We thank the individuals who have donated their bodies for the advancement of education and research. We are grateful to the OneLegacy Foundation, which formed the basis for obtaining donor hearts for research. We are also grateful to Anthony A. Smithson and Arvin Roque-Verdeflor of the UCLA Translational Research Imaging Center (Department of Radiology) for their support in CT data acquisition. This project was supported by the UCLA Amara Yad Project. We are thankful to Drs. Kalyanam Shivkumar and Olujimi A. Ajijola for establishing and maintaining a human heart pipeline for research. We appreciate our Research Operations Manager, Amiksha S. Gandhi for her dedication to support our projects. This work was made possible by support from NIH grants OT2OD023848 &#38; P01 HL164311 and Leducq grant 23CVD04 to Kalyanam Shivkumar, the American Heart Association Career Development Award 23CDA1039446 to PH, and the UCLA Amara-Yad Project (https://www.uclahealth.org/medical-services/heart/arrhythmia/about-us/amara-yad-project). The GNEXT microPET/CT scanner used in this study was funded by an NIH Shared Instrumentation for Animal Research Grant (1 S10 OD026917-01A1).

This study used de-identified tissue samples collected from non-failing donor human hearts and was approved by the Institutional Review Board of the University of California, Los Angeles (UCLA). Samples were obtained from non-failing hearts that were rejected for transplantation. The hearts were pressure-perfused, fixed in 4% paraformaldehyde (PFA), and imaged before tissue processing per the following methods. Figure 1 summarizes the flow chart of the order of the study. The details of the reagents and the equipment used in the study are listed in the Table of Materials.
1. Micro-scale examination
<ol>
	<li>Tissue clearing using modified immunolabeling-enabled 3D imaging of solvent-cleared organs&#160;(iDISCO+) protocol.
	<ol>
		<li>Dissect 4% PFA-fixed tissue with a scalpel to fit within the 3 mm &#215; 16 mm &#215; 25 mm chamber for confocal microscopy.&#160;To image thicker tissues, additional chambers and/or spacers may be stacked on the slide.</li>
		<li>Dehydrate specimens using graded methanol (MeOH) series (20%, 40%, 60%, 80%, and 100% MeOH in deionized H2O [vol/vol]) for 1 h each at room temperature (RT) with agitation.</li>
		<li>Wash with&#160;100%&#160;MeOH for 1 h at RT and immerse in 66% dichloromethane/33% MeOH at RT with agitation overnight.</li>
		<li>The next day, wash twice in MeOH (100%) for 1 h at RT, chill at 4 &#176;C, and treat with 5% H2O2 in MeOH (vol/vol) overnight at 4&#160;&#176;C.</li>
		<li>Rehydrate with graded MeOH series (80%, 60%, 40%, and 20% MeOH) and wash in 0.01 mol/L PBS for 1 h each at RT with agitation.</li>
		<li>Wash the tissues&#160;twice in 0.01 mol/L PBS with 0.2% Triton X-100 for 1 h at RT.</li>
		<li>Prepare for immunolabeling by permeabilizing in 0.01 mol/L PBS, 20% dimethyl sulfoxide (DMSO), 0.2% Triton X-100, and 0.3 mol/L glycine for 2 days at 37&#160;&#176;C with agitation.</li>
		<li>Block in 0.01 mol/L PBS with 10% DMSO, 0.2% Triton X-100, and 5% normal donkey serum for another 2 days at 37 &#176;C with agitation.</li>
		<li>Label with a primary antibody that is compatible with MeOH conjugated to fluorophores diluted in 0.01 mol/L PBS with 10 mg/mL heparin (PTwH), 0.2% Tween-20, 5% DMSO, and 3% normal donkey serum for 3-4 days&#160;at 37&#160;&#176;C with agitation.</li>
		<li>Replenish the antibody solution and incubate for another 3-4 days at 37 &#176;C with agitation.</li>
		<li>After 1-week incubation in primary antibody solution, wash 4 to 5 times in PTwH overnight at RT.</li>
		<li>Incubate with secondary antibody conjugated to fluorophores diluted in PTwH, 3% normal donkey serum for 3 days at 37&#160;&#176;C with agitation.</li>
		<li>Replenish the secondary antibody solution incubate for another 3&#160;days at 37 &#176;C with agitation.</li>
