This study is supported by the Glaucoma Research Foundation Shaffer Grant, 4-CA Cavalier Collaborative Award, R01EY029121, R01EY035088, and Knights Templar Eye Foundation.&#8195;

All animal procedures were approved by the Institutional Animal Care and Use Committee at the University of Virginia and conformed to the guideline on Use of Animals from the National Institute of Health (NIH). See the Table of Materials for details related to all materials, reagents, and instruments used in this protocol.
1. In vivo vis-OCT imaging
<ol>
	<li>The vis-OCT system
	<ol>
		<li>Image the mice eyes using a small animal vis-OCT system that uses a supercontinuum light source, which delivers visible-light illumination between 480 nm and 650 nm. Ensure that the power incident on the cornea is 1 mW and use an A-line rate of 25 kHz and an integration time of 39.3 &#181;s per A-line.</li>
		<li>Ensure that the spectral detection range of the spectrometer is between 508 nm and 613 nm, which provides an axial resolution of 1.3 &#181;m in the retina. The total imaging volume is approximately 700 &#181;m (x) x 700 &#181;m (y) x 1,500 &#181;m (z). The lateral resolution is between 4.5 &#181;m at the center of the field of view and 8.7 &#181;m at 350 &#181;m from the center11,13.</li>
	</ol>
	</li>
	<li>Mouse anesthesia
	<ol>
		<li>Anesthetize mice of C57BL/6 background and either sex with an intraperitoneal injection of Ketamine (114 mg/kg) and Xylazine (17 mg/kg) cocktail and dilate their pupils using 1% tropicamide drops. Confirm adequate anesthetization by loss of pedal reflex after a firm toe pinch.</li>
		<li>During imaging, keep the mouse warm by using an infrared heat lamp. After each image acquisition, apply artificial tears to prevent corneal dehydration.</li>
	</ol>
	</li>
	<li>Positioning of the mouse for imaging
	<ol>
		<li>Place the anesthetized mouse on the animal holder and keep the mouse in position with the help of two Velcro straps. 
		NOTE: The animal holder allows movement in three dimensions (vertical adjustment, fine horizontal adjustment, as well as pitch and yaw adjustments) to place the laser into the mouse&#39;s eye.</li>
	</ol>
	</li>
	<li>Adjusting imaging parameters
	<ol>
		<li>Turn on the computer and open the referenced software, which will turn on the laser automatically.</li>
		<li>Adjust the animal holder until the laser is stable and centered into the mouse&#39;s eye. Visualize the posterior part of the eye through an En Face preview in the software interface, the field of view (FOV) of the superficial vascular plexus, and a B-scan, the cross-section of the retina within the FOV.</li>
		<li>Acquire a vis-OCT volume by clicking on the Acquire button on the software interface after performing minor adjustments of the optical focus, which consists of 512 A-lines/B-scan and 512 B-scans/volume. 
		NOTE: This process takes ~10.5 s. Image acquisition is guided by a built-in quality index (QI) estimator to ensure that images below a predetermined threshold (QI &#60; 45) are not included.
		<ol>
			<li>For each mouse, acquire four vis-OCT volumes from the same eye. Align the optic nerve head (ONH) in each of the four corners in the FOV to cover different areas of the retina. 
			NOTE: Such placement minimizes the retinal curvature, which maximizes RNFL reflectance throughout the FOV. It requires ~1 min to reposition the eye between each acquisition (Figure 1A,B).</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Vis-OCTF analysis 
	NOTE: MATLAB is used to perform image analysis.
	<ol>
		<li>To generate vis-OCT fibergrams from the vis-OCT volume, use an intensity-based threshold method (MATLAB code line&#160;808) to detect the surface of the retina. 
		NOTE: These lines use the imadjust function to adjust the intensity values of the bscan. The [0.0087 0.08] argument passed to imadjust specifies the range of intensities to map to the full dynamic range of the output image.</li>
		<li>Crop the RNFL by selecting the first ~16 &#181;m in depth. See Matlab code line 782. 
		NOTE: The typical in vivo RNFL thickness in an adult wild-type C57BL/6 mouse is ~14 &#181;m and can vary among different segmentation methods13.</li>
