1
|
Catanese J, Murakami T, Kenny PJ, Ibanez-Tallon I. Precise 3D Localization of Intracerebral Implants with a simple Brain Clearing Method. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.22.573088. [PMID: 38187775 PMCID: PMC10769389 DOI: 10.1101/2023.12.22.573088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Determining the localization of intracerebral implants in rodent brain stands as a critical final step in most physiological and behaviroral studies, especially when targeting deep brain nuclei. Conventional histological approaches, reliant on manual estimation through sectioning and slice examination, are error-prone, potentially complicating data interpretation. Leveraging recent advances in tissue-clearing techniques and light-sheet fluorescence microscopy, we introduce a method enabling virtual brain slicing in any orientation, offering precise implant localization without the limitations of traditional tissue sectioning. To illustrate the method's utility, we present findings from the implantation of linear silicon probes into the midbrain interpeduncular nucleus (IPN) of anesthetized transgenic mice expressing chanelrhodopsin-2 and enhanced yellow fluorescent protein under the choline acetyltransferase (ChAT) promoter/enhancer regions (ChAT-Chr2-EYFP mice). Utilizing a fluorescent dye applied to the electrode surface, we visualized both the targeted area and the precise localization, enabling enhanced inter-subject comparisons. Three dimensional (3D) brain renderings, presented effortlessly in video format across various orientations, showcase the versatility of this approach.
Collapse
|
2
|
Mizes KGC, Lindsey J, Escola GS, Ölveczky BP. Dissociating the contributions of sensorimotor striatum to automatic and visually guided motor sequences. Nat Neurosci 2023; 26:1791-1804. [PMID: 37667040 PMCID: PMC11187818 DOI: 10.1038/s41593-023-01431-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/14/2023] [Indexed: 09/06/2023]
Abstract
The ability to sequence movements in response to new task demands enables rich and adaptive behavior. However, such flexibility is computationally costly and can result in halting performances. Practicing the same motor sequence repeatedly can render its execution precise, fast and effortless, that is, 'automatic'. The basal ganglia are thought to underlie both types of sequence execution, yet whether and how their contributions differ is unclear. We parse this in rats trained to perform the same motor sequence instructed by cues and in a self-initiated overtrained, or 'automatic,' condition. Neural recordings in the sensorimotor striatum revealed a kinematic code independent of the execution mode. Although lesions reduced the movement speed and affected detailed kinematics similarly, they disrupted high-level sequence structure for automatic, but not visually guided, behaviors. These results suggest that the basal ganglia are essential for 'automatic' motor skills that are defined in terms of continuous kinematics, but can be dispensable for discrete motor sequences guided by sensory cues.
Collapse
Affiliation(s)
- Kevin G C Mizes
- Program in Biophysics, Harvard University, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jack Lindsey
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York City, NY, USA
| | - G Sean Escola
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York City, NY, USA
- Department of Psychiatry, Columbia University, New York City, NY, USA
| | - Bence P Ölveczky
- Department of Organismic and Evolutionary Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
3
|
Mizes KGC, Lindsey J, Escola GS, Ölveczky BP. Motor cortex is required for flexible but not automatic motor sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.05.556348. [PMID: 37732225 PMCID: PMC10508748 DOI: 10.1101/2023.09.05.556348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
How motor cortex contributes to motor sequence execution is much debated, with studies supporting disparate views. Here we probe the degree to which motor cortex's engagement depends on task demands, specifically whether its role differs for highly practiced, or 'automatic', sequences versus flexible sequences informed by external events. To test this, we trained rats to generate three-element motor sequences either by overtraining them on a single sequence or by having them follow instructive visual cues. Lesioning motor cortex revealed that it is necessary for flexible cue-driven motor sequences but dispensable for single automatic behaviors trained in isolation. However, when an automatic motor sequence was practiced alongside the flexible task, it became motor cortex-dependent, suggesting that subcortical consolidation of an automatic motor sequence is delayed or prevented when the same sequence is produced also in a flexible context. A simple neural network model recapitulated these results and explained the underlying circuit mechanisms. Our results critically delineate the role of motor cortex in motor sequence execution, describing the condition under which it is engaged and the functions it fulfills, thus reconciling seemingly conflicting views about motor cortex's role in motor sequence generation.
