1
|
Nikitin V, Wildenberg G, Mittone A, Shevchenko P, Deriy A, De Carlo F. Laminography as a tool for imaging large-size samples with high resolution. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:851-866. [PMID: 38771775 PMCID: PMC11226144 DOI: 10.1107/s1600577524002923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/03/2024] [Indexed: 05/23/2024]
Abstract
Despite the increased brilliance of the new generation synchrotron sources, there is still a challenge with high-resolution scanning of very thick and absorbing samples, such as a whole mouse brain stained with heavy elements, and, extending further, brains of primates. Samples are typically cut into smaller parts, to ensure a sufficient X-ray transmission, and scanned separately. Compared with the standard tomography setup where the sample would be cut into many pillars, the laminographic geometry operates with slab-shaped sections significantly reducing the number of sample parts to be prepared, the cutting damage and data stitching problems. In this work, a laminography pipeline for imaging large samples (>1 cm) at micrometre resolution is presented. The implementation includes a low-cost instrument setup installed at the 2-BM micro-CT beamline of the Advanced Photon Source. Additionally, sample mounting, scanning techniques, data stitching procedures, a fast reconstruction algorithm with low computational complexity, and accelerated reconstruction on multi-GPU systems for processing large-scale datasets are presented. The applicability of the whole laminography pipeline was demonstrated by imaging four sequential slabs throughout an entire mouse brain sample stained with osmium, in total generating approximately 12 TB of raw data for reconstruction.
Collapse
Affiliation(s)
- Viktor Nikitin
- Advanced Photon SourceArgonne National LaboratoryLemontIL60439USA
| | | | - Alberto Mittone
- Advanced Photon SourceArgonne National LaboratoryLemontIL60439USA
| | - Pavel Shevchenko
- Advanced Photon SourceArgonne National LaboratoryLemontIL60439USA
| | - Alex Deriy
- Advanced Photon SourceArgonne National LaboratoryLemontIL60439USA
| | | |
Collapse
|
2
|
Imenez Silva PH, Pepin M, Figurek A, Gutiérrez-Jiménez E, Bobot M, Iervolino A, Mattace-Raso F, Hoorn EJ, Bailey MA, Hénaut L, Nielsen R, Frische S, Trepiccione F, Hafez G, Altunkaynak HO, Endlich N, Unwin R, Capasso G, Pesic V, Massy Z, Wagner CA. Animal models to study cognitive impairment of chronic kidney disease. Am J Physiol Renal Physiol 2024; 326:F894-F916. [PMID: 38634137 DOI: 10.1152/ajprenal.00338.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/11/2024] [Accepted: 04/04/2024] [Indexed: 04/19/2024] Open
Abstract
Mild cognitive impairment (MCI) is common in people with chronic kidney disease (CKD), and its prevalence increases with progressive loss of kidney function. MCI is characterized by a decline in cognitive performance greater than expected for an individual age and education level but with minimal impairment of instrumental activities of daily living. Deterioration can affect one or several cognitive domains (attention, memory, executive functions, language, and perceptual motor or social cognition). Given the increasing prevalence of kidney disease, more and more people with CKD will also develop MCI causing an enormous disease burden for these individuals, their relatives, and society. However, the underlying pathomechanisms are poorly understood, and current therapies mostly aim at supporting patients in their daily lives. This illustrates the urgent need to elucidate the pathogenesis and potential therapeutic targets and test novel therapies in appropriate preclinical models. Here, we will outline the necessary criteria for experimental modeling of cognitive disorders in CKD. We discuss the use of mice, rats, and zebrafish as model systems and present valuable techniques through which kidney function and cognitive impairment can be assessed in this setting. Our objective is to enable researchers to overcome hurdles and accelerate preclinical research aimed at improving the therapy of people with CKD and MCI.