		<li>Change the paths of the RAW file (line 9), Files for reconstruction (line 11), and file name (line 15), click Run, and wait for the OCT image to be analyzed by the MATLAB code. Calculate the mean intensity projection along the axial (z) direction (MATLAB code lines 905-908) to generate the fibergram image composed of RGC axon bundles and surrounding vasculature. Montage the four images after fibergram processing for each FOV by aligning the blood vessels with a graphics editor of choice, covering ~1.2 x 1.2 mm in total. The RAW files are usually saved in the folder: Halo Data, under the date of OCT imaging (e.g., 0606 Opticent). 
		&#8203;NOTE: The MATLAB codes are available in Supplementary File 1.</li>
	</ol>
	</li>
</ol>
2. Ex vivo confocal imaging
<ol>
	<li>Mouse euthanasia
	<ol>
		<li>After acquiring vis-OCT data, euthanize the mice with a mixture of pentobarbital sodium (390 mg/mL) and phenytoin sodium (50mg/mL).&#160;Phenytoin sodium functions by amplifying the effects of pentobarbital sodium, which has been widely applied in rodent euthanasia14,15. For each mouse, use 0.2 mL/20 g of the diluted mixture (156 mg/mL) and perfuse with 20 mL of phosphate-buffered saline (PBS) and then, 20 mL of 4% paraformaldehyde (PFA) in PBS16,17.</li>
	</ol>
	</li>
	<li>Eye dissection and orientation
	<ol>
		<li>Enucleate the eyes and make a mark on the temporal side to indicate the orientation.</li>
		<li>After carefully removing the anterior chamber,&#160;the ocular lens, vitreous, and fix the eyecups in PFA for 30 min.</li>
		<li>Wash the eyecups with PBS for 30 min, and replace the PBS solution 3x during the washing. Then, wash with 0.5% Triton X-100 in PBS (pH 7.5) for 30 min.</li>
		<li>Incubate the eyecups in blocking buffer (5% donkey serum with 2.5% bovine serum albumin and 0.5% Triton X-100 in Tris-buffered saline [pH 7.5]) for 2 h at room temperature.</li>
	</ol>
	</li>
	<li>Immunostaining 
	NOTE: The eyecups are now ready to be stained with the primary antibodies of mouse anti-Tuj1 to detect RGC axon bundles and rat anti-ICAM-2 to detect blood vessels.
	<ol>
		<li>Incubate the eye cups overnight with the primary antibodies, mouse anti-Tuj1 (1:200 in blocking buffer) and rat anti-ICAM-2 (1:500 in blocking buffer), at 4 &#176;C.</li>
		<li>Wash the eyecups 3-5x for 1 h each time, with a phosphate-buffered saline solution containing 0.5% Triton X-100 (PBST) to minimize background and remove any unbound antibody.</li>
		<li>After washing, incubate the eye cups overnight with the secondary antibodies, donkey anti-mouse Immunoglobulin G conjugated to Alexa Fluor 488 dye (green fluorescence) and donkey anti-rat IgG conjugated to Alexa Fluor 594 dye (red fluorescence), all diluted 1:1000 in blocking buffer, at 4 &#176;C.</li>
		<li>The following day, wash the eyecups 3-5x for 1 h each with PBST to minimize background and remove unbound antibody.</li>
		<li>Transfer the eyecups to a Petri dish of PBS before the flat mount.</li>
	</ol>
	</li>
	<li>Flat-mounted retina
	<ol>
		<li>After the immunostaining process, isolate the retinas from the eyecups under the microscope.</li>
		<li>Cut the retinas into four leaves and flat mount them with the RGC layer facing up. Leave the mark on the temporal side attached to the retina to indicate orientation.</li>
		<li>Coverslip the retinas with mounting medium13,18. Seal the slides with nail polish13,18,19.</li>
	</ol>
	</li>
	<li>Confocal imaging 
	NOTE: The image processing of confocal images was performed using ZEN Microscopy Software.
	<ol>
		<li>Turn on the confocal microscope, and under Locate mode, find the area of interest using the eyepiece of the microscope.</li>
		<li>Under acquisition mode, set up tiles to cover the whole retina and z-stack slices to cover all layers of information. Image a least 25 tiles across the whole retina to cover the total volume of 5.99 mm (x) x 5.88 mm (y) x 30 &#181;m (z) at a pixel size of 1.24 &#181;m/pixel.</li>
		<li>Project the Z-stack slices to create two-dimensional en face confocal microscopy images (Figure 1C,D)11,13,19,20,21.</li>
	</ol>
	</li>
</ol>
3. Alignment of in vivo and ex vivo images
<ol>
	<li>After processing the fibergram, create a composite image that includes the four images acquired from each mouse by aligning all the blood vessels with a graphics editor of choice. 
	NOTE: On average, the final composite image is approximately 1.2 mm (x) x 1.2 mm (y), as shown in Figure 1B.</li>
	<li>Use the optic nerve head (ONH) and the pattern of blood vessels as landmarks to align the composite fibergram. Obtain the in vivo and ex vivo alignment by overlapping the blood vessel pattern of the composite OCT images with the confocal images of the same retina stained with ICAM-2.</li>
</ol>