Collapse
Affiliation(s)
- Kevin G. C. Mizes
- Program in Biophysics, Harvard University, Cambridge, MA 02138,
USA
- Department of Organismic and Evolutionary Biology and Center for
Brain Science, Harvard University, Cambridge, MA, USA
| | - Jack Lindsey
- Zuckerman Mind Brain and Behavior Institute, Columbia
University, New York, NY, 10027, USA
| | - G. Sean Escola
- Zuckerman Mind Brain and Behavior Institute, Columbia
University, New York, NY, 10027, USA
- Department of Psychiatry, Columbia University, New York, NY,
10032, USA
| | - Bence P. Ölveczky
- Department of Organismic and Evolutionary Biology and Center for
Brain Science, Harvard University, Cambridge, MA, USA
| |
Collapse
|
4
|
Papazoglou AS, Karagiannidis E, Liatsos A, Bompoti A, Moysidis DV, Arvanitidis C, Tsolaki F, Tsagkaropoulos S, Theocharis S, Tagarakis G, Michaelson JS, Herrmann MD. Volumetric Tissue Imaging of Surgical Tissue Specimens Using Micro-Computed Tomography: An Emerging Digital Pathology Modality for Nondestructive, Slide-Free Microscopy-Clinical Applications of Digital Pathology in 3 Dimensions. Am J Clin Pathol 2023; 159:242-254. [PMID: 36478204 DOI: 10.1093/ajcp/aqac143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/14/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES Micro-computed tomography (micro-CT) is a novel, nondestructive, slide-free digital imaging modality that enables the acquisition of high-resolution, volumetric images of intact surgical tissue specimens. The aim of this systematic mapping review is to provide a comprehensive overview of the available literature on clinical applications of micro-CT tissue imaging and to assess its relevance and readiness for pathology practice. METHODS A computerized literature search was performed in the PubMed, Scopus, Web of Science, and CENTRAL databases. To gain insight into regulatory and financial considerations for performing and examining micro-CT imaging procedures in a clinical setting, additional searches were performed in medical device databases. RESULTS Our search identified 141 scientific articles published between 2000 and 2021 that described clinical applications of micro-CT tissue imaging. The number of relevant publications is progressively increasing, with the specialties of pulmonology, cardiology, otolaryngology, and oncology being most commonly concerned. The included studies were mostly performed in pathology departments. Current micro-CT devices have already been cleared for clinical use, and a Current Procedural Terminology (CPT) code exists for reimbursement of micro-CT imaging procedures. CONCLUSIONS Micro-CT tissue imaging enables accurate volumetric measurements and evaluations of entire surgical specimens at microscopic resolution across a wide range of clinical applications.
Collapse
Affiliation(s)
| | - Efstratios Karagiannidis
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alexandros Liatsos
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreana Bompoti
- Diagnostic Imaging, Peterborough City Hospital, North West Anglia NHS Foundation Trust, Peterborough, UK
| | - Dimitrios V Moysidis
- First Department of Cardiology, AHEPA University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christos Arvanitidis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece.,LifeWatch ERIC, Sector II-II, Seville, Spain
| | - Fani Tsolaki
- Department of Cardiothoracic Surgery, AHEPA University Hospital, Thessaloniki, Greece
| | | | - Stamatios Theocharis
- First Department of Pathology, National and Kapoditrian University of Athens, Athens, Greece
| | - Georgios Tagarakis
- Department of Cardiothoracic Surgery, AHEPA University Hospital, Thessaloniki, Greece
| | - James S Michaelson
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Markus D Herrmann
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| |
Collapse
|
5
|
Balcaen T, Piens C, Mwema A, Chourrout M, Vandebroek L, Des Rieux A, Chauveau F, De Borggraeve WM, Hoffmann D, Kerckhofs G. Revealing the three-dimensional murine brain microstructure by contrast-enhanced computed tomography. Front Neurosci 2023; 17:1141615. [PMID: 37034159 PMCID: PMC10076597 DOI: 10.3389/fnins.2023.1141615] [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: 01/10/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
To improve our understanding of the brain microstructure, high-resolution 3D imaging is used to complement classical 2D histological assessment techniques. X-ray computed tomography allows high-resolution 3D imaging, but requires methods for enhancing contrast of soft tissues. Applying contrast-enhancing staining agents (CESAs) ameliorates the X-ray attenuating properties of soft tissue constituents and is referred to as contrast-enhanced computed tomography (CECT). Despite the large number of chemical compounds that have successfully been applied as CESAs for imaging brain, they are often toxic for the researcher, destructive for the tissue and without proper characterization of affinity mechanisms. We evaluated two sets of chemically related CESAs (organic, iodinated: Hexabrix and CA4+ and inorganic polyoxometalates: 1:2 hafnium-substituted Wells-Dawson phosphotungstate and Preyssler anion), for CECT imaging of healthy murine hemispheres. We then selected the CESA (Hexabrix) that provided the highest contrast between gray and white matter and applied it to a cuprizone-induced demyelination model. Differences in the penetration rate, effect on tissue integrity and affinity for tissue constituents have been observed for the evaluated CESAs. Cuprizone-induced demyelination could be visualized and quantified after Hexabrix staining. Four new non-toxic and non-destructive CESAs to the field of brain CECT imaging were introduced. The added value of CECT was shown by successfully applying it to a cuprizone-induced demyelination model. This research will prove to be crucial for further development of CESAs for ex vivo brain CECT and 3D histopathology.
