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Structural and molecular interrogation of intact biological systems

(PDF) Structural and molecular interrogation of intact

Structural and molecular interrogation of intact biological systems Nature. 2013 May 16;497(7449):332-7. doi: 10.1038/nature12107. intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.. intact biological systems has long been a fundamental challenge across fields of investigation, and has spurred considerable technolo-gical innovation1-8. The study of brain structure-function relation-ships in particular may benefit from intact-system tools9-12, and in general, much valuable information on intra-system relationship But removing lipid membranes that intact biological systems has long been a fundamental challenge provide structural integrity and retain biomolecules would inevitably across fields of investigation, and has spurred considerable technolo- damage tissue with profound loss of cellular and molecular informa- gical innovation1-8 Structural and molecular interrogation of intact biological systems Kwanghun Chung , 1, 2 Jenelle Wallace , 1 Sung-Yon Kim , 1 Sandhiya Kalyanasundaram , 2 Aaron S. Andalman , 1, 2 Thomas J. Davidson , 1, 2 Julie J. Mirzabekov , 1 Kelly A. Zalocusky , 1, 2 Joanna Mattis , 1 Aleksandra K. Denisin , 1 Sally Pak , 1 Hannah Bernstein , 1 Charu.

(PDF) Structural and molecular interrogation of intact

Structural and molecular interrogation of intact biological systems. Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact. Structural and molecular interrogation of intact biological systems. Posted on May 17, 2013. Abstract Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology

Structural and molecular interrogation of intact biological systems. by Kwanghun Chung, Jenelle Wallace, Sung-Yon Kim, Sandhiya Kalyanasundaram, Aaron S Andalman, Thomas J Davidson, Julie J Mirzabekov, Kelly A Zalocusky, Joanna Mattis, Aleksandra K Denisin, Sally Pak, Hannah Bernstein, Charu Ramakrishnan, Logan Grosenick, Viviana Gradinaru, Karl Deisseroth structural and molecular interrogation of intact biological systems Journal Club 23rd April 2013 Despina Goniotaki . Imaging of intact tissue Clearing Human Brain structural/molecular phenotyping Human frontal lobe (BA10), 500µm thick, intact blocks Single axonal tracing -rendering o Structural and molecular interrogation of intact biological systems Kwanghun Chung1,2, Jenelle Wallace1, Sung-Yon Kim1, The extraction of detailed structural and molecular information from intact biological systems has long been a fundamental challenge across fields of investigation, and ha

Structural and molecular interrogation of intact biological systems. Structural and molecular interrogation of intact biological systems. Apr 30th. Brain Control with Light. Apr 21st. Structural and molecular interrogation of intact b... Video 1 Maximum projection of Department of Bioengineering, Stanford University, Stanford, California 94305, have come up with a way to make whole brains transparent, so they can be label.. We are not allowed to display external PDFs yet. You will be redirected to the full text document in the repository in a few seconds, if not click here.click here Structural and molecular interrogation of intact biological systems. Notice: Users may be experiencing issues with displaying some pages on stanfordhealthcare.org. We are working closely with our technical teams to resolve the issue as quickly as possible

rounds of molecular, structural and activity-history interrogation throughout intact adult mammalian brains; this is of relevance not only for neuroscience but also for research into any intact biological system. Thus far, CLARITY has been used to inter-rogate mouse brains, adult zebrafish and postmortem human Figure 1 | CLARITY pipeline. Structural and molecular interrogation of intact biological systems. Event time: 11:30am Event date: 25th October 2013 Speaker: Jakub Pastuszak (Formerly School of Physics & Astronomy, University of Edinburgh) Location: Room 2511, James Clerk Maxwell Building (JCMB) James Clerk Maxwell Building Peter Guthrie Tait Road Edinburgh EH9 3FD G Original Article Kwanghun Chung, Jenelle Wallace, Sung-Yon Kim, Sandhiya Kalyanasundaram, Aaron Andalman, Tom J. Davidson, Kelly A. Zalocusky, Joanna Mattis, Sally Pak, Viviana Gradinaru, Hannah Bernstein, Julie Mirzabekov, Charu Ramakrishnan, and Karl Deisseroth, Structural and molecular interrogation of intact biological systems, Nature, 2013, 497, 332-337 (This paper was featured in. biomolecules and structural integrity of the tissue. Lipid membranes are removed by passive thermal clearing in SBC solution at 37°C or by electrophoretic tissue clearing (ETC). The resulting intact tissue-hydrogel hybrid can undergo multiple rounds of molecular and structural interrogation using immunohistochemistry and light microscopy Biological Engineering Cellular, Developmental, Systems Biology Evolutionary and Organismal Biology Microbiology and Immunology Molecular Biology, Biochemistry, and Biophysics Neuroscience Research Centers Beckman Institute Center for Environmental Microbial Interactions (CEMI) Merkin Institute for Translational Research Resnick Sustainability.