Mouse Retina OCT Fibergram Alignment with Confocal Images

<ol>
	<li>Sernagor, E., Eglen, S. J., Wong, R. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+retinal+ganglion+cell+structure+and+function.">Development of retinal ganglion cell structure and function.</a> Progress in Retinal and Eye Research. 20 (2), 139-174 (2001).</li><li>Sanes, J. R., Masland, R. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+types+of+retinal+ganglion+cells:+current+status+and+implications+for+neuronal+classification.">The types of retinal ganglion cells: current status and implications for neuronal classification.</a> Annual Review of Neuroscience. 38, 221-246 (2015).</li><li>Seabrook, T. A., Burbridge, T. J., Crair, M. C., Huberman, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Architecture,+function,+and+assembly+of+the+mouse+visual+system.">Architecture, function, and assembly of the mouse visual system.</a> Annual Review of Neuroscience. 40, 499-538 (2017).</li><li>Cang, J., Savier, E., Barchini, J., Liu, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visual+function,+organization,+and+development+of+the+mouse+superior+colliculus.">Visual function, organization, and development of the mouse superior colliculus.</a> Annual Review of Vision Science. 4, 239-262 (2018).</li><li>Quigley, H. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Understanding+glaucomatous+optic+neuropathy:+the+synergy+between+clinical+observation+and+investigation.">Understanding glaucomatous optic neuropathy: the synergy between clinical observation and investigation.</a> Annual Review of Vision Science. 2, 235-254 (2016).</li><li>Whitmore, A. V., Libby, R. T., John, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Glaucoma:+thinking+in+new+ways-a+role+for+autonomous+axonal+self-destruction+and+other+compartmentalised+processes.">Glaucoma: thinking in new ways-a role for autonomous axonal self-destruction and other compartmentalised processes.</a> Progress in Retinal and Eye Research. 24 (6), 639-662 (2005).</li><li>Syc-Mazurek, S. B., Libby, R. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Axon+injury+signaling+and+compartmentalized+injury+response+in+glaucoma.">Axon injury signaling and compartmentalized injury response in glaucoma.</a> Progress in Retinal and Eye Research. 73, 100769 (2019).</li><li>Puyang, Z., Chen, H., Liu, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Subtype-dependent+morphological+and+functional+degeneration+of+retinal+ganglion+cells+in+mouse+models+of+experimental+glaucoma.">Subtype-dependent morphological and functional degeneration of retinal ganglion cells in mouse models of experimental glaucoma.</a> Journal of Nature and Science. 1 (5), (2015).</li><li>Tatham, A. J., Medeiros, F. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detecting+structural+progression+in+glaucoma+with+optical+coherence+tomography.">Detecting structural progression in glaucoma with optical coherence tomography.</a> Ophthalmology. 124, S57-S65 (2017).</li><li>Shu, X., Beckmann, L., Zhang, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visible-light+optical+coherence+tomography:+a+review.">Visible-light optical coherence tomography: a review.</a> Journal of Biomedical Optics. 22 (12), 1-14 (2017).</li><li>Miller, D. 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=Visible-light+optical+coherence+tomography+fibergraphy+for+quantitative+imaging+of+retinal+ganglion+cell+axon+bundles.">Visible-light optical coherence tomography fibergraphy for quantitative imaging of retinal ganglion cell axon bundles.</a> Translational Vision Science and Technology. 9 (11), (2020).</li><li>Beckmann, 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=In+vivo+imaging+of+the+inner+retinal+layer+structure+in+mice+after+eye-opening+using+visible-light+optical+coherence+tomography.">In vivo imaging of the inner retinal layer structure in mice after eye-opening using visible-light optical coherence tomography.</a> Experimental Eye Research. 211, 108756 (2021).</li><li>Grannonico, 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=Global+and+regional+damages+in+retinal+ganglion+cell+axon+bundles+monitored+non-invasively+by+visible-light+optical+coherence+tomography+fibergraphy.">Global and regional damages in retinal ganglion cell axon bundles monitored non-invasively by visible-light optical coherence tomography fibergraphy.</a> Journal of Neuroscience. 41 (49), 10179-10193 (2021).</li><li>Allen-Worthington, K. H., Brice, A. K., Marx, J. O., Hankenson, F. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intraperitoneal+Injection+of+Ethanol+for+the+Euthanasia+of+Laboratory+Mice+(Mus+musculus)+and+Rats+(Rattus+norvegicus).">Intraperitoneal Injection of Ethanol for the Euthanasia of Laboratory Mice (Mus musculus) and Rats (Rattus norvegicus).</a> J Am Assoc Lab Anim Sci. 54 (6), 769-778 (2015).</li><li>Boivin, G. P., Bottomley, M. A., Schiml, P. A., Goss, L., Grobe, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Physiologic,+Behavioral,+and+Histologic+Responses+to+Various+Euthanasia+Methods+in+C57BL/6NTac+Male+Mice.">Physiologic, Behavioral, and Histologic Responses to Various Euthanasia Methods in C57BL/6NTac Male Mice.</a> J Am Assoc Lab Anim Sci. 56 (1), 69-78 (2017).</li><li>Chen, 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=Progressive+degeneration+of+retinal+and+superior+collicular+functions+in+mice+with+sustained+ocular+hypertension.">Progressive degeneration of retinal and superior collicular functions in mice with sustained ocular hypertension.</a> Investigative Ophthalmology and Visual Science. 56 (3), 1971-1984 (2015).</li><li>Feng, L., Chen, H., Suyeoka, G., Liu, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+laser-induced+mouse+model+of+chronic+ocular+hypertension+to+characterize+visual+defects.">A laser-induced mouse model of chronic ocular hypertension to characterize visual defects.</a> Journal of Visualized Experiments: JoVE. 78 (78), (2013).</li><li>Gao, 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=Differential+effects+of+experimental+glaucoma+on+intrinsically+photosensitive+retinal+ganglion+cells+in+mice.">Differential effects of experimental glaucoma on intrinsically photosensitive retinal ganglion cells in mice.</a> Journal of Comparative Neurology. 530 (9), 1494-1506 (2022).</li><li>Thomson, B. 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=Angiopoietin-1+knockout+mice+as+a+genetic+model+of+open-angle+glaucoma.">Angiopoietin-1 knockout mice as a genetic model of open-angle glaucoma.</a> Translational Vision Science and Technology. 9 (4), (2020).</li><li>Feng, 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=Sustained+ocular+hypertension+induces+dendritic+degeneration+of+mouse+retinal+ganglion+cells+that+depends+on+cell+type+and+location.">Sustained ocular hypertension induces dendritic degeneration of mouse retinal ganglion cells that depends on cell type and location.</a> Investigative Ophthalmology and Visual Science. 54 (2), 1106-1117 (2013).</li><li>Grannonico, 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=Longitudinal+analysis+of+retinal+ganglion+cell+damage+at+individual+axon+bundle+level+in+mice+using+visible-light+optical+coherence+tomography+fibergraphy.">Longitudinal analysis of retinal ganglion cell damage at individual axon bundle level in mice using visible-light optical coherence tomography fibergraphy.</a> Translational Vision Science and Technology. 12 (5), (2023).</li></ol>