Collapse
Affiliation(s)
- Pedro H Imenez Silva
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Marion Pepin
- Institut National de la Santé et de la Recherche Médicale U-1018 Centre de Recherche en Épidémiologie et Santé des Population, Équipe 5, Paris-Saclay University, Versailles Saint-Quentin-en-Yvelines University, Villejuif, France
- Department of Geriatrics, Centre Hospitalier Universitaire Ambroise Paré, Assistance Publique-Hôpitaux de Paris Université Paris-Saclay, Paris, France
| | - Andreja Figurek
- Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Eugenio Gutiérrez-Jiménez
- Center for Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Mickaël Bobot
- Centre de Néphrologie et Transplantation Rénale, Hôpital de la Conception, Assistance Publique-Hopitaux de Marseille, and INSERM 1263, Institut National de la Recherche Agronomique 1260, C2VN, Aix-Marseille Universitaire, Marseille, France
| | - Anna Iervolino
- Department of Translational Medical Sciences, University of Campania 'Luigi Vanvitelli,' Naples, Italy
| | - Francesco Mattace-Raso
- Division of Geriatrics, Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ewout J Hoorn
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus Medical Center, University Medical Center, Rotterdam, The Netherlands
| | - Matthew A Bailey
- Edinburgh Kidney, Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, United Kingdom
| | - Lucie Hénaut
- UR UPJV 7517, Jules Verne University of Picardie, Amiens, France
| | - Rikke Nielsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Francesco Trepiccione
- Department of Translational Medical Sciences, University of Campania 'Luigi Vanvitelli,' Naples, Italy
| | - Gaye Hafez
- Department of Pharmacology, Faculty of Pharmacy, Altinbas University, Istanbul, Turkey
| | - Hande O Altunkaynak
- Department of Pharmacology, Gulhane Faculty of Pharmacy, University of Health Sciences, Istanbul, Turkey
| | - Nicole Endlich
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Robert Unwin
- Department of Renal Medicine, Royal Free Hospital, University College London, London, United Kingdom
| | - Giovambattista Capasso
- Department of Translational Medical Sciences, University of Campania 'Luigi Vanvitelli,' Naples, Italy
- Biogem Research Institute, Ariano Irpino, Italy
| | - Vesna Pesic
- Department of Physiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Ziad Massy
- Centre for Research in Epidemiology and Population Health, INSERM UMRS 1018, Clinical Epidemiology Team, University Paris-Saclay, University Versailles-Saint Quentin, Villejuif, France
- Department of Nephrology, Centre Hospitalier Universitaire Ambroise Paré, Assistance Publique-Hôpitaux de Paris Université Paris-Saclay, Paris, France
| | - Carsten A Wagner
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| |
Collapse
|
3
|
Reichmann J, Sarrazin C, Schmale S, Blaurock C, Balkema-Buschmann A, Schmitzer B, Salditt T. 3D imaging of SARS-CoV-2 infected hamster lungs by X-ray phase contrast tomography enables drug testing. Sci Rep 2024; 14:12348. [PMID: 38811688 PMCID: PMC11137149 DOI: 10.1038/s41598-024-61746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
X-ray Phase Contrast Tomography (XPCT) based on wavefield propagation has been established as a high resolution three-dimensional (3D) imaging modality, suitable to reconstruct the intricate structure of soft tissues, and the corresponding pathological alterations. However, for biomedical research, more is needed than 3D visualisation and rendering of the cytoarchitecture in a few selected cases. First, the throughput needs to be increased to cover a statistically relevant number of samples. Second, the cytoarchitecture has to be quantified in terms of morphometric parameters, independent of visual impression. Third, dimensionality reduction and classification are required for identification of effects and interpretation of results. To address these challenges, we here design and implement a novel integrated and high throughput XPCT imaging and analysis workflow for 3D histology, pathohistology and drug testing. Our approach uses semi-automated data acquisition, reconstruction and statistical quantification. We demonstrate its capability for the example of lung pathohistology in Covid-19. Using a small animal model, different Covid-19 drug candidates are administered after infection and tested in view of restoration of the physiological cytoarchitecture, specifically the alveolar morphology. To this end, we then use morphometric parameter determination followed by a dimensionality reduction and classification based on optimal transport. This approach allows efficient discrimination between physiological and pathological lung structure, thereby providing quantitative insights into the pathological progression and partial recovery due to drug treatment. Finally, we stress that the XPCT image chain implemented here only used synchrotron radiation for validation, while the data used for analysis was recorded with laboratory μ CT radiation, more easily accessible for pre-clinical research.
