Name: whole-brain single-cell imaging and analysis of intact neonatal mouse brains using mri, tissue clearing, and light-sheet microscopy
Uploaded: 2022-08-01T14:00:00
Description: Watch this Scientific Journal Video about Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy at JoVE.com

This work was supported by the NIH (R01MH121433, R01MH118349, and R01MH120125 to JLS and R01NS110791 to GW) and the Foundation of Hope. We thank Pablo Ariel of the Microscopy Services Laboratory for assisting in sample imaging. The Microscopy Services Laboratory in the Department of Pathology and Laboratory Medicine is supported in part by Cancer Center Core Support Grant P30 CA016086 to the University of North Carolina (UNC) Lineberger Comprehensive Cancer Center. The Neuroscience Microscopy Core is supported by grant P30 NS045892.&#160;Research reported in this publication was supported in part by the North Carolina Biotech Center Institutional Support Grant 2016-IDG-1016.

All mice were used in accordance with and approved by the Institutional Animal Care and Use Committee (IACUC) at the University of North Carolina at Chapel Hill.
1. Mouse dissection and perfusion
NOTE: The following dissections were performed on P4 and P14 mice using a syringe. The volume of perfusion fluid will vary depending on the age of the animal.
<ol>
	<li>Perfusion 
	CAUTION: Paraformaldehyde (PFA) is a hazardous chemical. Perform all ...