Chang, S., None; Xu, W., None; Fan, W., None; McDaniel, J.A., None; D.A. Miller, None; M. Grannonico, None; M. Liu, None; X. Liu, None; H.F. Zhang has financial interests in Opticent Health, which did not support this work.

There are two steps in this protocol that require attention. First, it is necessary to ensure that the animal is under deep anesthesia and that their eyes are fully dilated before vis-OCT imaging. If the mice are not adequately anesthetized, their fast breathing may lead to unstable movements of the en face images, which can adversely affect the quality of the fibergram. Moreover, insufficient dilation can also have a negative impact on image quality since the iris may obstruct the light, preventing it from reac...

Retinal ganglion cells (RGCs) play a critical role in visual information processing, receiving synaptic inputs through their dendritic trees in the inner plexiform layer (IPL) and transmitting the information via their axons in the retinal nerve fiber layer (RNFL) to the brain1,2,3,4. In diseased conditions such as glaucoma, early RGC degeneration may result in subtle changes in the RNFL, the ganglion cell layer (GCL), the IPL, and the optic nerve in both patients and rodent models5,6,7,8,9. Early detection of these morphological changes in RGCs is thus essential for timely intervention to prevent RGC and vision loss.
We have recently developed a new clinical-ready imaging technology called visible-light optical coherence tomography (vis-OCT) to satisfy the need for in vivo monitoring of RGC damage. Vis-OCT improved the axial resolution, reaching 1.3 &#181;m in the retina10, 11, allowing for the visualization of individual RGC axon bundles in the RNFL. Subsequently, vis-OCT fibergraphy (vis-OCTF) was established to track and quantify RGC damage at the single axon bundle level in mice11,12,13. However, ex vivo confocal imaging of the same retina as the gold standard is often necessary to validate the in vivo findings. Therefore, this study will demonstrate how to align in vivo images acquired by vis-OCTF with ex vivo confocal images of the same mouse retina. The protocol aims to validate the in vivo findings by ex vivo confocal imaging and establish a foundation for examining the molecular and cellular changes underlying RGC damage in diseased conditions.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Halo 100</td>
			<td>Opticent Health, Evanston, IL</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Zeiss LSM800 microscope</td>
			<td>Carl Zeiss</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Drugs and antibodies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>4% paraformaldehyde (PFA)</td>
			<td>Santz Cruz Biotechnology, SC-281692</td>
			<td></td>
			<td>1-2 drops</td>
		</tr>
		<tr>
			<td>Bovine serum albumin powder</td>
			<td>Fisher Scientific, BP9706-100</td>
			<td></td>
			<td>1:10</td>
		</tr>
		<tr>
			<td>Donkey anti Mouse Alexa Fluor 488 dye</td>
			<td>Thermo Fisher Scientific, Cat# A-21202</td>
			<td></td>
			<td>1:1,000</td>
		</tr>
		<tr>
			<td>Donkey anti rat Alexa Fluor 594 dye</td>
			<td>Thermo Fisher Scientific, Cat# A-21209</td>
			<td></td>
			<td>1:1,000</td>
		</tr>
		<tr>
			<td>Euthasol (a mixture of pentobarbital sodium (390 mg/mL) and phenytoin sodium (50 mg/mL))</td>
			<td>Covetrus, NDC 11695-4860-1</td>
			<td></td>
			<td>15.6 mg/mL</td>
		</tr>
		<tr>
			<td>Ketamine</td>
			<td>Covetrus, NADA043304</td>
			<td></td>
			<td>114 mg/kg</td>
		</tr>
		<tr>
			<td>Mouse anti-Tuj1</td>
			<td>A gift from Anthony J. Spano, University of Virginia</td>
			<td></td>
			<td>1:200</td>
		</tr>
		<tr>
			<td>Normal donkey serum(NDS)</td>
			<td>Millipore Sigma, S30-100 mL</td>
			<td></td>
			<td>1:100</td>
		</tr>
		<tr>
			<td>Phosphate-buffered saline (PBS, 10x), pH 7.4 
			(Contains 1370 mM NaCl, 27 mM KCl, 80 mM Na2HPO4, and 20 mM KH2PO4)</td>
			<td>Thermo Fisher Scientific, Cat# J62036.K3</td>
			<td></td>
			<td>1:10</td>
		</tr>
		<tr>
			<td>Rat anti-ICAM-2</td>
			<td>BD Pharmingen, Cat#553325</td>
			<td></td>
			<td>1:500</td>
		</tr>
		<tr>
			<td>Tropicamide drops&#160;</td>
			<td>Covetrus, NDC17478-102-12</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100 
			(Reagent Grade)</td>
			<td>VWR, CAS: 9002-93-1</td>
			<td></td>
			<td>1:20</td>
		</tr>
		<tr>
			<td>Vectashield mounting medium</td>
			<td>Vector Laboratories Inc. H2000-10</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Xylazine</td>
			<td>Covetrus, NDC59399-110-20</td>
			<td></td>
			<td>17 mg/kg</td>
		</tr>
	</tbody>
</table>

alignment of visible-light optical coherence tomography fibergrams with confocal images of the same mouse retina