Collapse
Affiliation(s)
- Tim Balcaen
- MolDesignS, Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, Leuven, Belgium
- ContrasT Team, Institute of Mechanics, Materials and Civil Engineering, Mechatronic, Electrical Energy and Dynamic Systems, UCLouvain, Louvain-la-Neuve, Belgium
- Pole of Morphology, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
| | - Catherine Piens
- ContrasT Team, Institute of Mechanics, Materials and Civil Engineering, Mechatronic, Electrical Energy and Dynamic Systems, UCLouvain, Louvain-la-Neuve, Belgium
| | - Ariane Mwema
- Advanced Drug Delivery and Biomaterials, UCLouvain, Brussels, Belgium
- Bioanalysis and Pharmacology of Bioactive Lipids, UCLouvain, Brussels, Belgium
| | - Matthieu Chourrout
- Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre de Recherche en Neurosciences de Lyon U1028 UMR 5292, Bron, France
| | - Laurens Vandebroek
- Laboratory of Biomolecular Modelling and Design (LBMD), Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Anne Des Rieux
- Advanced Drug Delivery and Biomaterials, UCLouvain, Brussels, Belgium
| | - Fabien Chauveau
- Université Claude Bernard Lyon 1, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Centre de Recherche en Neurosciences de Lyon U1028 UMR 5292, Bron, France
| | - Wim M. De Borggraeve
- MolDesignS, Sustainable Chemistry for Metals and Molecules, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Delia Hoffmann
- Pole of Morphology, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
- Prometheus, Division of Skeletal Tissue Engineering, KU Leuven, Leuven, Belgium
- Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium
| | - Greet Kerckhofs
- ContrasT Team, Institute of Mechanics, Materials and Civil Engineering, Mechatronic, Electrical Energy and Dynamic Systems, UCLouvain, Louvain-la-Neuve, Belgium
- Pole of Morphology, Institute of Experimental and Clinical Research, UCLouvain, Brussels, Belgium
- Department Materials Engineering, KU Leuven, Leuven, Belgium
- *Correspondence: Greet Kerckhofs,
| |
Collapse
|
6
|
Censoni L, Halje P, Axelsson J, Skovgård K, Ramezani A, Malinina E, Petersson P. Verification of multi-structure targeting in chronic microelectrode brain recordings from CT scans. J Neurosci Methods 2022; 382:109719. [PMID: 36195238 DOI: 10.1016/j.jneumeth.2022.109719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/07/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Large-scale microelectrode recordings offer a unique opportunity to study neurophysiological processes at the network level with single cell resolution. However, in the small brains of many experimental animals, it is often technically challenging to verify the correct targeting of the intended structures, which inherently limits the reproducibility of acquired data. NEW METHOD To mitigate this problem, we have developed a method to programmatically segment the trajectory of electrodes arranged in larger arrays from acquired CT-images and thereby determine the position of individual recording tips with high spatial resolution, while also allowing for coregistration with an anatomical atlas, without pre-processing of the animal samples or post-imaging histological analyses. RESULTS Testing the technical limitations of the developed method, we found that the choice of scanning angle influences the achievable spatial resolution due to shadowing effects caused by the electrodes. However, under optimal acquisition conditions, individual electrode tip locations within arrays with 250 µm inter-electrode spacing were possible to reliably determine. COMPARISON TO EXISTING METHODS Comparison to a histological verification method suggested that, under conditions where individual wires are possible to track in slices, a 90% correspondence could be achieved in terms of the number of electrodes groups that could be reliably assigned to the same anatomical structure. CONCLUSIONS The herein reported semi-automated procedure to verify anatomical targeting of brain structures in the rodent brain could help increasing the quality and reproducibility of acquired neurophysiological data by reducing the risk of assigning recorded brain activity to incorrectly identified anatomical locations. DATA AVAILABILITY The tools developed in this study are freely available as a software package at: https://github.com/NRC-Lund/ct-tools.