		<li>After 6-day&#160;incubation in secondary antibody solution, wash in PTwH 4-5 times overnight at RT.</li>
		<li>Dehydrate with a graded MeOH series (20%, 40%, 60%, 80%, 100%, and 100% MeOH). The sample may be stored overnight at RT.</li>
		<li>Incubate in 66% dichloromethane/33% MeOH for 3 h at RT with agitation.</li>
		<li>Wash twice in 100% dichloromethane for 15 min at RT with agitation.</li>
		<li>Incubate and store specimens in benzyl ether. Fill the tube to minimize air from oxidizing the sample.</li>
	</ol>
	</li>
	<li>Imaging tissue-cleared specimen
	<ol>
		<li>Affix a chamber containing adhesive to a slide and apply nail polish around the perimeter of the chamber.&#160;For thicker tissues, additional chambers and/or spacers may be stacked on the slide.</li>
		<li>Place cleared tissue in the chamber, fill&#160;with benzyl ether, and apply a coverslip.</li>
		<li>Apply nail polish around the coverslip to create a&#160;seal.</li>
		<li>Obtain tilescan and Z stack images using an upright laser scanning confocal microscope with a 5x or 10x lens to image at a depth up to the working distance of the lens.</li>
		<li>Image at a resolution of 1024 x 1024 using laser lines appropriate for emission spectra of fluorophores used. Muscle autofluorescence is visible using the 488 nm laser line.</li>
		<li>Ensure that the z-axis step size is commensurate with Nyquist sampling based on the numerical aperture of the specified objective11.</li>
		<li>Stitch images and use software for 3D visualization.</li>
		<li>Create figures using maximum intensity projection (MIP) images of Z stacks for individual and merged channels (Figure 2).</li>
	</ol>
	</li>
	<li>Immunohistochemistry 
	NOTE: After the tissue is paraffin-embedded22, the following procedure is used to create slides for immunohistochemical study.
	<ol>
		<li>Preparation of refractive index matching solution (RIMS).
		<ol>
			<li>Prepare 0.1 mol/L phosphate buffer by adding 10.9 g of Na2HPO4 (anhydrous) and 3.1 g of NaH2PO4 (monohydrate) to deionized H2O to a total volume of 1 L (pH 7.4). Filter-sterilize the solution and store it at RT.</li>
			<li>Dilute the phosphate buffer to 0.02 mol/L.</li>
			<li>Dissolve Histodenz in 30 mL of 0.02 mol/L phosphate buffer by stirring the solution for 10 min with a magnetic stir bar in the final storage bottle that may be sealed to minimize evaporation and contamination.</li>
			<li>Add sodium azide to a total concentration of 0.01% (w/v) and adjust the pH to 7.5 with NaOH.</li>
			<li>Adjust the RI by varying the final concentration of Histodenz.</li>
			<li>Store the RIMS at RT for months. Discard if microbial contamination is noted. 
			NOTE: Do NOT autoclave any solutions containing sodium azide.</li>
		</ol>
		</li>
		<li>Preparation of slides for immunohistochemical study
		<ol>
			<li>Create sections of 5 &#181;m thickness with microtome. Apply tissue section to charged slides.</li>
			<li>Remove paraffin by incubating the slides in &#62;75% xylene for 10 min. Move slides to a second container with xylene for an additional 10 min.</li>
			<li>Remove xylene by immersing the slides in 100% EtOH for 10 min, then in 95% EtOH for 5 min and 70% EtOH for 5 min.</li>
			<li>Rinse the slides with deionized H2O for 5 min.</li>
			<li>Immerse slides in antigen retrieval buffer for 25 min at 90-95&#176;C.</li>
			<li>Allow the container to cool to RT for 1 h with agitation.</li>
			<li>Immerse the slides in soaking buffer (0.01 mol/L PBS + 0.4% Triton X-100) for 30 min at 4&#176;C.</li>
			<li>Encircle the tissue with a PAP pen. Add PBS to each slide and place it in a humidified chamber to prevent desiccation.</li>
			<li>Wash slides with PBS at RT with agitation for 5 min.</li>
			<li>Block with blocking buffer (0.01 mol/L PBS + 10% Donkey Serum + 0.1% TX-100) for 1 h with agitation.</li>
			<li>Incubate with a primary antibody diluted in blocking buffer overnight at 4&#176;C.</li>
			<li>The next day, allow slides to warm to RT for 15 min.</li>