<ol>
	<li>Dodt, H. U., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultramicroscopy:+Three-dimensional+visualization+of+neuronal+networks+in+the+whole+mouse+brain.">Ultramicroscopy: Three-dimensional visualization of neuronal networks in the whole mouse brain.</a> Nature Methods. 4 (4), 331-336 (2007).</li><li>H&#228;gerling, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+multistep+mechanism+for+initial+lymphangiogenesis+in+mouse+embryos+based+on+ultramicroscopy.">A novel multistep mechanism for initial lymphangiogenesis in mouse embryos based on ultramicroscopy.</a> The EMBO Journal. 32 (5), 629-644 (2013).</li><li>Tomer, R., Khairy, K., Keller, P. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Shedding+light+on+the+system:+studying+embryonic+development+with+light+sheet+microscopy.">Shedding light on the system: studying embryonic development with light sheet microscopy.</a> Current Opinion in Genetics &amp; Development. 21 (5), 558-565 (2011).</li><li>Li, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Micro-optical+sectioning+tomography+to+obtain+a+high-resolution+atlas+of+the+mouse+brain.">Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain.</a> Science. 330 (6009), 1404-1408 (2010).</li><li>Stoner, R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Patches+of+disorganization+in+the+neocortex+of+children+with+autism.">Patches of disorganization in the neocortex of children with autism.</a> The New England Journal of Medicine. 370 (13), 1209-1219 (2014).</li><li>Renier, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IDISCO:+A+simple,+rapid+method+to+immunolabel+large+tissue+samples+for+volume+imaging.">IDISCO: A simple, rapid method to immunolabel large tissue samples for volume imaging.</a> Cell. 159 (4), 896-910 (2014).</li><li>Susaki, E. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole-brain+imaging+with+single-cell+resolution+using+chemical+cocktails+and+computational+analysis.">Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.</a> Cell. 157 (3), 726-739 (2014).</li><li>Richardson, D. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+clearing.">Tissue clearing.</a> Nature Reviews. Methods Primers. 1 (1), 84 (2021).</li><li>Richardson, D. S., Lichtman, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clarifying+tissue+clearing.">Clarifying tissue clearing.</a> Cell. 162 (2), 246-257 (2015).</li><li>Renier, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mapping+of+brain+activity+by+automated+volume+analysis+of+immediate+early+genes.">Mapping of brain activity by automated volume analysis of immediate early genes.</a> Cell. 165 (7), 1789-1802 (2016).</li><li>Santi, P. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Light+sheet+fluorescence+microscopy:+a+review.">Light sheet fluorescence microscopy: a review.</a> The Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society. 59 (2), 129-138 (2011).</li><li>Girkin, J. M., Carvalho, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+light-sheet+microscopy+revolution.">The light-sheet microscopy revolution.</a> Journal of Optics. 20 (5), 053002 (2018).</li><li>Budday, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanical+properties+of+gray+and+white+matter+brain+tissue+by+indentation.">Mechanical properties of gray and white matter brain tissue by indentation.</a> Journal of the Mechanical Behavior of Biomedical Materials. 46, 318-330 (2015).</li><li>Johnson, G. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-throughput+morphologic+phenotyping+of+the+mouse+brain+with+magnetic+resonance+histology.">High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology.</a> NeuroImage. 37 (1), 82-89 (2007).</li><li>Herculano-Houzel, S., Mota, B., Lent, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellular+scaling+rules+for+rodent+brains.">Cellular scaling rules for rodent brains.</a> Proceedings of the National Academy of Sciences of the United States of America. 103 (32), 12138-12143 (2006).</li><li>Matsumoto, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advanced+CUBIC+tissue+clearing+for+whole-organ+cell+profiling.">Advanced CUBIC tissue clearing for whole-organ cell profiling.</a> Nature Protocols. 14 (12), 3506-3537 (2019).</li><li>F&#252;rth, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+interactive+framework+for+whole-brain+maps+at+cellular+resolution.">An interactive framework for whole-brain maps at cellular resolution.</a> Nature Neuroscience. 21 (1), 139-149 (2018).</li><li>Chandrashekhar, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CloudReg:+automatic+terabyte-scale+cross-modal+brain+volume+registration.">CloudReg: automatic terabyte-scale cross-modal brain volume registration.</a> Nature Methods. 18 (8), 845-846 (2021).</li><li>Krupa, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=NuMorph:+Tools+for+cortical+cellular+phenotyping+in+tissue-cleared+whole-brain+images.">NuMorph: Tools for cortical cellular phenotyping in tissue-cleared whole-brain images.</a> Cell Reports. 37 (2), 109802 (2021).</li><li>Petiet, A., Delatour, B., Dhenain, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Models+of+neurodegenerative+disease+-+Alzheimer's+anatomical+and+amyloid+plaque+imaging.">Models of neurodegenerative disease - Alzheimer's anatomical and amyloid plaque imaging.