Transparent Brains- Structural and molecular interrogation

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  1. Structural and molecular interrogation of intact biological systems. Nature (2013) 497: 332-337. ↑ K Chung and K Deisseroth. CLARITY for mapping the nervous system. Nature Methods (2013) 10(6): 508-513
  2. Institute of Molecular Biology and Genetics, Seoul National University CONTACT INFORMATION 1 Gwanak-ro, Gwanak-gu Proteomic Imaging for High-Dimensional Profiling of Intact Systems. (2015). Cell 163(6) Deisseroth K. (2013). Structural and molecular interrogation of intact biological systems. Nature. 497(7449):332-7. 19
  3. In his time in the Karl Deisseroth Lab, he invented a novel technology termed CLARITY, which enables system-wide structural and molecular analysis of large-scale intact biological samples including rodent brains and human clinical samples. He was a Burroughs Wellcome Fund Career Award at Scientific Interface (BWF-CASI) Postdoctoral Fellow

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CLARITY — Chung Lab Resource

Biochemistry, Structural, and Molecular Cell Biology Biological Engineering Developmental Biology and Genetics Evolutionary and Organismal Biology Microbiology and Immunology Neuroscience Systems Biology Research Centers Merkin Institute for Translational Research Resnick Sustainability Institute Tianqiao and Chrissy Chen Institute for. Sodium dodecyl sulfate (SDS) or sodium lauryl sulfate (SLS), sometimes written sodium laurilsulfate, is a synthetic organic compound with the formula C H 3 (CH 2) 11 SO 4 Na.It is an anionic surfactant used in many cleaning and hygiene products. This molecule is an organosulfate and a salt. It consists of a 12-carbon tail attached to a sulfate group, that is, it is the sodium salt of dodecyl. Structural and molecular interrogation of intact biological systems. Nature Chung, K., Wallace, J., Kim, S The structural and functional complexity of multicellular biological systems, such as the brain, are beyond the reach of human design or assembly capabilities. molecular and structural insights into dACRs and nACRs will be critical. A molecular calcium integrator reveals a striatal cell type driving aversion. Grosenick L, Broxton M, Yang S, Deisseroth K. SPED light sheet microscopy: fast mapping of biological system structure and function A.K., Pak S., Bernstein H., Ramakrishnan C., Grosenick L., Gradinaru V., Deisseroth K. Structural and molecular interrogation of.

Advanced CLARITY Methods for Rapid and High-Resolution

Expansion microscopy allows nanoscale precise single cell interrogation in intact tissues. Expansion microscopy (ExM) is a recently developed strategy for imaging molecular information throughout large cell and tissue samples, in 3-D and with nanoscale resolution, on ordinary diffraction-limited microscopes . This is achieved by embedding the. Structural and molecular interrogation of intact biological systems Chun et al., Nature 2013; 497: 332-337; doi 10.1038/Nature12107 Fluorescence microscopy is an immensely valuable tool for determining the localization of biomolecules within tissues. Genetically modified animals expressing fluorescent reporte CLARITY is the technique developed in the Deisseroth lab at Stanford University. This protocol transforms intact tissues including whole organs into an optically transparent hydrogel-hybridized form, ready for molecular phenotyping and high resolution 3D imaging. FUJIFILM Wako's VA-044 is used to initiate hydrogel polymerization Wallace et al. (2013) Structural and molecular interrogation of intact biological systems. Nature 497 332. PMID: 23575631; Kurokawa et al. (2011) Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat Neurosci 14 1481. PMID: 2187893

