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17
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Nguyen D, Uhlmann V, Planchette AL, Marchand PJ, Van De Ville D, Lasser T, Radenovic A. Supervised learning to quantify amyloidosis in whole brains of an Alzheimer's disease mouse model acquired with optical projection tomography. BIOMEDICAL OPTICS EXPRESS 2019; 10:3041-3060. [PMID: 31259073 PMCID: PMC6583328 DOI: 10.1364/boe.10.003041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/19/2019] [Accepted: 05/19/2019] [Indexed: 05/14/2023]
Abstract
Alzheimer's disease (AD) is characterized by amyloidosis of brain tissues. This phenomenon is studied with genetically-modified mouse models. We propose a method to quantify amyloidosis in whole 5xFAD mouse brains, a model of AD. We use optical projection tomography (OPT) and a random forest voxel classifier to segment and measure amyloid plaques. We validate our method in a preliminary cross-sectional study, where we measure 6136 ± 1637, 8477 ± 3438, and 17267 ± 4241 plaques (AVG ± SD) at 11, 17, and 31 weeks. Overall, this method can be used in the evaluation of new treatments against AD.
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Affiliation(s)
- David Nguyen
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
- Medical Image Processing Lab, École Polytechnique Fédérale de Lausanne, Genève, Genève,
Switzerland
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Virginie Uhlmann
- Biomedical Imaging Group, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
- European Bioinformatics Institute, EMBL-EBI, Cambridge,
United Kingdom
| | - Arielle L. Planchette
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Paul J. Marchand
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Dimitri Van De Ville
- Medical Image Processing Lab, École Polytechnique Fédérale de Lausanne, Genève, Genève,
Switzerland
- Department of Radiology and Medical Informatics, University of Geneva, Genève, Genève,
Switzerland
| | - Theo Lasser
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, École Polytechnique Fédérale de Lausanne, Lausanne, Vaud,
Switzerland
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18
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Kim YY, Chao JR, Kim C, Jung H, Kim B, Kang TC, Chang J, Park HS, Suh JG, Lee JH. Comparing the Superficial Vasculature of the Central Nervous System in Six Laboratory Animals: A Hypothesis About the Role of the "Circle of Willis". Anat Rec (Hoboken) 2019; 302:2049-2061. [PMID: 31087813 DOI: 10.1002/ar.24146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 03/05/2019] [Accepted: 03/23/2019] [Indexed: 11/08/2022]
Abstract
We provide images of the entire central nervous system vasculature, and compare the anatomical findings in six different laboratory animals. A detailed understanding of the specific anatomy for each is important in the design of experimental modeling and for understanding the specific function of each target organ. Six different types of animals, the Korean wild mouse, C57BL/6J mouse, F344 rat, mongolian gerbil, Syrian hamsters, and guinea pigs, were included. To stain the blood vessels in each of the animals, Alcian blue reagent was used to perfuse each species. The bifurcation and anastomotic patterns of the anterior cerebral arteries differed in each species. The vascular supply to the olfactory nerve was visualized as a single artery supplying both olfactory nerves, and arteries supplying the lateral portion of the olfactory nerves originating from the olfactory bulb area. The posterior communicating arteries of the six animals demonstrated unique morphologies. The shape of the hypophyseal portal system varied by species. Most animals used in this study had a hexagonal Circle of Willis, except for the Korean wild mouse. Using this approach, we successfully mapped the brain vascular system in six different species of animals. This information and the images created can guide other researchers as they design research studies and create experimental models for new surgical procedures and approaches. Anat Rec, 2019. © 2019 Wiley Periodicals, Inc. Anat Rec, 302:2049-2061, 2019. © 2019 American Association for Anatomy.