</a> Methods in Molecular Biology. 771, 293-308 (2011).</li><li>Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., Smith, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=FSL.">FSL.</a> NeuroImage. 62, 782-790 (2012).</li><li>Jenkinson, M., Bannister, P., Brady, M., Smith, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+optimization+for+the+robust+and+accurate+linear+registration+and+motion+correction+of+brain+images.">Improved optimization for the robust and accurate linear registration and motion correction of brain images.</a> NeuroImage. 17 (2), 825-841 (2002).</li><li>Avants, B. B., Epstein, C. L., Grossman, M., Gee, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Symmetric+diffeomorphic+image+registration+with+cross-correlation:+evaluating+automated+labeling+of+elderly+and+neurodegenerative+brain.">Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain.</a> Medical Image Analysis. 12 (1), 26-41 (2008).</li><li>. iDISCO method Available from: <a target="_blank" href="https://idisco.info/">https://idisco.info/</a> (2022)</li><li>Ariel, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=UltraMicroscope+II+-+A+User+Guide.">UltraMicroscope II - A User Guide.</a> University of North Carolina at Chapel Hill. , (2019).</li><li>. Anaconda Distribution - Anaconda documentation Available from: <a target="_blank" href="https://docs.anaconda.com/anaconda/">https://docs.anaconda.com/anaconda/</a> (2022)</li><li>Peng, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+BaSiC+tool+for+background+and+shading+correction+of+optical+microscopy+images.">A BaSiC tool for background and shading correction of optical microscopy images.</a> Nature Communications. 8, 14836 (2017).</li><li>Klein, S., Staring, M., Murphy, K., Viergever, M. A., Pluim, J. P. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=elastix:+a+toolbox+for+intensity-based+medical+image+registration.">elastix: a toolbox for intensity-based medical image registration.</a> IEEE Transactions on Medical Imaging. 29, 196-205 (2010).</li><li>Lowe, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sift-the+scale+invariant+feature+transform.">Sift-the scale invariant feature transform.</a> International Journal. 2 (91-110), 2 (2004).</li><li>Young, D. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole-brain+image+analysis+and+anatomical+atlas+3D+generation+using+MagellanMapper.">Whole-brain image analysis and anatomical atlas 3D generation using MagellanMapper.</a> Current Protocols in Neuroscience. 94 (1), 104 (2020).</li><li>Schindelin, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fiji:+an+open-source+platform+for+biological-image+analysis.">Fiji: an open-source platform for biological-image analysis.</a> Nature Methods. 9 (7), 676-682 (2012).</li><li>Vel&#237;&#353;ek, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Under+the+(Light)+sheet+after+the+iDISCO.">Under the (Light) sheet after the iDISCO.</a> Epilepsy Currents / American Epilepsy Society. 16 (6), 405-407 (2016).</li><li>Young, D. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Constructing+and+optimizing+3D+atlases+from+2D+data+with+application+to+the+developing+mouse+brain.">Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain.</a> eLife. 10, (2021).</li><li>Yun, D. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrafast+immunostaining+of+organ-scale+tissues+for+scalable+proteomic+phenotyping.">Ultrafast immunostaining of organ-scale tissues for scalable proteomic phenotyping.</a> bioRxiv. , (2019).</li><li>Silvestri, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Universal+autofocus+for+quantitative+volumetric+microscopy+of+whole+mouse+brains.">Universal autofocus for quantitative volumetric microscopy of whole mouse brains.</a> Nature Methods. 18 (8), 953-958 (2021).</li><li>Frasconi, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+automated+identification+of+mouse+brain+cells+in+confocal+light+sheet+microscopy+images.">Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images.</a> Bioinformatics. 30 (17), 587 (2014).</li><li>Kruskal, J. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+shortest+spanning+subtree+of+a+graph+and+the+traveling+salesman+problem.">On the shortest spanning subtree of a graph and the traveling salesman problem.</a> Proceedings of the American Mathematical Society. American Mathematical Society. 7 (1), 48-50 (1956).</li><li>Wang, Q., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+allen+mouse+brain+common+coordinate+framework:+A+3D+reference+atlas.">The allen mouse brain common coordinate framework: A 3D reference atlas.</a> Cell. 181, 936-953 (2020).</li><li>Borland, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Segmentor:+a+tool+for+manual+refinement+of+3D+microscopy+annotations.">Segmentor: a tool for manual refinement of 3D microscopy annotations.</a> BMC Bioinformatics. 22 (1), 260 (2021).</li><li>Kumar, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dual-view+plane+illumination+microscopy+for+rapid+and+spatially+isotropic+imaging.">Dual-view plane illumination microscopy for rapid and spatially isotropic imaging.</a> Nature Protocols. 9 (11), 2555-2573 (2014).</li></ol>