Studying intact systems with this sort of molecular resolution and global scope -- to be able to see the fine detail and the big picture at the same time -- has been a major unmet goal in biology. Hearing loss is a prevalent disorder that affects people of all ages. On top of the existing hearing aids and cochlear implants, there is a growing effort to regenerate functional tissues and restore hearing. However, studying and evaluating these regenerative medicine approaches in a big animal model (e.g. pigs) whose anatomy, physiology, and organ size are similar to a human is challenging Cel Cell Biology Mol Molecular Biology Intact-Brain Analyses Reveal Distinct Information Carried by SNc Dopamine Subcircuits. Cell. 2015 Jul 30; 162(3):635-47. Structural and molecular interrogation of intact biological systems. Nature. 2013 May 16; 497(7449):332-7 The research was published under the title 'Structural and molecular interrogation of intact biological systems' in the on-line version of Nature (more videos can be found at the above link). Some source material came from the io9.com article: Scientists can now turn brains invisible by Robert T. Gonzalez. Photos and video by Chung et al.

Viviana Gradinaru Biology and Biological Engineerin

Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, and Deisseroth K: Structural and molecular interrogation of intact biological systems. Nature 497 (7449): 332-7 (2013) Combining neuroscience and chemical engineering, researchers at Stanford University have developed a process that renders a mouse brain transparent. The postmortem brain remains whole — not sliced or sectioned in any way — with its three-dimensional complexity of fine wiring and molecular structures completely intact and able to be measured and probed at will with visible light and chemicals This left behind a porous, yet fully assembled system of cell parts, amenable to imaging and labeling of different cellular molecules. Though other intact-imaging techniques have extended the depth of light microscopy (e.g., Hama et al., 2011), they do not offer a preparation permeable enough for labeling. Call it CLARIT By using emulsion systems linking flanking regions to amplicons within the CNV, this led to the reconstruction of a 59kb haplotype across the DEFA1A3 CNV in HapMap individuals. CONCLUSION: This study has demonstrated a novel use for emulsion haplotype fusion PCR in addressing the issue of reconstructing structural haplotypes at multiallelic. An intact mouse brain stained with fluorescent labels for different proteins. Each colour represents a different molecular label. Credit: Kwanghun Chung and Karl Deisseroth, Howard Hughes Medical.

27776-21-2・VA-044, Azo Initiator・LB-VA044-50GS・LB-VA044A sensitive and specific nanosensor for monitoring

Fig. 1: Brain cells: A 3-D visualization of fluorescently-labeled brain cells within an intact brain tissue. Through the use of this novel whole-body clearing and staining method, researchers can make an organism's tissues transparent - allowing them to look through the tissues of an organism for specific cells that have been labeled or stained (Credit: Bin Yang and Viviana Gradinaru) CLARITY is a method of making tissue transparent using acrylamide-based hydrogels built from within, and linked to, the tissue, and as defined in the initial paper, represents transformation of intact biological tissue into a hybrid form in which specific components are replaced with exogenous elements that provide new accessibility or functionality Wavefront shaping holds great potential for high-resolution imaging or light delivery either through or deep inside living tissue. However, one of the biggest barriers that must be overcome to unleash the full potential of wavefront shaping for practical biomedical applications is the fact that wavefront shaping, especially based on iterative feedback, requires lengthy measurements to obtain. Imaging gene expression levels with single-cell resolution in intact tissues is essential for understanding the genetic programs in many systems, such as developing embryos and dynamic brain circuits. Structural and molecular interrogation of intact biological systems