Collapse
Affiliation(s)
- Luciano Censoni
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Pär Halje
- The Group for Integrative Neurophysiology and Neurotechnology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Jan Axelsson
- Department of Radiation Science, Umeå University, Umeå, Sweden
| | - Katrine Skovgård
- The Group for Integrative Neurophysiology and Neurotechnology, Department of Experimental Medical Science, Lund University, Lund, Sweden; Basal Ganglia Pathophysiology Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Arash Ramezani
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Evgenya Malinina
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Per Petersson
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden; The Group for Integrative Neurophysiology and Neurotechnology, Department of Experimental Medical Science, Lund University, Lund, Sweden.
| |
Collapse
|
7
|
Tennant SA, Clark H, Hawes I, Tam WK, Hua J, Yang W, Gerlei KZ, Wood ER, Nolan MF. Spatial representation by ramping activity of neurons in the retrohippocampal cortex. Curr Biol 2022; 32:4451-4464.e7. [PMID: 36099915 DOI: 10.1016/j.cub.2022.08.050] [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: 01/14/2022] [Revised: 07/05/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022]
Abstract
Neurons in the retrohippocampal cortices play crucial roles in spatial memory. Many retrohippocampal neurons have firing fields that are selectively active at specific locations, with memory for rewarded locations associated with reorganization of these firing fields. Whether this is the sole strategy for representing spatial memories is unclear. Here, we demonstrate that during a spatial memory task retrohippocampal neurons encode location through ramping activity that extends across segments of a linear track approaching and following a reward, with the rewarded location represented by offsets or switches in the slope of the ramping activity. Ramping representations could be maintained independently of trial outcome and cues marking the reward location, indicating that they result from recall of the track structure. When recorded in an open arena, neurons that generated ramping activity during the spatial memory task were more numerous than grid or border cells, with a majority showing spatial firing that did not meet criteria for classification as grid or border representations. Encoding of rewarded locations through offsets and switches in the slope of ramping activity also emerged in recurrent neural network models trained to solve a similar spatial memory task. Impaired performance of model networks following disruption of outputs from ramping neurons is consistent with this coding strategy supporting navigation to recalled locations of behavioral significance. Our results suggest that encoding of learned spaces by retrohippocampal networks employs both discrete firing fields and continuous ramping representations. We hypothesize that retrohippocampal ramping activity mediates readout of learned models for goal-directed navigation.
Collapse
Affiliation(s)
- Sarah A Tennant
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Harry Clark
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Ian Hawes
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Wing Kin Tam
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Junji Hua
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Wannan Yang
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Klara Z Gerlei
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Emma R Wood
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Matthew F Nolan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK; Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK; Centre for Statistics, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
8
|
Andree A, Li N, Butenko K, Kober M, Chen JZ, Higuchi T, Fauser M, Storch A, Ip CW, Kühn AA, Horn A, van Rienen U. Deep brain stimulation electrode modeling in rats. Exp Neurol 2022; 350:113978. [PMID: 35026227 DOI: 10.1016/j.expneurol.2022.113978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/13/2021] [Accepted: 01/06/2022] [Indexed: 11/26/2022]
Abstract
Deep Brain Stimulation (DBS) is an efficacious treatment option for an increasing range of brain disorders. To enhance our knowledge about the mechanisms of action of DBS and to probe novel targets, basic research in animal models with DBS is an essential research base. Beyond nonhuman primate, pig, and mouse models, the rat is a widely used animal model for probing DBS effects in basic research. Reconstructing DBS electrode placement after surgery is crucial to associate observed effects with modulating a specific target structure. Post-mortem histology is a commonly used method for reconstructing the electrode location. In humans, however, neuroimaging-based electrode localizations have become established. For this reason, we adapt the open-source software pipeline Lead-DBS for DBS electrode localizations from humans to the rat model. We validate our localization results by inter-rater concordance and a comparison with the conventional histological method. Finally, using the open-source software pipeline OSS-DBS, we demonstrate the subject-specific simulation of the VTA and the activation of axon models aligned to pathways representing neuronal fibers, also known as the pathway activation model. Both activation models yield a characterization of the impact of DBS on the target area. Our results suggest that the proposed neuroimaging-based method can precisely localize DBS electrode placements that are essentially rater-independent and yield results comparable to the histological gold standard. The advantages of neuroimaging-based electrode localizations are the possibility of acquiring them in vivo and combining electrode reconstructions with advanced imaging metrics, such as those obtained from diffusion or functional magnetic resonance imaging (MRI). This paper introduces a freely available open-source pipeline for DBS electrode reconstructions in rats. The presented initial validation results are promising.