Tissue clearing methods are useful techniques for measuring 3D cellular organization of the brain. There are a host of tissue clearing methods described in the literature, each with its advantages and limitations6,7,8,9. The options for computational tools to analyze the cell types in the tissue-cleared images are relatively limited. Other available tools have been implemented to sparse cell po...

Whole-brain imaging at single-cell resolution is an important challenge in neuroscience. Cellular-resolution brain images allow for detailed analysis and system-level mapping of brain circuitry and how that circuitry is disrupted by genetic or environmental risk factors for neuropsychiatric disorders, cellular behavior in developing embryos, as well as neural circuits in the adult brain1,2,3. There are multiple histological methods that allow for high-resolution images of the reconstructed 3D brain; however, these techniques require expensive, specialized equipment, may not be compatible with immunolabeling, and the two-dimensional (2D) nature of some methods may lead to tissue damage and shearing during sectioning4,5.
Recent advancements have provided an alternative approach for imaging entire brains that does not require tissue sectioning; they involve using tissue clearing to make brains transparent. Transparency is achieved in most tissue clearing methods by both removing lipids, as they are a major source of light scattering, and matching the refractive index (RI) of the object with the RI of the sample immersion solution during imaging. Light can then pass through the boundary between materials without being scattered6,7,8,9.
Tissue clearing methods, such as iDISCO+, are often combined with rapid 3D imaging using single-photon excitation microscopy, such as LSFM6,7,10. Within transparent tissues labeled with a fluorophore, light-sheet fluorescence microscopy images sections by excitation with a thin plane of light11. The main advantage of LSFM is that a single optical section is illuminated at a time, with all the fluorescence from the molecules within that section being excited, which minimizes photobleaching. Moreover, imaging an entire optical slice enables camera-based detection of that excited slice, increasing speed relative to point scanning12. LSFM nondestructively produces well-registered optical sections that are suitable for 3D reconstruction.
While the iDISCO+ method allows for inexpensive tissue clearing within ~3 weeks, dehydration steps within the protocol may lead to tissue shrinkage and potential alteration of the sample morphology, thus affecting volumetric measurements6,10. Adding a secondary imaging method, such as MRI, to be used prior to the tissue clearing procedure can measure the degree of tissue clearing-induced shrinkage across the sample. During the dehydration steps, differences in mechanical properties between gray and white matter may lead to nonuniform brain matter deformations, resulting in dissimilar tissue clearing-induced volume deformations between wild-type and mutant samples and may confound interpretations of volumetric differences in these samples10,13. MRI is performed by first perfusing the animal with a contrast agent (e.g., gadolinium), followed by incubating the extracted tissue of interest in an immersion solution (e.g., fomblin) before imaging14. MRI is compatible with tissue clearing and performing LSFM on the same sample.
LSFM is often used to create large-scale microscopy images for qualitative visualization of the brain tissue of interest rather than quantitative evaluation of brain structure (Figure 1). Without quantitative evaluation, it is difficult to demonstrate structural differences resulting from genetic or environmental insults. As tissue-clearing and imaging technologies improve, along with decreased costs of storage and computing power, quantifying cell type localizations within the tissue of interest is becoming more accessible, allowing more researchers to include these data in their studies.