Intact and whole-mount palps (labial, maxillary), antennae and legs were freshly dissected from ice-chilled adult C. populi beetles that were injected beforehand with dsLac2, dsTH or dsGfp as control. Three independent biological replicates from each appendage and injected dsRNA were used for FISH Imaging intact tissue is critical to gain a complete understanding of biological mechanisms in health and disease. However, biological tissues are heterogeneous structures with non-uniform light absorption, scattering, attenuation patterns, and refractive index (RI), making it challenging to image deep Ensured 100% data integrity on the data reported to agencies by performing system configurations. Structural and molecular interrogation of intact biological systems, Nature (2013. Alon, S. et al. Expansion sequencing: spatially precise in situ transcriptomics in intact biological systems. Science 371 , eaax2656 (2021). CAS PubMed PubMed Central Article Google Schola 1. CLARITY A technique for structural and molecular interrogation of intact biological systems Based on the work of Kwanghun Chung and Karl Deisseroth Published on Nature Methods 2013 2. Studying intact systems with molecular resolution and global scope remains an unmet goal in biology CONFOCALTWO-PHOTON max penetration 700 um 3

Multiplexed Intact-Tissue Transcriptional Analysis at

UltraMicroscope II - A User Guid

  1. density in a.
  2. Systems biology is a data-heavy field that focuses on systems-wide depictions of biological phenomena necessarily sacrificing a detailed characterization of individual components. As an example, genome-wide protein interaction networks are widely used in systems biology and continuously extended and refined as new sources of evidence become available
  3. Below is a selected list of papers that best describe our research. You can see all our papers on Pubmed or Google Scholar.. Kim M, Heo G, Kim, S. -Y. Neural signaling of gut mechanosensation for the control of ingestion and digestion.Nature Reviews Neuroscience. In press
  4. 1 Structural and molecular interrogation of intact biological systems. Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AJ, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, and K Deisseroth. Nature 497, 332-337 (16 May 2013) eYFP PV GFAP Cortex alv DG CA3 CA

This system removes lipids electrophoretically from the tissue-hydrogel hybrids. K., et al. Structural and molecular interrogation of intact biological systems. The primary commercial. The Deisseroth Lab is part of the Bioengineering Department at Stanford University. We develop and apply tools for controlling and mapping specific elements within intact biological systems. We are interested both in natural behaviorally-relevant neural circuit dynamics, and in pathological dynamics underlying neuropsychiatric disease symptomatology and treatment structural and molecular level information. The barrier to the visualization of intact systems is the lipid bilayers in biological tissues, which hinder our molecular probing and limit our ability to image the tissue by rendering the tissue opaque.1 Removing them is challenging because of their importance for the structural integrity of the tissue

CLARITY Protocol and Tissue Clearing Guide Abca

• Combining network structure and function. . . Davi Bock Clay Reid. . . Viren Jain Sebastian Seung. Logan Grosenick, Viviana Gradinaru, and Karl Deisseroth. Structural and molecular interrogation of intact biological systems. Nature, 10, 2013. Miniature Fluorescence Microscope Barretto RPJ, Messerschmidt B, Schnitzer MJ. Monte-Carlo. Researchers seek CLARITY for scientific questions from a transparent brain. Imagine if Miss Frizzle, science teacher extraordinaire, and the Magic School Bus really existed. We could all shrink down to the size of microscopic particles, fly up someone's nose and enter their brain to investigate the inner workings of the mind - all in IRB. Structural analysis of microscale three-dimensional tissues (3D microtissues) in high-throughput is becoming increasingly important in drug discovery, regenerative medicine, and other biomedical areas because they recapitulate many in vivo biological features not present in 2D models. This can be done by using microfluidic technology to control and apply external forces to on-chip 3D.