Collapse
Affiliation(s)
- Jakob Reichmann
- Georg-August-University of Göttingen, Institute for X-Ray Physics, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany
| | - Clement Sarrazin
- Georg-August-University of Göttingen, Institute of Computer Science, Goldschmidtstraße 7, 37077, Göttingen, Germany
- Equipe RAPSODI, Centre INRIA de l'université de Lille, F-59000, Lille, France
| | - Sebastian Schmale
- Georg-August-University of Göttingen, Institute of Computer Science, Goldschmidtstraße 7, 37077, Göttingen, Germany
| | - Claudia Blaurock
- Friedrich-Loeffler-Institute, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | | | - Bernhard Schmitzer
- Georg-August-University of Göttingen, Institute of Computer Science, Goldschmidtstraße 7, 37077, Göttingen, Germany.
| | - Tim Salditt
- Georg-August-University of Göttingen, Institute for X-Ray Physics, Friedrich-Hund-Platz 1, 37077, Göttingen, Germany.
| |
Collapse
|
4
|
Paukner D, Wildenberg GA, Badalamente GS, Littlewood PB, Kronforst MR, Palmer SE, Kasthuri N. Synchrotron-source micro-x-ray computed tomography for examining butterfly eyes. Ecol Evol 2024; 14:e11137. [PMID: 38571794 PMCID: PMC10985371 DOI: 10.1002/ece3.11137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 11/30/2023] [Accepted: 01/09/2024] [Indexed: 04/05/2024] Open
Abstract
Comparative anatomy is an important tool for investigating evolutionary relationships among species, but the lack of scalable imaging tools and stains for rapidly mapping the microscale anatomies of related species poses a major impediment to using comparative anatomy approaches for identifying evolutionary adaptations. We describe a method using synchrotron source micro-x-ray computed tomography (syn-μXCT) combined with machine learning algorithms for high-throughput imaging of Lepidoptera (i.e., butterfly and moth) eyes. Our pipeline allows for imaging at rates of ~15 min/mm3 at 600 nm3 resolution. Image contrast is generated using standard electron microscopy labeling approaches (e.g., osmium tetroxide) that unbiasedly labels all cellular membranes in a species-independent manner thus removing any barrier to imaging any species of interest. To demonstrate the power of the method, we analyzed the 3D morphologies of butterfly crystalline cones, a part of the visual system associated with acuity and sensitivity and found significant variation within six butterfly individuals. Despite this variation, a classic measure of optimization, the ratio of interommatidial angle to resolving power of ommatidia, largely agrees with early work on eye geometry across species. We show that this method can successfully be used to determine compound eye organization and crystalline cone morphology. Our novel pipeline provides for fast, scalable visualization and analysis of eye anatomies that can be applied to any arthropod species, enabling new questions about evolutionary adaptations of compound eyes and beyond.