With over 100 million cells in the mouse brain15 and whole-brain imaging sessions that can generate terabytes of data, there is increased demand for advanced image analysis tools that allow accurate quantification of features within the images, such as cells. A host of segmentation methods exist for tissue-cleared images that apply thresholding for nuclear staining intensity and filter objects with predefined shapes, sizes, or densities10,16,17,18. However, inaccurate interpretations of results can arise from variations in parameters such as cell size, image contrast, and labeling intensity. This paper describes our established protocol to quantify cell nuclei in the mouse brain. First, we detail steps for tissue collection of the P4 mouse brain, followed by a tissue clearing and immunolabeling protocol optimized from the publicly available iDISCO+ method10. Second, we describe image acquisition using MRI and light-sheet microscopy, including the parameters used for capturing images. Finally, we describe and demonstrate NuMorph19, a set of image analysis tools our group has developed that allows cell-type specific quantification after tissue clearing, immunolabeling with nuclear markers, and light-sheet imaging of annotated regions.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Bruker 9.4T/30 cm MRI Scanner</td>
			<td>Bruker Biospec</td>
			<td></td>
			<td>Horizontal Bore Animal MRI System</td>
		</tr>
		<tr>
			<td>Dibenzyl ether</td>
			<td>Sigma-Aldrich</td>
			<td>108014-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>Dichloromethane (DCM)</td>
			<td>Sigma-Aldrich</td>
			<td>270997-1L</td>
			<td></td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxide (DMSO)</td>
			<td>Fisher-Scientific</td>
			<td>ICN19605590</td>
			<td></td>
		</tr>
		<tr>
			<td>Donkey serum</td>
			<td>Sigma-Aldrich</td>
			<td>S30-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>EVO 860 4TB external SSD</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Fomblin Y</td>
			<td>Speciality Fluids Company</td>
			<td>YL-VAC-25-6</td>
			<td>perfluoropolyether lubricant</td>
		</tr>
		<tr>
			<td>gadolinium contrast agent (ProHance)</td>
			<td>Bracco Diagnostics</td>
			<td>A9576</td>
			<td></td>
		</tr>
		<tr>
			<td>gadolinium contrast agent(ProHance)</td>
			<td>Bracco Diagnostics</td>
			<td>0270-1111-03</td>
			<td></td>
		</tr>
		<tr>
			<td>GeForce GTX 1080 Ti 11GB GPU</td>
			<td>EVGA</td>
			<td>08G-P4-6286-KR</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma-Aldrich</td>
			<td>G7126-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Heparin sodium salt</td>
			<td>Sigma-Aldrich</td>
			<td>H3393-10KU</td>
			<td>Dissolved in H2O to 10 mg/mL</td>
		</tr>
		<tr>
			<td>Hydrogen peroxide solution, 30%</td>
			<td>Sigma-Aldrich</td>
			<td>H1009-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>ImSpector Pro</td>
			<td>LaVision BioTec</td>
			<td></td>
			<td>Microscope image acquisition software</td>
		</tr>
		<tr>
			<td>ITK Snap</td>
			<td></td>
			<td></td>
			<td>segmentation software</td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Fisher-Scientific</td>
			<td>A412SK-4</td>
			<td></td>
		</tr>
		<tr>
			<td>MVPLAPO 2x/0.5 NA Objective</td>
			<td>Olympus</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde, powder, 95% (PFA)</td>
			<td>Sigma-Aldrich</td>
			<td>30525-89-4</td>
			<td>Dissolved in 1x PBS to 4%</td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline 10x (PBS)</td>
			<td>Corning</td>
			<td>46-013-CM</td>
			<td>Diluted to 1x in H2O</td>
		</tr>
		<tr>
			<td>Sodium Azide</td>
			<td>Sigma-Aldrich</td>
			<td>S2002-100G</td>
			<td>Dissolved in H2O to 10%</td>
		</tr>
		<tr>
			<td>Sodium deoxycholate</td>
			<td>Sigma-Aldrich</td>
			<td>D6750-10G</td>
			<td></td>
		</tr>
		<tr>
			<td>Tergitol type NP-40</td>
			<td>Sigma-Aldrich</td>
			<td>NP40S-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>TritonX-100</td>
			<td>Sigma-Aldrich</td>
			<td>T8787-50ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Fisher-Scientific</td>
			<td>BP337 500</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultramicroscope II Light Sheet Microscope</td>
			<td>LaVision BioTec</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Xeon Processor E5-2690 v4</td>
			<td>Intel</td>
			<td>E5-2690</td>
			<td></td>
		</tr>
		<tr>
			<td>Zyla sCMOS Camera</td>
			<td>Andor</td>
			<td></td>
			<td>Complementary metal oxide semiconductor camera</td>
		</tr>
		<tr>
			<td>Antibody</td>
			<td></td>
			<td></td>
			<td>Working concentration</td>
		</tr>
		<tr>
			<td>Alexa Fluor Goat 790 Anti-Rabbit</td>
			<td>Thermofisher Scientific</td>
			<td>A11369</td>
			<td>(1:50)</td>
		</tr>
		<tr>
			<td>Alexa Fluor Goat 568 Anti-Rat</td>
			<td>Thermofisher Scientific</td>
			<td>A11077</td>
			<td>(1:200)</td>
		</tr>
		<tr>
			<td>Rat anti-Ctip2</td>
			<td>Abcam</td>
			<td>ab18465</td>
			<td>(1:400)</td>
		</tr>
		<tr>
			<td>Rabbit anti-Brn2</td>
			<td>Cell Signaling Technology</td>
			<td>12137</td>
			<td>(1:100)</td>
		</tr>
		<tr>
			<td>To-Pro 3 (TP3)</td>
			<td>Thermofisher Scientific</td>
			<td>T3605</td>
			<td>(1:400)</td>
		</tr>
	</tbody>
</table>