Collapse
Affiliation(s)
- Andrea Andree
- Institute of General Electrical Engineering, University of Rostock, Albert-Einstein-Straße 2, 18059 Rostock, Germany.
| | - Ningfei Li
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Germany; Berlin Institute of Health, Movement Disorders and Neuromodulation Unit, Department for Neurology, Charitéplatz 1, 10117 Berlin, Germany.
| | - Konstantin Butenko
- Institute of General Electrical Engineering, University of Rostock, Albert-Einstein-Straße 2, 18059 Rostock, Germany.
| | - Maria Kober
- Department of Neurology, Rostock University Medical Center, Gehlsheimer Straße 20, 18147 Rostock, Germany.
| | - Jia Zhi Chen
- Department of Neurology, University Hospital of Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany.
| | - Takahiro Higuchi
- Department of Nuclear Medicine and Comprehensive Heart Failure Center, University Hospital of Würzburg, Oberdürrbacher Straße 6, 97080 Würzburg, Germany.
| | - Mareike Fauser
- Department of Neurology, Rostock University Medical Center, Gehlsheimer Straße 20, 18147 Rostock, Germany.
| | - Alexander Storch
- Department of Neurology, Rostock University Medical Center, Gehlsheimer Straße 20, 18147 Rostock, Germany; German Centre for Neurodegenerative Diseases (DZNE) Rostock/Greifswald, Gehlsheimer, Straße 20, 18147 Rostock, Germany; Department Ageing of Individuals and Society, University of Rostock, Gehlsheimer Straße 20, 18147 Rostock, Germany.
| | - Chi Wang Ip
- Department of Neurology, University Hospital of Würzburg, Josef-Schneider-Straße 11, 97080 Würzburg, Germany.
| | - Andrea A Kühn
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Germany; Berlin Institute of Health, Movement Disorders and Neuromodulation Unit, Department for Neurology, Charitéplatz 1, 10117 Berlin, Germany.
| | - Andreas Horn
- Charité, Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Germany; Berlin Institute of Health, Movement Disorders and Neuromodulation Unit, Department for Neurology, Charitéplatz 1, 10117 Berlin, Germany.
| | - Ursula van Rienen
- Institute of General Electrical Engineering, University of Rostock, Albert-Einstein-Straße 2, 18059 Rostock, Germany; Department Ageing of Individuals and Society, University of Rostock, Gehlsheimer Straße 20, 18147 Rostock, Germany; Department Life, Light & Matter, University of Rostock, Albert-Einstein-Straße 25, 18059 Rostock, Germany.
| |
Collapse
|
9
|
Du M, Di Z(W, Gürsoy D, Xian RP, Kozorovitskiy Y, Jacobsen C. Upscaling X-ray nanoimaging to macroscopic specimens. J Appl Crystallogr 2021; 54:386-401. [PMID: 33953650 PMCID: PMC8056767 DOI: 10.1107/s1600576721000194] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/06/2021] [Indexed: 11/10/2022] Open
Abstract
Upscaling X-ray nanoimaging to macroscopic specimens has the potential for providing insights across multiple length scales, but its feasibility has long been an open question. By combining the imaging requirements and existing proof-of-principle examples in large-specimen preparation, data acquisition and reconstruction algorithms, the authors provide imaging time estimates for howX-ray nanoimaging can be scaled to macroscopic specimens. To arrive at this estimate, a phase contrast imaging model that includes plural scattering effects is used to calculate the required exposure and corresponding radiation dose. The coherent X-ray flux anticipated from upcoming diffraction-limited light sources is then considered. This imaging time estimation is in particular applied to the case of the connectomes of whole mouse brains. To image the connectome of the whole mouse brain, electron microscopy connectomics might require years, whereas optimized X-ray microscopy connectomics could reduce this to one week. Furthermore, this analysis points to challenges that need to be overcome (such as increased X-ray detector frame rate) and opportunities that advances in artificial-intelligence-based 'smart' scanning might provide. While the technical advances required are daunting, it is shown that X-ray microscopy is indeed potentially applicable to nanoimaging of millimetre- or even centimetre-size specimens.