Collapse
Affiliation(s)
- Dawn Paukner
- Department of NeurobiologyUniversity of ChicagoChicagoIllinoisUSA
- Argonne National LaboratoryLemontIllinoisUSA
- Department of Organismal Biology and AnatomyUniversity of ChicagoChicagoIllinoisUSA
| | - Gregg A. Wildenberg
- Department of NeurobiologyUniversity of ChicagoChicagoIllinoisUSA
- Argonne National LaboratoryLemontIllinoisUSA
| | - Griffin S. Badalamente
- Department of NeurobiologyUniversity of ChicagoChicagoIllinoisUSA
- Department of ZoologyThe Old Schools, University of CambridgeCambridgeUK
| | | | | | - Stephanie E. Palmer
- Department of Organismal Biology and AnatomyUniversity of ChicagoChicagoIllinoisUSA
- Department of PhysicsUniversity of ChicagoChicagoIllinoisUSA
| | - Narayanan Kasthuri
- Department of NeurobiologyUniversity of ChicagoChicagoIllinoisUSA
- Argonne National LaboratoryLemontIllinoisUSA
| |
Collapse
|
5
|
Liu Z, Zhu Y, Zhang L, Jiang W, Liu Y, Tang Q, Cai X, Li J, Wang L, Tao C, Yin X, Li X, Hou S, Jiang D, Liu K, Zhou X, Zhang H, Liu M, Fan C, Tian Y. Structural and functional imaging of brains. Sci China Chem 2022; 66:324-366. [PMID: 36536633 PMCID: PMC9753096 DOI: 10.1007/s11426-022-1408-5] [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] [Received: 07/27/2022] [Accepted: 09/28/2022] [Indexed: 12/23/2022]
Abstract
Analyzing the complex structures and functions of brain is the key issue to understanding the physiological and pathological processes. Although neuronal morphology and local distribution of neurons/blood vessels in the brain have been known, the subcellular structures of cells remain challenging, especially in the live brain. In addition, the complicated brain functions involve numerous functional molecules, but the concentrations, distributions and interactions of these molecules in the brain are still poorly understood. In this review, frontier techniques available for multiscale structure imaging from organelles to the whole brain are first overviewed, including magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), serial-section electron microscopy (ssEM), light microscopy (LM) and synchrotron-based X-ray microscopy (XRM). Specially, XRM for three-dimensional (3D) imaging of large-scale brain tissue with high resolution and fast imaging speed is highlighted. Additionally, the development of elegant methods for acquisition of brain functions from electrical/chemical signals in the brain is outlined. In particular, the new electrophysiology technologies for neural recordings at the single-neuron level and in the brain are also summarized. We also focus on the construction of electrochemical probes based on dual-recognition strategy and surface/interface chemistry for determination of chemical species in the brain with high selectivity and long-term stability, as well as electrochemophysiological microarray for simultaneously recording of electrochemical and electrophysiological signals in the brain. Moreover, the recent development of brain MRI probes with high contrast-to-noise ratio (CNR) and sensitivity based on hyperpolarized techniques and multi-nuclear chemistry is introduced. Furthermore, multiple optical probes and instruments, especially the optophysiological Raman probes and fiber Raman photometry, for imaging and biosensing in live brain are emphasized. Finally, a brief perspective on existing challenges and further research development is provided.
Collapse
Affiliation(s)
- Zhichao Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Ying Zhu
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Liming Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Weiping Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Yawei Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
| | - Qiaowei Tang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Xiaoqing Cai
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Jiang Li
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Lihua Wang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Changlu Tao
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | | | - Xiaowei Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shangguo Hou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055 China
| | - Dawei Jiang
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| |
Collapse
|
6
|
Abstract
Fluorescence microscopy is a highly effective tool for interrogating biological structure and function, particularly when imaging across multiple spatiotemporal scales. Here we survey recent innovations and applications in the relatively understudied area of multiscale fluorescence imaging of living samples. We discuss fundamental challenges in live multiscale imaging and describe successful examples that highlight the power of this approach. We attempt to synthesize general strategies from these test cases, aiming to help accelerate progress in this exciting area.
Collapse
Affiliation(s)
- Yicong Wu
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Hari Shroff
- Laboratory of High-Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| |
Collapse
|
7
|
Poeta LS, Ordóñez MP, Fournier E, Nelson AJ. Correlative tomography and authentication features of a shrunken head (tsantsa). PLoS One 2022; 17:e0270305. [PMID: 35921270 PMCID: PMC9348654 DOI: 10.1371/journal.pone.0270305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Museum personnel and the general public have become quite familiar with the presence of shrunken heads in museum collections, but the procedures to authenticate the history and origin of these unique cultural items are not yet reliable. These shrunken heads, called tsantsas, are meant to be the cultural material remains of ceremonies conducted by the Shuar and Achuar Peoples of South America. This project seeks to integrate the use of micro-computed tomography (micro-CT) scanning with methods used in previous studies (clinical computed tomography (CT) and visual inspections) to examine authentication procedures of shrunken heads (tsantsas) held in contemporary museum collections. We use a correlative tomographic approach using several scans at successively higher resolutions to determine whether a tsantsa was created from human remains, and if so, what key features can best contribute to its authentication. Conclusively, our correlative tomographic approaches provide new insights into the determination process of whether a tsantsa was created from real human remains or not. Also, this study questions whether the previously conceptualized dichotomy of ceremonial or commercial might be better thought of as a continuum of practice. Investigating and redefining the examination and authentication procedures of tsantsas is crucial for future ethical curation, management, and repatriation efforts of this unique cultural material of the Shuar and Achuar Peoples.