whole-brain single-cell imaging and analysis of intact neonatal mouse brains using mri, tissue clearing, and light-sheet microscopy

Tissue clearing followed by light-sheet microscopy (LSFM) enables cellular-resolution imaging of intact brain structure, allowing quantitative analysis of structural changes caused by genetic or environmental perturbations. Whole-brain imaging results in more accurate quantification of cells and the study of region-specific differences that may be missed with commonly used microscopy of physically sectioned tissue. Using light-sheet microscopy to image cleared brains greatly increases acquisition speed as compared to confocal microscopy. Although these images produce very large amounts of brain structural data, most computational tools that perform feature quantification in images of cleared tissue are limited to counting sparse cell populations, rather than all nuclei.
Here, we demonstrate NuMorph (Nuclear-Based Morphometry), a group of analysis tools, to quantify all nuclei and nuclear markers within annotated regions of a postnatal day 4 (P4) mouse brain after clearing and imaging on a light-sheet microscope. We describe magnetic resonance imaging (MRI) to measure brain volume prior to shrinkage caused by tissue clearing dehydration steps, tissue clearing using the iDISCO+ method, including immunolabeling, followed by light-sheet microscopy using a commercially available platform to image mouse brains at cellular resolution. We then demonstrate this image analysis pipeline using NuMorph, which is used to correct intensity differences, stitch image tiles, align multiple channels, count nuclei, and annotate brain regions through registration to publicly available atlases.
We designed this approach using publicly available protocols and software, allowing any researcher with the necessary microscope and computational resources to perform these techniques. These tissue clearing, imaging, and computational tools allow measurement and quantification of the three-dimensional (3D) organization of cell-types in the cortex and should be widely applicable to any wild-type/knockout mouse study design.

As the iDISCO+ protocol introduces significant tissue shrinkage, which is easily noticeable by eye (Figure 2B), we added an MRI step to this pipeline prior to tissue clearing to quantify the shrinkage induced by tissue clearing. The workflow starts with removal of the non-brain tissue from the MR image (Figure 2C). Next, a rigid transformation (3 translation and 3 rotation angles) is applied to align the MR image to the light-sheet image (Fi...

Watch this Scientific Journal Video about Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy at JoVE.com

Whole-Brain Single-Cell Imaging and Analysis of Intact Neonatal Mouse Brains Using MRI, Tissue Clearing, and Light-Sheet Microscopy

This protocol describes methods for conducting magnetic resonance imaging, clearing, and immunolabeling of intact mouse brains using iDISCO+, followed by a detailed description of imaging using light-sheet microscopy, and downstream analyses using NuMorph.

Tissue clearing followed by light-sheet microscopy (LSFM) enables cellular-resolution imaging of intact brain structure, allowing quantitative analysis of ...

Research

JoVE Journal

Neuroscience

Multiple-mouse Neuroanatomical Magnetic Resonance Imaging

The field of mouse phenotyping with magnetic resonance imaging (MRI) is rapidly growing, motivated by the need for improved tools for characterizing and ...

Functional Neuroimaging Using Ultrasonic Blood-brain Barrier Disruption and Manganese-enhanced MRI

Although mice are the dominant model system for studying the genetic and molecular underpinnings of neuroscience, functional neuroimaging in mice remains ...

Micron-scale Resolution Optical Tomography of Entire Mouse Brains with Confocal Light Sheet Microscopy

Understanding the architecture of mammalian  brain at single-cell resolution is one of the key issues of neuroscience.  However, mapping neuronal soma and ...

Stereotaxic Surgery for Genetic Manipulation in Striatal Cells of Neonatal Mouse Brains

Many genes are expressed in embryonic brains, and some of them are continuously expressed in the brain after birth. For such persistently expressed genes, ...

Visualization of Motor Axon Navigation and Quantification of Axon Arborization In Mouse Embryos Using Light Sheet Fluorescence Microscopy

Spinal motor neurons (MNs) extend their axons to communicate with their innervating targets, thereby controlling movement and complex tasks in ...

Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing

Probing an individual cell&#39;s gene expression enables the identification of cell type and cell state. Single-cell RNA sequencing has emerged as a ...

Whole-Brain 3D Activation and Functional Connectivity Mapping in Mice using Transcranial Functional Ultrasound Imaging

Functional ultrasound (fUS) imaging is a novel brain imaging modality that relies on the high-sensitivity measure of the cerebral blood volume achieved by ...

Imaging and Quantification of Intact Neuronal Dendrites via CLARITY Tissue Clearing

Brain activity, the electrochemical signals passed between neurons, is determined by the connectivity patterns of neuronal networks, and from the ...

Deep-Tissue Three-Photon Fluorescence Microscopy in Intact Mouse and Zebrafish Brain

Multiphoton microscopy techniques, such as two-photon microscopy (2PM) and three-photon microscopy (3PM), are powerful tools for deep-tissue in vivo ...

A Tissue Clearing Method for Neuronal Imaging from Mesoscopic to Microscopic Scales

A detailed protocol is provided here to visualize neuronal structures from mesoscopic to microscopic levels in brain tissues. Neuronal structures ranging ...