Collapse
Affiliation(s)
- Ming Du
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Zichao (Wendy) Di
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Doǧa Gürsoy
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL 60208, USA
| | - R. Patrick Xian
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Yevgenia Kozorovitskiy
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
10
|
Rodrigues PV, Tostes K, Bosque BP, de Godoy JVP, Amorim Neto DP, Dias CSB, Fonseca MDC. Illuminating the Brain With X-Rays: Contributions and Future Perspectives of High-Resolution Microtomography to Neuroscience. Front Neurosci 2021; 15:627994. [PMID: 33815039 PMCID: PMC8010130 DOI: 10.3389/fnins.2021.627994] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 02/26/2021] [Indexed: 12/27/2022] Open
Abstract
The assessment of three-dimensional (3D) brain cytoarchitecture at a cellular resolution remains a great challenge in the field of neuroscience and constant development of imaging techniques has become crucial, particularly when it comes to offering direct and clear obtention of data from macro to nano scales. Magnetic resonance imaging (MRI) and electron or optical microscopy, although valuable, still face some issues such as the lack of contrast and extensive sample preparation protocols. In this context, x-ray microtomography (μCT) has become a promising non-destructive tool for imaging a broad range of samples, from dense materials to soft biological specimens. It is a new supplemental method to be explored for deciphering the cytoarchitecture and connectivity of the brain. This review aims to bring together published works using x-ray μCT in neurobiology in order to discuss the achievements made so far and the future of this technique for neuroscience.
Collapse
Affiliation(s)
- Paulla Vieira Rodrigues
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Katiane Tostes
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Beatriz Pelegrini Bosque
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - João Vitor Pereira de Godoy
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Dionisio Pedro Amorim Neto
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Department of Structural and Functional Biology, State University of Campinas, Campinas, Brazil
| | - Carlos Sato Baraldi Dias
- Brazilian Synchrotron Light National Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Matheus de Castro Fonseca
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| |
Collapse
|
11
|
Kastner DB, Kharazia V, Nevers R, Smyth C, Astudillo-Maya DA, Williams GM, Yang Z, Holobetz CM, Santina LD, Parkinson DY, Frank LM. Scalable method for micro-CT analysis enables large scale quantitative characterization of brain lesions and implants. Sci Rep 2020; 10:20851. [PMID: 33257721 PMCID: PMC7705725 DOI: 10.1038/s41598-020-77796-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 11/17/2020] [Indexed: 12/18/2022] Open
Abstract
Anatomic evaluation is an important aspect of many studies in neuroscience; however, it often lacks information about the three-dimensional structure of the brain. Micro-CT imaging provides an excellent, nondestructive, method for the evaluation of brain structure, but current applications to neurophysiological or lesion studies require removal of the skull as well as hazardous chemicals, dehydration, or embedding, limiting their scalability and utility. Here we present a protocol using eosin in combination with bone decalcification to enhance contrast in the tissue and then employ monochromatic and propagation phase-contrast micro-CT imaging to enable the imaging of brain structure with the preservation of the surrounding skull. Instead of relying on descriptive, time-consuming, or subjective methods, we develop simple quantitative analyses to map the locations of recording electrodes and to characterize the presence and extent of hippocampal brain lesions.
