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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.
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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.
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Király B, Balázsfi D, Horváth I, Solari N, Sviatkó K, Lengyel K, Birtalan E, Babos M, Bagaméry G, Máthé D, Szigeti K, Hangya B. In vivo localization of chronically implanted electrodes and optic fibers in mice. Nat Commun 2020; 11:4686. [PMID: 32943633 PMCID: PMC7499215 DOI: 10.1038/s41467-020-18472-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 08/24/2020] [Indexed: 12/20/2022] Open
Abstract
Electrophysiology provides a direct readout of neuronal activity at a temporal precision only limited by the sampling rate. However, interrogating deep brain structures, implanting multiple targets or aiming at unusual angles still poses significant challenges for operators, and errors are only discovered by post-hoc histological reconstruction. Here, we propose a method combining the high-resolution information about bone landmarks provided by micro-CT scanning with the soft tissue contrast of the MRI, which allowed us to precisely localize electrodes and optic fibers in mice in vivo. This enables arbitrating the success of implantation directly after surgery with a precision comparable to gold standard histology. Adjustment of the recording depth with micro-drives or early termination of unsuccessful experiments saves many working hours, and fast 3-dimensional feedback helps surgeons avoid systematic errors. Increased aiming precision enables more precise targeting of small or deep brain nuclei and multiple targeting of specific cortical or hippocampal layers.
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Affiliation(s)
- Bálint Király
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Diána Balázsfi
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
| | - Ildikó Horváth
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Nicola Solari
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
| | - Katalin Sviatkó
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
- János Szentágothai Doctoral School of Neurosciences, Semmelweis University, Budapest, Hungary
| | - Katalin Lengyel
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
| | - Eszter Birtalan
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
| | - Magor Babos
- Mediso Medical Imaging Systems Ltd., Budapest, Hungary
| | | | - Domokos Máthé
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- CROmed Translational Research Centers, Budapest, Hungary
| | - Krisztián Szigeti
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Balázs Hangya
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary.
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Marinković I, Tatlisumak T, Abo-Ramadan U, Brkić BG, Aksić M, Marinković S. A basic MRI anatomy of the rat brain in coronal sections for practical guidance to neuroscientists. Brain Res 2020; 1747:147021. [PMID: 32755602 DOI: 10.1016/j.brainres.2020.147021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
Abstract
Identification of the brain structures in the magnetic resonance imaging (MRI) of the rat is very important for the experimental work of many neuroscientists. Our intention was to recognize most of the structures without overlapping the MRI sections with the histological templates. Three live rats were used for this study who were examined in a micro-MRI apparatus by performing T2-weighted sequences in serial brain sections. Most of the white matter structures were easily identified, e.g. the anterior commissure, corpus callosum with forceps minor and major, cingulum, external and internal capsules, fornix, stria medullaris and terminalis, cranial nerves, mammillothalamic tract, fasciculus retroflexus, medial and lateral lemniscus, posterior commissure, commissures of the superior and inferior colliculi, medial longitudinal fasciculus, and the cerebral peduncle. Large and small gray matter structures were recognized as well, for example, the anterior olfactory structures, nucleus accumbens, caudate putamen, claustrum, bed nucleus of the stria terminalis, pituitary gland, globus pallidus, amygdala, some midline and intralaminar thalamic nuclei, certain hypothalamic nuclei, hippocampal formation, pineal body, periaqueductal gray matter, lateral and medial geniculate bodies, superior and inferior colliculi, and cranial nerves nuclei. All in all, of the total 160 recognized brain structures, 77 were identified without using the corresponding histological atlases. We believe that our labeled MRI pictures could be an important way for quick orientation for evaluating the effects of the experimental work regarding the rat brain.
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Affiliation(s)
- Ivan Marinković
- Clinical Neuroscience, Neurology, Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland.
| | - Turgut Tatlisumak
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Blå Stråket 7, Plan 3, Sahlgrenska 41345, Gothenburg, Sweden; Department of Neurology, Sahlgrenska University Hospital, Blå Stråket 7, Plan 3, Sahlgrenska 41345, Gothenburg, Sweden.
| | - Usama Abo-Ramadan
- VTT Technical Research Centre of Finland Ltd, University of Helsinki, Tietotie 4E, 02150 Espoo, Finland
| | | | - Milan Aksić
- Department of Neuroanatomy, Institute of Anatomy, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Slobodan Marinković
- Department of Neuroanatomy, Institute of Anatomy, Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
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Ramadi KB, Dagdeviren C, Bhagchandani P, Nunez-Lopez C, Kim MJ, Langer R, Graybiel AM, Cima MJ. Simultaneous recording and marking of brain microstructures. J Neural Eng 2020; 17:044001. [PMID: 32604074 DOI: 10.1088/1741-2552/aba161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The vast majority of techniques to study the physiology of the nervous system involve inserting probes into the brain for stimulation, recording, or sampling. Research is increasingly uncovering the fine microstructure of the brain, each of its regions with dedicated functions. Accurate knowledge of the placement of probes interrogating these regions is critical. We have developed a customizable concentric marking electrode (CME) consisting of an iron core within a 125 μm-stainless steel (SS) sheath for co-localization of targeted regions in the brain. We used a dielectric layer stack of SiO2, Al2O3, SiO2 to electrically encapsulate the iron core and minimize exposure area to avoid significant increases in inflammatory response triggered by the probes. The CME can record multi-neuronal extracellular firing patterns. Appropriate electrical polarity of the iron and SS components controls the deposition of iron microdeposits on brain tissue. We show that in vivo labels by this method can be as small as 100 μm, visible via noninvasive magnetic resonance imaging (MRI) as well as post-mortem histology, and illustrate how deposit size can be tuned by varying stimulus parameters. We targeted the CA3 area of the hippocampus in adult rats and demonstrate that iron microdeposits are remarkably stable and persist up to 10 months post-deposition. Using a single probe for recording and marking avoids inaccuracies with re-insertion of separate probes and utilizes iron microdeposits as valuable fiducial markers in vivo and ex vivo.