Collapse
Affiliation(s)
| | - Maria Patricia Ordóñez
- Colegio de Ciencias Sociales y Humanidades, Universidad San Fransisco de Quito, Quito, Ecuador
| | | | | |
Collapse
|
8
|
Bosch C, Ackels T, Pacureanu A, Zhang Y, Peddie CJ, Berning M, Rzepka N, Zdora MC, Whiteley I, Storm M, Bonnin A, Rau C, Margrie T, Collinson L, Schaefer AT. Functional and multiscale 3D structural investigation of brain tissue through correlative in vivo physiology, synchrotron microtomography and volume electron microscopy. Nat Commun 2022; 13:2923. [PMID: 35614048 PMCID: PMC9132960 DOI: 10.1038/s41467-022-30199-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Understanding the function of biological tissues requires a coordinated study of physiology and structure, exploring volumes that contain complete functional units at a detail that resolves the relevant features. Here, we introduce an approach to address this challenge: Mouse brain tissue sections containing a region where function was recorded using in vivo 2-photon calcium imaging were stained, dehydrated, resin-embedded and imaged with synchrotron X-ray computed tomography with propagation-based phase contrast (SXRT). SXRT provided context at subcellular detail, and could be followed by targeted acquisition of multiple volumes using serial block-face electron microscopy (SBEM). In the olfactory bulb, combining SXRT and SBEM enabled disambiguation of in vivo-assigned regions of interest. In the hippocampus, we found that superficial pyramidal neurons in CA1a displayed a larger density of spine apparati than deeper ones. Altogether, this approach can enable a functional and structural investigation of subcellular features in the context of cells and tissues.
Collapse
Affiliation(s)
- Carles Bosch
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK.
| | - Tobias Ackels
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
| | - Alexandra Pacureanu
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
- ESRF, The European Synchrotron, Grenoble, France
| | - Yuxin Zhang
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
| | | | - Manuel Berning
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt am Main, Germany
- Scalable minds GmbH, Potsdam, Germany
| | | | - Marie-Christine Zdora
- Department of Physics and Astronomy, University College London, London, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- School of Physics and Astronomy, University of Southampton, Highfield Campus, Southampton, UK
| | - Isabell Whiteley
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
| | - Malte Storm
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Institute of Materials Physics, Helmholtz-Zentrum Hereon, Geesthacht, Germany
| | - Anne Bonnin
- Paul Scherrer Institut, Villigen, Switzerland
| | - Christoph Rau
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Troy Margrie
- Sainsbury Wellcome Centre, University College London, London, UK
| | - Lucy Collinson
- Electron Microscopy STP, The Francis Crick Institute, London, UK
| | - Andreas T Schaefer
- Sensory Circuits and Neurotechnology Lab., The Francis Crick Institute, London, UK.
- Department of Neuroscience, Physiology and Pharmacology, University College, London, UK.