Collapse
Affiliation(s)
- David B Kastner
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA. .,Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA.
| | - Viktor Kharazia
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Rhino Nevers
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Clay Smyth
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Daniela A Astudillo-Maya
- Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA
| | - Greer M Williams
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA
| | - Zhounan Yang
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA
| | - Cristofer M Holobetz
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA
| | - Luca Della Santina
- Deparment of Ophthalmology, University of California, San Francisco, CA, 94143, USA.,Bakar Computational Health Science Unit, University of California, San Francisco, CA, 94158, USA
| | - Dilworth Y Parkinson
- Advanced Light Source, Lawrence Berkeley National Labs, Berkeley, CA, 94720, USA
| | - Loren M Frank
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, 94143, USA.,Kavli Institute for Fundamental Neuroscience and Department of Physiology, University of California, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| |
Collapse
|
12
|
Guitchounts G, Masís J, Wolff SB, Cox D. Encoding of 3D Head Orienting Movements in the Primary Visual Cortex. Neuron 2020; 108:512-525.e4. [DOI: 10.1016/j.neuron.2020.07.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/11/2020] [Accepted: 07/13/2020] [Indexed: 10/23/2022]
|
13
|
Barbone GE, Bravin A, Mittone A, Kraiger MJ, Hrabě de Angelis M, Bossi M, Ballarini E, Rodriguez-Menendez V, Ceresa C, Cavaletti G, Coan P. Establishing sample-preparation protocols for X-ray phase-contrast CT of rodent spinal cords: Aldehyde fixations and osmium impregnation. J Neurosci Methods 2020; 339:108744. [DOI: 10.1016/j.jneumeth.2020.108744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022]
|
14
|
Gabričević M, Lente G, Fábián I. Kinetic detection of osmium(VI) ester intermediates during the OsO
4
‐mediated aqueous dihydroxylation of chloroethylenes. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mario Gabričević
- Faculty of Pharmacy and BiochemistryUniversity of Zagreb Zagreb Croatia
| | - Gábor Lente
- Department of General and Physical ChemistryUniversity of Pécs Pécs Hungary
| | - István Fábián
- Department of Inorganic and Analytical ChemistryUniversity of Debrecen Debrecen Hungary
- MTA‐DE Redox and Homogeneous Catalytic Reaction Mechanisms Research Group Debrecen Hungary
| |
Collapse
|
15
|
Udagawa S, Miyara K, Takekata H, Takeuchi Y, Takemura A. Investigation on the validity of 3D micro-CT imaging in the fish brain. J Neurosci Methods 2019; 328:108416. [PMID: 31472188 DOI: 10.1016/j.jneumeth.2019.108416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Micro-computed tomography (CT) is a non-invasive technique that is used to obtain three-dimensional (3D) images of tissue structure in small animals. Compared with extensive mammal studies, few 3D imaging studies of fish have been conducted using micro-CT. An optimized method for imaging fish tissue structure is necessary, because they have adapted to diverse environments via functional and structural specialization. NEW METHOD Brains of three species with different sizes and habitats were fixed in 4% paraformaldehyde and immersed in non-ionic iodinated contrast agent (Iopamiron). We examined the relationship between Iopamiron concentration and immersion time to determine universally optimal conditions for use in fish. RESULTS We reconstructed 3D images of whole fish brains from cross-sections of brains from the Malabar grouper (Epinephelus malabaricus), bastard halibut (Paralichthys olivaceus), and threespot wrasse (Halichoeres trimaculatus). Developmental changes in brain structure were observed in the bastard halibut. Most brain regions of the threespot wrasse were distinguishable, although inner regions of the brain were less visible. COMPARISON WITH EXISTING METHODS Histological techniques are typically used to observe fish brain structure, despite its drawbacks in terms of tissue sample preparation (shrinkage and distortion) and image capture (3D image constriction). The technique examined in the present study solves these problems and allows for the simultaneous handling of multiple specimens. CONCLUSION Micro-CT imaging is suitable for observing the surfaces and inner structures of fish of various species.
Collapse
Affiliation(s)
- Shingo Udagawa
- Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Keitaro Miyara
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Hiroki Takekata
- Organization for Research Promotion, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan
| | - Yuki Takeuchi
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan; Okinawa Institute of Science and Technology Graduate University, 1919-1, Onna, Okinawa 904-0495, Japan
| | - Akihiro Takemura
- Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213, Japan.