In recent years, in vivo retinal imaging, which provides non-invasive, real-time, and longitudinal information about biological systems and processes, has been increasingly applied to obtain an objective assessment of neural damage in eye diseases. Ex vivo confocal imaging of the same retina is often necessary to validate the in vivo findings especially in animal research. In this study, we demonstrated a method for aligning an ex vivo confocal image of the mouse retina with its in vivo images. A new clinical-ready imaging technology called visible light optical coherence tomography fibergraphy (vis-OCTF) was applied to acquire in vivo images of the mouse retina. We then performed the confocal imaging of the same retina as the &#34;gold standard&#34; to validate the in vivo vis-OCTF images. This study not only enables further investigation of the molecular and cellular mechanisms but also establishes a foundation for a sensitive and objective evaluation of neural damage in vivo.

The composite vis-OCT fibergram is compared with the corresponding confocal image of flat-mounted retina immunostained with Tuj-1 for RGC axons (Figure 1D, top panel). Axon bundles imaged by vis-OCTF can be matched with the Tu-j1-labeled axon bundles on the confocal image. Blood vessels usually exhibit distinguishable branching structures compared with surrounding axon bundles in fibergram images, which can be matched with the ICAM-2-labeled blood vessels on the confocal image (<strong class...

Watch this Scientific Journal Video about Advancements in In Vivo and Ex Vivo Retinal Imaging for Improved Glaucoma Diagnosis and Treatment at JoVE.com

Author Spotlight: Advancements in In Vivo and Ex Vivo Retinal Imaging for Improved Glaucoma Diagnosis and Treatment 

The present protocol outlines the steps for aligning in vivo visible-light optical coherence tomography fibergraphy (vis-OCTF) images with ex vivo confocal images of the same mouse retina for the purpose of verifying the observed retinal ganglion cell axon bundle morphology in the in vivo images.

Alignment of Visible-Light Optical Coherence Tomography Fibergrams with Confocal Images of the Same Mouse Retina

In recent years, in vivo retinal imaging, which provides non-invasive, real-time, and longitudinal information about biological systems and processes, has ...

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JoVE Journal

Neuroscience

1.4K Views.  University of Virginia. The present protocol outlines the steps for aligning in vivo visible-light optical coherence tomography fibergraphy (vis-OCTF) images with ex vivo confocal images of the same mouse retina for the purpose of verifying the observed retinal ganglion cell axon bundle morphology in the in vivo images. 

Video: Author Spotlight: Advancements in In Vivo and Ex Vivo Retinal Imaging for Improved Glaucoma Diagnosis and Treatment 

Quantifying the Activity of cis-Regulatory Elements in the Mouse Retina by Explant Electroporation

Transcription factors within cellular gene networks control the spatiotemporal pattern and levels of expression of their target genes by binding to cis-regulatory elements (CREs), short (&tilde;300-600 bp) stretches of genomic DNA which can lie upstream, downstream, or within the introns of the genes they control. CREs (i.e., enhancers/promoters) typically consist of multiple clustered binding sites for both transcriptional activators and repressors1-3. They serve as logical integrators of transcriptional input giving a unitary output in the form of spatiotemporally precise and quantitatively exact promoter activity. Most studies of mammalian cis-regulation to date have relied on mouse transgenesis as a means of assaying the enhancer function of CREs4-5. This technique is time-consuming, costly and, on account of insertion site effects, largely non-quantitative. On the other hand, quantitative assays for mammalian CRE function have been developed in tissue culture systems (e.g., dual luciferase assays), but the in vivo relevance of these results is often uncertain. 
Electroporation offers an excellent alternative to traditional mouse transgenesis in that it permits both spatiotemporal and quantitative assessment of cis-regulatory activity in living mammalian tissue. This technique has been particularly useful in the analysis of cis-regulation in the central nervous system, especially in the cerebral cortex and the retina6-8. While mouse retinal electroporation, both in vivo and ex vivo, has been developed and extensively described by Matsuda and Cepko6-7,9, we have recently developed a simple approach to quantify the activity of photoreceptor-specific CREs in electroporated mouse retinas10. Given that the amount of DNA that is introduced into the retina by electroporation can vary from experiment to experiment, it is necessary to include a co-electroporated 'loading control' in all experiments. In this respect, the technique is very similar to the dual luciferase assay used to quantify promoter activity in cultured cells. 
When assaying photoreceptor cis-regulatory activity, electroporation is usually performed in newborn mice (postnatal day 0, P0) which is the time of peak rod production11-12. Once retinal cell types become post-mitotic, electroporation is much less efficient. Given the high rate of rod birth in newborn mice and the fact that rods constitute more than 70% of the cells in the adult mouse retina, the majority of cells that are electroporated at P0 are rods. For this reason, rod photoreceptors are the easiest retinal cell type to study via electroporation. The technique we describe here is primarily useful for quantifying the activity of photoreceptor CREs.