| |
Collapse
|
9
|
Rodgers G, Tanner C, Schulz G, Migga A, Kuo W, Bikis C, Scheel M, Kurtcuoglu V, Weitkamp T, Müller B. Virtual histology of an entire mouse brain from formalin fixation to paraffin embedding. Part 2: Volumetric strain fields and local contrast changes. J Neurosci Methods 2022; 365:109385. [PMID: 34637810 DOI: 10.1016/j.jneumeth.2021.109385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/07/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Fixation and embedding of post mortem brain tissue is a pre-requisite for both gold-standard conventional histology and X-ray virtual histology. This process alters the morphology and density of the brain microanatomy. NEW METHOD To quantify these changes, we employed synchrotron radiation-based hard X-ray tomography with 3 μm voxel length to visualize the same mouse brain after fixation in 4% formalin, immersion in ethanol solutions (50%, 70%, 80%, 90%, and 100%), xylene, and finally after embedding in a paraffin block. The volumetric data were non-rigidly registered to the initial formalin-fixed state to align the microanatomy within the entire mouse brain. RESULTS Volumetric strain fields were used to characterize local shrinkage, which was found to depend on the anatomical region and distance to external surface. X-ray contrast was altered and enhanced by preparation-induced inter-tissue density changes. The preparation step can be selected to highlight specific anatomical features. For example, fiber tract contrast is amplified in 100% ethanol. COMPARISON WITH EXISTING METHODS Our method provides volumetric strain fields, unlike approaches based on feature-to-feature or volume measurements. Volumetric strain fields are produced by non-rigid registration, which is less labor-intensive and observer-dependent than volume change measurements based on manual segmentations. X-ray microtomography provides spatial resolution at least an order of magnitude higher than magnetic resonance microscopy, allowing for analysis of morphology and density changes within the brain's microanatomy. CONCLUSION Our approach belongs to three-dimensional virtual histology with isotropic micrometer spatial resolution and therefore complements atlases based on a combination of magnetic resonance microscopy and optical micrographs of serial histological sections.
Collapse
Affiliation(s)
- Griffin Rodgers
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Christine Tanner
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland.
| | - Georg Schulz
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Alexandra Migga
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| | - Willy Kuo
- The Interface Group, Institute of Physiology, University of Zurich, 8057 Zurich, Switzerland; National Centre of Competence in Research, Kidney.CH, 8057 Zurich, Switzerland
| | - Christos Bikis
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland; Integrierte Psychiatrie Winterthur - Zürcher Unterland, 8408 Winterthur, Switzerland
| | - Mario Scheel
- Synchrotron Soleil, 91192 Gif-sur-Yvette, France
| | - Vartan Kurtcuoglu
- The Interface Group, Institute of Physiology, University of Zurich, 8057 Zurich, Switzerland; National Centre of Competence in Research, Kidney.CH, 8057 Zurich, Switzerland
| | | | - Bert Müller
- Biomaterials Science Center, Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland; Biomaterials Science Center, Department of Clinical Research, University Hospital Basel, 4031 Basel, Switzerland
| |
Collapse
|
10
|
Quesada J, Sathidevi L, Liu R, Ahad N, Jackson JM, Azabou M, Xiao J, Liding C, Jin M, Urzay C, Gray-Roncal W, Johnson EC, Dyer EL. MTNeuro: A Benchmark for Evaluating Representations of Brain Structure Across Multiple Levels of Abstraction. ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 2022; 35:5299-5314. [PMID: 38414814 PMCID: PMC10898440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
There are multiple scales of abstraction from which we can describe the same image, depending on whether we are focusing on fine-grained details or a more global attribute of the image. In brain mapping, learning to automatically parse images to build representations of both small-scale features (e.g., the presence of cells or blood vessels) and global properties of an image (e.g., which brain region the image comes from) is a crucial and open challenge. However, most existing datasets and benchmarks for neuroanatomy consider only a single downstream task at a time. To bridge this gap, we introduce a new dataset, annotations, and multiple downstream tasks that provide diverse ways to readout information about brain structure and architecture from the same image. Our multi-task neuroimaging benchmark (MTNeuro) is built on volumetric, micrometer-resolution X-ray microtomography images spanning a large thalamocortical section of mouse brain, encompassing multiple cortical and subcortical regions. We generated a number of different prediction challenges and evaluated several supervised and self-supervised models for brain-region prediction and pixel-level semantic segmentation of microstructures. Our experiments not only highlight the rich heterogeneity of this dataset, but also provide insights into how self-supervised approaches can be used to learn representations that capture multiple attributes of a single image and perform well on a variety of downstream tasks. Datasets, code, and pre-trained baseline models are provided at: https://mtneuro.github.io/.
Collapse
Affiliation(s)
| | | | - Ran Liu
- Georgia Institute of Technology
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|