Publications - Gradinaru La

Following his graduation in 2009, Dr. Chung joined the Karl Deisseroth Lab at Stanford University for post-doctoral training in 2010, where he invented a novel technology termed CLARITY, which enables system-wide structural and molecular analysis of large-scale intact biological samples Structural and molecular interrogation of intact biological systems more. by Aaron Andalman, Kelly a. Zalocusky, Charu Ramakrishnan, Logan Grosenick, and Sally Pak. Publication Date: 2013 Publication Name: Nature. Research Interests Kwanghun Chung, Ph.D. The Picower Institute Massachusetts Institute of Technology. Obtaining detailed structural and molecular information from complex biological systems while simultaneously maintaining the global perspective has long been a fundamental challenge in neuroscience and throughout biology

CLARITY Technique - CLARITY Wik

Clearing Tissues - Providing a Clearer View on Brain Function. As studies move to larger and deeper 3D samples such as brain sections, organoids and a range of model organisms, it creates a new set of challenges. Issues with imaging thicker samples include light scattering, absorption and autofluoresence which can make it almost impossible to. Biological tissues show complex bioelectrical impedance which depends on the tissue compositions, tissue structure, tissue health and signal frequency. As the tissue composition, structure and health are significantly changed during boiling, there will be a significant change in tissue electrical properties in the boiled tissues Complete dendritic structure of adult-born granule cells and relationship to axonal development. SEBI also enables reconstruction of complete dendritic arbors without sectioning artifact; this allowed for the first full-structure characterization of intact newborn granule cell dendritic development in the adult mouse hippocampus (Fig. 5 A. Yang et al. reported that PARS method, a method that provides tissue clearance of intact whole-organisms, could provide access to integrated structural and molecular information from the brain and other intact biological systems . Although, organs with a higher cell density (e.g., kidney and liver) required up to 22 days for tissue clearance.

CLARITY Protocol and Tissue Clearing Guide | Abcam

Three-dimensional microscopy in the NIR-II window (1,000 to 1,700 nm) allows noninvasive deep-tissue optical sectioning of live mammals with high spatiotemporal resolution due to suppressed light scattering and reduced tissue autofluorescence. Herein, we present a NIR-II structured-illumination light-sheet microscopy (NIR-II SIM) with both excitation and emission wavelengths in the NIR-IIb. Three-dimensional cell cultures are able to better mimic the physiology and cellular environments found in tissues in vivo compared to cells grown in two dimensions. In order to study the structure and function of cells in 3-D cultures, light microscopy is frequently used. The preparation of 3-D cell cultures for light microscopy is often destructive, including physical sectioning of the. Skin histology is traditionally carried out using two-dimensional tissue sections, which allows for rapid staining, but these sections cannot accurately represent three-dimensional structures in skin such as nerves, vasculature, hair follicles, and sebaceous glands. Although it may be ideal to image skin in a three-dimensional manner, it is technically challenging to image deep into tissue. 1. Introduction. Three-dimensional (3-D) imaging of intact brain is indispensable for high-resolution mapping of neuronal networks, which is valuable for understanding brain structural-functional relationships. 1 - 3 Except for the widespread histological sectioning methods and emerging automated serial-sectioning and imaging approaches, optical imaging techniques make the 3-D imaging of. Structural preservation of complex biological systems from the subcellular to whole organism level in robust forms, enabling dissection and imaging while preserving 3D context, represents an enduring grand challenge in biology. Here we report a simple immersion method for structurally preserving.

The CLARITY process protects 3D structure whilst retaining antigenicity, permitting immunohistochemistry, in situ hybridization, and other molecular phenotyping methods. The report incudes many elegant 3D reconstructions of intact mouse brains demonstrating both long and short-range connections, cellular and subcellular structures, protein. Cells can sense mechanical cues, amongst others, via integrin-mediated signal transduction and focal adhesions, a molecular complex that is able to deform its environment, dynamically remodel in response to external loads, and trigger signaling cascades with a wide array of biological ramifications 31, 41, 46-48 You can see a video here that shows the power of the CLARITY technique for high resolution 3D visualisation of tissue and organ structure. Further Reading. Richardson & Lichtman (2205) Clarifying tissue clearing. Cell 162: 246-257. Chung et al (2013) Structural and molecular interrogation of intact biological systems. Nature 497: 332-337

Simple, Scalable Proteomic Imaging for High-Dimensional

Advances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy. Image: Caption: CLARITY allows molecular analysis of the intact brain. Each color represents a different molecular label; this labeling can happen after the brain is clarified but still fully intact. Hippocampus is shown, a structure important for many important roles including learning, memory, and emotion