| |
Collapse
|
16
|
Sakurai Y, Ikeda Y. Development of a contrast-enhanced micro computed tomography protocol for the oval squid (Sepioteuthis lessoniana) brain. Microsc Res Tech 2019; 82:1941-1952. [PMID: 31411804 DOI: 10.1002/jemt.23363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/28/2019] [Accepted: 08/01/2019] [Indexed: 01/13/2023]
Abstract
Coleoid cephalopods (squid, cuttlefish, and octopus) have a well-developed and complex central nervous system. Its absolute size is the largest among invertebrates, and the brain-to-body mass ratio is larger than that of fish and reptiles and equivalent to that of birds and mammals. Although a number of histological studies have been conducted on the brains of cephalopods, most of them used a light microscope or an electron microscope, which show the microstructure of the brain, but often cannot image the whole brain instantaneously. Of late, micro computed tomography (CT) has gained popularity for imaging animal brains because it allows for noninvasive three-dimensional (3D) reconstruction and preprocessing that are not cumbersome. To perform micro-CT on cephalopod brains, we first tested conditions suitable for preprocessing, paying special attention to staining conditions that would provide high contrast images. Four agents, iodine in 99.5% ethanol, iodine potassium iodide in water (IKI), phosphotungstic acid in 70% ethanol, and nonionic iodinated contrast agent in water, were tested at various concentrations and durations on brain of juvenile oval squid. To evaluate the quality of staining, we calculated the contrast ratio of the two-dimensional (2D) images and compared 3D segmentation of the best and worst 2D images. We concluded that 3% IKI staining for 7 days was the best combination to enhance the images contrast of the oval squid brain, in which each brain lobe was clearly detected and 3D segmentation of the whole brain was possible. The wider applicability of this preprocessing method for micro-CT of the brains of other cephalopods is discussed.
Collapse
Affiliation(s)
- Yuma Sakurai
- Department of Marine and Environmental Sciences, Graduate School of Engineering and Science, University of the Ryukyus, Okinawa, Japan
| | - Yuzuru Ikeda
- Faculty of Science, Department of Chemistry, Biology, and Marine Science, University of the Ryukyus, Okinawa, Japan
| |
Collapse
|
17
|
Gulino M, Kim D, Pané S, Santos SD, Pêgo AP. Tissue Response to Neural Implants: The Use of Model Systems Toward New Design Solutions of Implantable Microelectrodes. Front Neurosci 2019; 13:689. [PMID: 31333407 PMCID: PMC6624471 DOI: 10.3389/fnins.2019.00689] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 06/18/2019] [Indexed: 01/28/2023] Open
Abstract
The development of implantable neuroelectrodes is advancing rapidly as these tools are becoming increasingly ubiquitous in clinical practice, especially for the treatment of traumatic and neurodegenerative disorders. Electrodes have been exploited in a wide number of neural interface devices, such as deep brain stimulation, which is one of the most successful therapies with proven efficacy in the treatment of diseases like Parkinson or epilepsy. However, one of the main caveats related to the clinical application of electrodes is the nervous tissue response at the injury site, characterized by a cascade of inflammatory events, which culminate in chronic inflammation, and, in turn, result in the failure of the implant over extended periods of time. To overcome current limitations of the most widespread macroelectrode based systems, new design strategies and the development of innovative materials with superior biocompatibility characteristics are currently being investigated. This review describes the current state of the art of in vitro, ex vivo, and in vivo models available for the study of neural tissue response to implantable microelectrodes. We particularly highlight new models with increased complexity that closely mimic in vivo scenarios and that can serve as promising alternatives to animal studies for investigation of microelectrodes in neural tissues. Additionally, we also express our view on the impact of the progress in the field of neural tissue engineering on neural implant research.
Collapse
Affiliation(s)
- Maurizio Gulino
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB – Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- FEUP – Faculdade de Engenharia, Universidade do Porto, Porto, Portugal
| | - Donghoon Kim
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, Zurich, Switzerland
| | - Salvador Pané
- Multi-Scale Robotics Lab (MSRL), Institute of Robotics and Intelligent Systems (IRIS), ETH Zurich, Zurich, Switzerland
| | - Sofia Duque Santos
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB – Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
| | - Ana Paula Pêgo
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- INEB – Instituto de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
- FEUP – Faculdade de Engenharia, Universidade do Porto, Porto, Portugal
- ICBAS – Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| |
Collapse
|
18
|
Shakeri-Zadeh A. How can molecular micro-CT imaging revolutionize drug discovery? Expert Opin Drug Discov 2019; 14:849-853. [DOI: 10.1080/17460441.2019.1623203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ali Shakeri-Zadeh
- Finetech in Medicine Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Medical Physics Department, School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
| |
Collapse
|