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Affiliation(s)
- Yoo Yeon Kim
- Department of Medical Genetics, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Janet Ren Chao
- Department of Surgery, Division of Otolaryngology, Yale School of Medicine, New Haven, Connecticut
| | - Chulho Kim
- Department of Neurology, Chuncheon Sacred Heart Hospital, Hallym University, Chuncheon, Republic of Korea
| | - Harry Jung
- Institute of New Frontier Research, Hallym University College of Medicine, Chuncheon, Republic of Korea
| | - Boyoung Kim
- Department of Medical Genetics, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Tae-Cheon Kang
- Department of Anatomy and Neurobiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jiwon Chang
- Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Hae Sang Park
- Institute of New Frontier Research, Hallym University College of Medicine, Chuncheon, Republic of Korea.,Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jun-Gyo Suh
- Department of Medical Genetics, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Jun Ho Lee
- Institute of New Frontier Research, Hallym University College of Medicine, Chuncheon, Republic of Korea.,Department of Otorhinolaryngology-Head and Neck Surgery, College of Medicine, Hallym University, Chuncheon, Republic of Korea
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19
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Abstract
The global population is ageing at an accelerating speed. The ability to perform working memory tasks together with rapid processing becomes increasingly difficult with increases in age. With increasing national average life spans and a rise in the prevalence of age-related disease, it is pertinent to discuss the unique perspectives that can be gained from imaging the aged brain. Differences in structure, function, blood flow, and neurovascular coupling are present in both healthy aged brains and in diseased brains and have not yet been explored to their full depth in contemporary imaging studies. Imaging methods ranging from optical imaging to magnetic resonance imaging (MRI) to newer technologies such as photoacoustic tomography each offer unique advantages and challenges in imaging the aged brain. This paper will summarize first the importance and challenges of imaging the aged brain and then offer analysis of potential imaging modalities and their representative applications. The potential breakthroughs in brain imaging are also envisioned.
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Affiliation(s)
- Hannah Humayun
- Photoacoustic Imaging Laboratory, Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Junjie Yao
- Photoacoustic Imaging Laboratory, Department of Biomedical Engineering, Duke University, Durham, NC, USA
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20
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Dou S, Liu J, Yang L. Dual-modality optical projection tomography reconstruction method from fewer views. JOURNAL OF BIOPHOTONICS 2019; 12:e201800407. [PMID: 30578626 DOI: 10.1002/jbio.201800407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
In optical projection tomography (OPT), for longitudinal living model studies, multiple measurements of the same sample are required at different time points. It is important to decrease both the total acquisition time and the light dose to the sample. We improved the ordered subsets expectation maximization reconstruction algorithm for OPT, which reduces the acquisition time and number of projections greatly compared with filtered back projection (FBP), and obtained satisfactory reconstructed images. Using zebrafish, in transmission and fluorescence mode, we demonstrate the capability of the method to reconstruct image from downsampled projection subsets. The result shows that the reconstruction image quality of the proposed method using 30 projections is comparable to that of FBP using 720 projections. The total acquisition procedure can be finished in a few seconds. The method also provides OPT with the remarkable capability to resist noises and artifacts. Projection image and fused image of zebrafish.
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Affiliation(s)
- Shaobin Dou
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, China
| | - Jinhuai Liu
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, China
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21
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Upputuri PK, Pramanik M. Photoacoustic imaging in the second near-infrared window: a review. JOURNAL OF BIOMEDICAL OPTICS 2019; 24:1-20. [PMID: 30968648 PMCID: PMC6990072 DOI: 10.1117/1.jbo.24.4.040901] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/18/2019] [Indexed: 05/04/2023]
Abstract
Photoacoustic (PA) imaging is an emerging medical imaging modality that combines optical excitation and ultrasound detection. Because ultrasound scatters much less than light in biological tissues, PA generates high-resolution images at centimeters depth. In recent years, wavelengths in the second near-infrared (NIR-II) window (1000 to 1700 nm) have been increasingly explored due to its potential for preclinical and clinical applications. In contrast to the conventional PA imaging in the visible (400 to 700 nm) and the first NIR-I (700 to 1000 nm) window, PA imaging in the NIR-II window offers numerous advantages, including high spatial resolution, deeper penetration depth, reduced optical absorption, and tissue scattering. Moreover, the second window allows a fivefold higher light excitation energy density compared to the visible window for enhancing the imaging depth significantly. We highlight the importance of the second window for PA imaging and discuss the various NIR-II PA imaging systems and contrast agents with strong absorption in the NIR-II spectral region. Numerous applications of NIR-II PA imaging, including whole-body animal imaging and human imaging, are also discussed.
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Affiliation(s)
- Paul Kumar Upputuri
- Nanyang Technological University, School of Chemical and Biomedical Engineering, Singapore
| | - Manojit Pramanik
- Nanyang Technological University, School of Chemical and Biomedical Engineering, Singapore
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