Scientists report that they can now study the brain's finer workings while preserving its 3D structure and integrity of its circuitry and other biological machinery Previously, researchers had to choose either to study a fully intact brain, which involves a lengthy sample preparation process and potential structural dissimilarities compared to the original organ, or to study small sections of the brain where one can examine fine molecular and cellular interactions without knowledge of the original complex. Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature 497, 332-337 (2013). CAS PubMed PubMed Central Article Google Scholar 17. Yang, B. et al. Single-cell phenotyping within transparent intact tissue through whole-body clearing. Cell 158, 945-958 (2014). CAS PubMed PubMed Central Articl You do not have permission to edit this page, for the following reason This method renders the bone transparent and enables the detailed visualization of an intact tissue specimen at multiple spatial scales. molecular regulation of the osteoblast lineage. Nat Rev Mol Cell Biol 13:27-38. Structural and molecular interrogation of intact biological systems. Nature 497:332-337

The Brain: Now You See It, Soon You Won’t – NIH Director's

The Brain: Now You See It, Soon You Won't. Posted on April 11th, 2013 by Dr. Francis Collins. A post mortem brain is a white, fatty, opaque, three-pound mass. Traditionally scientists have looked inside it by cutting the brain into thin slices, but the relationships and connections of the tens of billions of neurons are then almost impossible to reconstruct CLARITY Makes Brains See-Through in News April 30th, 2013 The science community received big news out of California last week as Karl Deisseroth and his team of researchers from the Department of Bioengineering at Stanford University had their paper concerning their newly developed CLARITY brain imaging technique published in Nature.The most astounding aspect of the newly released.

Kwanghun Chung - Institute for Medical Engineering & Scienc

Neurobiologist Christopher Walsh describes a microscopy technique called CLARITY that makes it easier to see cells and structures inside the brain. This technique involves labeling neurons using fluorescent proteins and then treating brain tissue with acrylamide to make the tissue more transparent. Walsh also shows a 3D animation of the cortex. The Department of Molecular and Cellular Biology of Harvard University is located at the main Cambridge campus. We are a collegial and energetic community of researchers dedicated to providing a rich educational environment for our undergraduates, graduate students, and postdoctoral fellows, while keeping our faculty research at the highest levels of excellence

Imaris for Neuroscientists. This Introduction to Imaris for Neuroscientists webinar focussed on image analysis workflows ideal for researchers working in neuroscience. This included image processing tips and tricks to improve quality of the signal, automated and semi-manual methods of neuron tracing and an automated spine detection method 1. Introduction. In recent years, the interest in the study of cells in their three-dimensional (3D) tissue environment has increased rapidly. This development is fueled by the increase in in-vivo imaging methods and the rising demand for more complex 3D model systems for drug testing and development. 1 - 3 To circumvent time-consuming serial sectioning and to avoid misalignment artifacts in. CLARITY makes possible this 3D tour of an entire, intact mouse brain. It was imaged using a fluorescence technique that previously could only be performed with thinly-sliced brain tissue, making.

Chung K, Wallace J, Kim S-Y, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K (2013) Structural and molecular interrogation of intact biological systems. Nature 497: 332 - 337. doi: 10.1038/nature12107 pmid: 2357563 Cleared tissue imaging has emerged as a powerful technique for rendering centimeter sized biological tissues and organs transparent in order to enable three dimensional volume imaging via light microscopy. (2013). Structural and molecular interrogation of intact biological systems. Nature Harvard University Department of Molecular and. At first it was thought that the neurons in the dopamine system were all quite similar, but over the past decade it has become clear that they exhibit a range of molecular, anatomical and functional properties (Lammel et al., 2008; Margolis et al., 2008; Lammel et al., 2011).Moreover, it seems that distinct subsets of dopamine neurons belong to discrete circuits that carry out different.

【透ける科学 透明化技術まとめ】 - TogetterTissue clearing and its applications in neuroscienceCLARITY Tissue Clearing - ClearLight Biotechnologies