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Affiliation(s)
- Khalil B Ramadi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. Harvard-MIT Health Sciences and Technology Division, Massachusetts Institute of Technology, Cambridge, MA 02139, United States of America. These authors contributed equally to this work
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Masís J, Mankus D, Wolff SBE, Guitchounts G, Joesch M, Cox DD. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Sci Rep 2018; 8:5184. [PMID: 29581439 PMCID: PMC5980003 DOI: 10.1038/s41598-018-23247-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 03/08/2018] [Indexed: 12/26/2022] Open
Abstract
Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12-15 and 5-6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.
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Affiliation(s)
- Javier Masís
- Harvard University, Department of Molecular and Cellular Biology, Cambridge, MA, 02138, USA. .,Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA.
| | - David Mankus
- Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA
| | - Steffen B E Wolff
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA, 02138, USA.,Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA
| | - Grigori Guitchounts
- Harvard University, Department of Molecular and Cellular Biology, Cambridge, MA, 02138, USA.,Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA
| | - Maximilian Joesch
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - David D Cox
- Harvard University, Department of Molecular and Cellular Biology, Cambridge, MA, 02138, USA.,Harvard University, Center for Brain Science, Cambridge, MA, 02138, USA
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Streeter KA, Sunshine MD, Patel SR, Liddell SS, Denholtz LE, Reier PJ, Fuller DD, Baekey DM. Coupling multielectrode array recordings with silver labeling of recording sites to study cervical spinal network connectivity. J Neurophysiol 2016; 117:1014-1029. [PMID: 27974450 DOI: 10.1152/jn.00638.2016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/12/2016] [Indexed: 01/24/2023] Open
Abstract
Midcervical spinal interneurons form a complex and diffuse network and may be involved in modulating phrenic motor output. The intent of the current work was to enable a better understanding of midcervical "network-level" connectivity by pairing the neurophysiological multielectrode array (MEA) data with histological verification of the recording locations. We first developed a method to deliver 100-nA currents to electroplate silver onto and subsequently deposit silver from electrode tips after obtaining midcervical (C3-C5) recordings using an MEA in anesthetized and ventilated adult rats. Spinal tissue was then fixed, harvested, and histologically processed to "develop" the deposited silver. Histological studies verified that the silver deposition method discretely labeled (50-μm resolution) spinal recording locations between laminae IV and X in cervical segments C3-C5. Using correlative techniques, we next tested the hypothesis that midcervical neuronal discharge patterns are temporally linked. Cross-correlation histograms produced few positive peaks (5.3%) in the range of 0-0.4 ms, but 21.4% of neuronal pairs had correlogram peaks with a lag of ≥0.6 ms. These results are consistent with synchronous discharge involving mono- and polysynaptic connections among midcervical neurons. We conclude that there is a high degree of synaptic connectivity in the midcervical spinal cord and that the silver-labeling method can reliably mark metal electrode recording sites and "map" interneuron populations, thereby providing a low-cost and effective tool for use in MEA experiments. We suggest that this method will be useful for further exploration of midcervical network connectivity.NEW & NOTEWORTHY We describe a method that reliably identifies the locations of multielectrode array (MEA) recording sites while preserving the surrounding tissue for immunohistochemistry. To our knowledge, this is the first cost-effective method to identify the anatomic locations of neuronal ensembles recorded with a MEA during acute preparations without the requirement of specialized array electrodes. In addition, evaluation of activity recorded from silver-labeled sites revealed a previously unappreciated degree of connectivity between midcervical interneurons.
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Affiliation(s)
- K A Streeter
- Department of Physical Therapy, University of Florida, Gainesville, Florida
| | - M D Sunshine
- Department of Physical Therapy, University of Florida, Gainesville, Florida
| | - S R Patel
- Department of Physical Therapy, University of Florida, Gainesville, Florida
| | - S S Liddell
- Department of Neuroscience, University of Florida, Gainesville, Florida; and
| | - L E Denholtz
- Department of Neuroscience, University of Florida, Gainesville, Florida; and
| | - P J Reier
- Department of Neuroscience, University of Florida, Gainesville, Florida; and
| | - D D Fuller
- Department of Physical Therapy, University of Florida, Gainesville, Florida
| | - D M Baekey
- Department of Physiological Sciences, University of Florida, Gainesville, Florida
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