Quantifying the Activity of cis-Regulatory Elements in the Mouse Retina by Explant Electroporation

This protocol describes a simple and inexpensive way to quantify the activity of cis-regulatory elements (i.e., enhancer/promoters) in living mouse retinas via explant electroporation. DNA preparation, retinal dissection, electroporation, retinal explant culture, and post-fixation analysis and quantification are described.

Transcription factors within cellular gene networks control the spatiotemporal pattern and levels of expression of their target genes by binding to ...

In vivo Electroporation of Developing Mouse Retina

The functional characterization of genes expressed during mammalian retinal development remains a significant challenge. Gene targeting to generate constitutive or conditional loss of function knockouts remains cost and labor intensive, as well as time consuming. Adding to these challenges, retina expressed genes may have essential roles outside the retina leading to unintended confounds when using a knockout approach. Furthermore, the ability to ectopically express a gene in a gain of function experiment can be extremely valuable when attempting to identify a role in cell fate specification and/or terminal differentiation.
We present a method for the rapid and efficient incorporation of DNA plasmids into the neonatal mouse retina by electroporation. The application of short electrical impulses above a certain field strength results in a transient increase in plasma membrane permeability, facilitating the transfer of material across the membrane 1,2,3,4. Groundbreaking work demonstrated that electroporation could be utilized as a method of gene transfer into mammalian cells by inducing the formation of hydrophilic plasma membrane pores allowing the passage of highly charged DNA through the lipid bilayer 5. Continuous technical development has resulted in the viability of electroporation as a method for in vivo gene transfer in multiple mouse tissues including the retina, the method for which is described herein 6, 7, 8, 9, 10. 
DNA solution is injected into the subretinal space so that DNA is placed between the retinal pigmented epithelium and retina of the neonatal (P0) mouse and electrical pulses are applied using a tweezer electrode. The lateral placement of the eyes in the mouse allows for the easy orientation of the tweezer electrode to the necessary negative pole-DNA-retina-positive pole alignment. Extensive incorporation and expression of transferred genes can be identified by postnatal day 2 (P2). Due to the lack of significant lateral migration of cells in the retina, electroporated and non-electroporated regions are generated. Non-electroporated regions may serve as internal histological controls where appropriate. 
Retinal electroporation can be used to express a gene under a ubiquitous promoter, such as CAG, or to disrupt gene function using shRNA constructs or Cre-recombinase. More targeted expression can be achieved by designing constructs with cell specific gene promoters. Visualization of electroporated cells is achieved using bicistronic constructs expressing GFP or by co-electroporating a GFP expression construct. Furthermore, multiple constructs may be electroporated for the study of combinatorial gene effects or simultaneous gain and loss of function of different genes. Retinal electroporation may also be utilized for the analysis of genomic cis-regulatory elements by generating appropriate expression constructs and deletion mutants. Such experiments can be used to identify cis-regulatory regions sufficient or required for cell specific gene expression 11. Potential experiments are limited only by construct availability.

In vivo Electroporation of Developing Mouse Retina

A method for the incorporation of plasmid DNA into murine retinal cells for the purpose of performing either gain- or loss of function studies in vivo is presented. This method capitalizes on the transient increase in permeability of cell plasma membranes induced by the application of an external electrical field.

The functional characterization of genes expressed during mammalian retinal development remains a significant challenge.  Gene targeting to generate ...

Optical Recording of Suprathreshold Neural Activity with Single-cell and Single-spike Resolution

Signaling of information in the vertebrate central nervous system is often carried by populations of neurons rather than individual neurons. Also propagation of suprathreshold spiking activity involves populations of neurons. Empirical studies addressing cortical function directly thus require recordings from populations of neurons with high resolution. Here we describe an optical method and a deconvolution algorithm to record neural activity from up to 100 neurons with single-cell and single-spike resolution. This method relies on detection of the transient increases in intracellular somatic calcium concentration associated with suprathreshold electrical spikes (action potentials) in cortical neurons. High temporal resolution of the optical recordings is achieved by a fast random-access scanning technique using acousto-optical deflectors (AODs)1. Two-photon excitation of the calcium-sensitive dye results in high spatial resolution in opaque brain tissue2. Reconstruction of spikes from the fluorescence calcium recordings is achieved by a maximum-likelihood method. Simultaneous electrophysiological and optical recordings indicate that our method reliably detects spikes (&gt;97% spike detection efficiency), has a low rate of false positive spike detection (&lt; 0.003 spikes/sec), and a high temporal precision (about 3 msec) 3. This optical method of spike detection can be used to record neural activity in vitro and in anesthetized animals in vivo3,4.

Understanding the function of the vertebrate central nervous system requires recordings from many neurons because cortical function arises on the level of populations of neurons. Here we describe an optical method to record suprathreshold neural activity with single-cell and single-spike resolution, dithered random-access scanning. This method records somatic fluorescence calcium signals from up to 100 neurons with high temporal resolution. A maximum-likelihood algorithm deconvolves the underlying suprathreshold neural activity from the somatic fluorescence calcium signals. This method reliably detects spikes with high detection efficiency and a low rate of false positives and can be used to study neural populations in vitro and in vivo.

Signaling of information in the vertebrate central nervous system is often carried by populations of neurons rather than individual neurons. Also ...

Thinned-skull Cortical Window Technique for In Vivo Optical Coherence Tomography Imaging

Optical coherence tomography (OCT) is a biomedical imaging technique with high spatial-temporal resolution. With its minimally invasive approach OCT has been used extensively in ophthalmology, dermatology, and gastroenterology1-3. Using a thinned-skull cortical window (TSCW), we employ spectral-domain OCT (SD-OCT) modality as a tool to image the cortex in vivo. Commonly, an opened-skull has been used for neuro-imaging as it provides more versatility, however, a TSCW approach is less invasive and is an effective mean for long term imaging in neuropathology studies. Here, we present a method of creating a TSCW in a mouse model for in vivo OCT imaging of the cerebral cortex.

Thinned-skull Cortical Window Technique for In Vivo Optical Coherence Tomography Imaging

We present a method of creating a thinned-skull cortical window (TSCW) in a mouse model for in vivo OCT imaging of the cerebral cortex.

Optical coherence tomography (OCT) is a biomedical imaging technique  with high spatial-temporal resolution. With its minimally invasive approach OCT  has ...

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 projections throughout the whole brain is still challenging for imaging and data management technologies. Indeed, macroscopic volumes need to be reconstructed with high resolution and contrast in a reasonable time, producing datasets in the TeraByte range. We recently demonstrated an optical method (confocal light sheet microscopy, CLSM) capable of obtaining micron-scale reconstruction of entire mouse brains labeled with enhanced green fluorescent protein (EGFP). Combining light sheet illumination and confocal detection, CLSM allows deep imaging inside macroscopic cleared specimens with high contrast and speed. Here we describe the complete experimental pipeline to obtain comprehensive and human-readable images of entire mouse brains labeled with fluorescent proteins. The clearing and the mounting procedures are described, together with the steps to perform an optical tomography on its whole volume by acquiring many parallel adjacent stacks. We showed the usage of open-source custom-made software tools enabling stitching of the multiple stacks and multi-resolution data navigation. Finally, we illustrated some example of brain maps: the cerebellum from an L7-GFP transgenic mouse, in which all Purkinje cells are selectively labeled, and the whole brain from a thy1-GFP-M mouse, characterized by a random sparse neuronal labeling.

In this article we describe the full experimental procedure to reconstruct, with high resolution, the fine brain anatomy of fluorescently labeled mouse brains. The described protocol includes sample preparation and clearing, specimen mounting for imaging, data post-processing and multi-scale visualization.

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

Assessment of Vascular Regeneration in the CNS Using the Mouse Retina

The rodent retina is perhaps the most accessible mammalian system in which to investigate neurovascular interplay within the central nervous system (CNS). It is increasingly being recognized that several neurodegenerative diseases such as Alzheimer&#8217;s, multiple sclerosis, and amyotrophic lateral sclerosis present elements of vascular compromise. In addition, the most prominent causes of blindness in pediatric and working age populations (retinopathy of prematurity and diabetic retinopathy, respectively) are characterized by vascular degeneration and failure of physiological vascular regrowth. The aim of this technical paper is to provide a detailed protocol to study CNS vascular regeneration in the retina. The method can be employed to elucidate molecular mechanisms that lead to failure of vascular growth after ischemic injury. In addition, potential therapeutic modalities to accelerate and restore healthy vascular plexuses can be explored. Findings obtained using the described approach may provide therapeutic avenues for ischemic retinopathies such as that of diabetes or prematurity and possibly benefit other vascular disorders of the CNS.

The rodent retina has long been recognized as an accessible window to the brain. In this technical paper we provide a protocol that employs the mouse model of oxygen-induced retinopathy to study the mechanisms that lead to failure of vascular regeneration within the central nervous system after ischemic injury. The described system can also be harnessed to explore strategies to promote regrowth of functional blood vessels within the retina and CNS.

The rodent retina is perhaps the most accessible mammalian system in which to investigate neurovascular interplay within the central nervous system (CNS). ...

Imaging Ca2+ Dynamics in Cone Photoreceptor Axon Terminals of the Mouse Retina

Retinal cone photoreceptors (cones) serve daylight vision and are the basis of color discrimination. They are subject to degeneration, often leading to blindness in many retinal diseases. Calcium (Ca2+), a key second messenger in photoreceptor signaling and metabolism, has been proposed to be indirectly linked with photoreceptor degeneration in various animal models. Systematically studying these aspects of cone physiology and pathophysiology has been hampered by the difficulties of electrically recording from these small cells, in particular in the mouse where the retina is dominated by rod photoreceptors. To circumvent this issue, we established a two-photon Ca2+ imaging protocol using a transgenic mouse line that expresses the genetically encoded Ca2+ biosensor TN-XL exclusively in cones and can be crossbred with mouse models for photoreceptor degeneration. The protocol described here involves preparing vertical sections (&#8220;slices&#8221;) of retinas from mice and optical imaging of light stimulus-evoked changes in cone Ca2+ level. The protocol also allows &#8220;in-slice measurement&#8221; of absolute Ca2+ concentrations; as the recordings can be followed by calibration. This protocol enables studies into functional cone properties and is expected to contribute to the understanding of cone Ca2+ signaling as well as the potential involvement of Ca2+ in photoreceptor death and retinal degeneration.

Imaging Ca2+ Dynamics in Cone Photoreceptor Axon Terminals of the Mouse Retina

We describe a protocol to monitor Ca2+ dynamics in the axon terminals of cone photoreceptors using an ex-vivo&#160;slice preparation of the mouse retina. This protocol allows comprehensive studies of cone Ca2+ signaling in an important mammalian model system, the mouse.

Retinal cone photoreceptors (cones) serve daylight vision and are the basis of color discrimination. They are subject to degeneration, often leading to ...

Optical Coherence Tomography: Imaging Mouse Retinal Ganglion Cells In Vivo

Structural changes in the retina are common manifestations of ophthalmic diseases. Optical coherence tomography (OCT) enables their identification in vivo&#8212;rapidly, repetitively, and at a high resolution. This protocol describes OCT imaging in the mouse retina as a powerful tool to study optic neuropathies (OPN). The OCT system is an interferometry-based, non-invasive alternative to common post mortem histological assays. It provides a fast and accurate assessment of retinal thickness, allowing the possibility to track changes, such as retinal thinning or thickening. We present the imaging process and analysis with the example of the Opa1delTTAG mouse line. Three types of scans are proposed, with two quantification methods: standard and homemade calipers. The latter is best for use on the peripapillary retina during radial scans; being more precise, is preferable for analyzing thinner structures. All approaches described here are designed for retinal ganglion cells (RGC) but are easily adaptable to other cell populations. In conclusion, OCT is efficient in mouse model phenotyping and has the potential to be used for the reliable evaluation of therapeutic interventions.

Optical Coherence Tomography: Imaging Mouse Retinal Ganglion Cells In Vivo

This manuscript describes a protocol for the in vivo imaging of the mouse retina with high-resolution spectral domain optical coherence tomography (SD-OCT). It focuses on retinal ganglion cells (RGC) in the peripapillary region, with several scanning and quantifying approaches described.

Structural changes in the retina are common manifestations of ophthalmic diseases. Optical coherence tomography (OCT) enables their identification in ...

Live Images of GLUT4 Protein Trafficking in Mouse Primary Hypothalamic Neurons Using Deconvolution Microscopy

Type 2 diabetes mellitus (T2DM) is a global health crisis which is characterized by insulin signaling impairment and chronic inflammation in peripheral tissues. The hypothalamus in the central nervous system (CNS) is the control center for energy and insulin signal response regulation. Chronic inflammation in peripheral tissues and imbalances of certain chemokines (such as CCL5, TNF&#945;, and IL-6) contribute to diabetes and obesity. However, the functional mechanism(s) connecting chemokines and hypothalamic insulin signal regulation still remain unclear.
In vitro primary neuron culture models are convenient and simple models which can be used to investigate insulin signal regulation in hypothalamic neurons. In this study, we introduced exogeneous GLUT4 protein conjugated with GFP (GFP-GLUT4) into primary hypothalamic neurons to track GLUT4 membrane translocation upon insulin stimulation. Time-lapse images of GFP-GLUT4 protein trafficking were recorded by deconvolution microscopy, which allowed users to generate high-speed, high-resolution images without damaging the neurons significantly while conducting the experiment. The contribution of CCR5 in insulin regulated GLUT4 translocation was observed in CCR5 deficient hypothalamic neurons, which were isolated and cultured from CCR5 knockout mice. Our results demonstrated that the GLUT4 membrane translocation efficiency was reduced in CCR5 deficient hypothalamic neurons after insulin stimulation.

This protocol describes a technique for observation of real-time Green Fluorescence Protein (GFP) tagged Glucose Transporter 4 (GLUT4) protein trafficking upon insulin stimulation and characterization of the biological role of CCR5 in the insulin&#8211;GLUT4 signaling pathway with Deconvolution Microscopy.

Type 2 diabetes mellitus (T2DM) is a global health crisis which is characterized by insulin signaling impairment and chronic inflammation in peripheral ...

Using Optical Coherence Tomography and Optokinetic Response As Structural and Functional Visual System Readouts in Mice and Rats

Optical coherence tomography (OCT) is a fast, non-invasive, interferometric technique allowing high-resolution retinal imaging. It is an ideal tool for the investigation of processes of neurodegeneration, neuroprotection and neuro-repair involving the visual system, as these often correlate well with retinal changes. As a functional readout, visually evoked compensatory eye and head movements are commonly used in experimental models involving the visual function. Combining both techniques allows a quantitative in vivo investigation of structure and function, which can be used to investigate the pathological conditions or to evaluate the potential of novel therapeutics. A great benefit of the presented techniques is the possibility to perform longitudinal analyses allowing the investigation of dynamic processes, reducing variability and cuts down the number of animals needed for the experiments. The protocol described aims to provide a manual for acquisition and analysis of high quality retinal scans of mice and rats using a low cost customized holder with an option to deliver inhalational anesthesia. Additionally, the proposed guide is intended as an instructional manual for researchers using optokinetic response (OKR) analysis in rodents, which can be adapted to their specific needs and interests.

A detailed protocol for the assessment of structural and visual readouts in rodents by optical coherence tomography and optokinetic response is presented. The results provide valuable insights for ophthalmologic as well as neurologic research.

Optical coherence tomography (OCT) is a fast, non-invasive, interferometric technique allowing high-resolution retinal imaging. It is an ideal tool for ...