			<li>Wash the slides 3 times with 0.01 mol/L PBS + 0.2% TritonX-100 for 5 min.</li>
			<li>Incubate with a secondary antibody diluted in blocking buffer for 1 h at RT with agitation.</li>
			<li>Wash the slides 3 times with 0.01 mol/L PBS + 0.2% TritonX-100 for 5 min.</li>
			<li>Wash the slides 3 times with 0.01 mol/L PBS for 5 min.</li>
			<li>Place 1 drop of RIMS with a dropper and apply a coverslip.</li>
			<li>Apply nail polish around the coverslip to create the seal.</li>
			<li>As a negative control, run a sample without the primary antibody to demonstrate the absence of specific staining.</li>
		</ol>
		</li>
		<li>Imaging immunostained slides
		<ol>
			<li>Image the slides with a laser scanning confocal microscope with 10x, 20x and 40x objective lenses.</li>
			<li>Image at a resolution of 1024 x 1024 using laser lines appropriate for the emission spectra of the secondary antibodies used.</li>
			<li>Create figures using maximum intensity projection (MIP) images of Z stacks for individual and merged channels (Figure 3).</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
2. Meso-scale examination
<ol>
	<li>Stereoscopic dissection
	<ol>
		<li>Perform delicate dissections focusing on tiny or thin structures, such as atrioventricular node, atrioventricular node artery, and cardiac nerve plexus (submillimeter to millimeters in scale) with either a magnifying desk lamp with clamp, surgical telescopes, or stereomicroscope.</li>
	</ol>
	</li>
	<li>Micro-CT scanning 
	NOTE: CT imaging is performed after pressure perfusion and fixation and at any stages of dissection using a micro-positron emission tomography (PET)/CT scanner (Figure 4).
	<ol>
		<li>Warm up the CT X-ray source for 25 min before sample imaging.</li>
		<li>Place the heart sample on the scanner bed.</li>
		<li>Move the scanner bed to a horizontal position of 544 mm and a vertical position of 14 mm to center the heart in the CT field of view (FOV).</li>
		<li>Acquire CT image at 80 kVp, 150 &#181;A, with 720 projections during 1 min scan time at a spatial resolution of 200 &#181;m.</li>
		<li>Reconstruct the CT data with a 12 cm x 12 cm x 10&#160;cm field of view and a matrix of 600 x 600 x 500 voxels, and save as a DICOM file.</li>
	</ol>
	</li>
</ol>
3. Macro-scale examination
<ol>
	<li>Pressure perfusion and fixation 
	NOTE: The authors modify previously described pressure perfusion and fixation techniques and apply them to the non-failing human hearts rejected for transplantation14,19,20,21.
	<ol>
		<li>Use high-flow pumps for perfusion fixation. Use either 100% ethanol14, 4% PFA, or 10% formalin for the fixative. 
		NOTE: The heart is recovered with the ascending aorta, pulmonary trunk, and both vena cavae, and pulmonary veins&#160;resected as distally as possible and delivered in&#160;University of Wisconsin solution23.</li>
		<li>Use two 20-24 Fr surgical cannulas for right- and left-heart perfusion. For right-heart perfusion, cannulate the superior vena cava, and place a vent at the pulmonary trunk or pulmonary artery with half-cut 12-30 mL sized plastic syringes with Luer-Lock tips attached to three-way stopcocks.</li>
		<li>Occlude the inferior vena cava and the other pulmonary artery with twine after putting an appropriately sized locked half-cut plastic syringe or 1.5-5.0 mL centrifuge tube.
		<ol>
			<li>For antegrade perfusion of the left heart, cannulate one of the pulmonary veins and place a vent at the distal cut end of the aorta with the half-cut 12-30 mL sized plastic syringes with Luer-Lock tips attached to three-way stopcocks.</li>
			<li>For retrograde perfusion of the left heart, cannulate one of the aortic arch branches and place a vent at another branch of the aortic arch. Place the tips of the cannulas in both ventricles.</li>
		</ol>
		</li>
		<li>Occlude other vessel orifices with twine after inserting an appropriately sized locked half-cut plastic syringe or 1.5-5.0 mL microcentrifuge tube. Use a thin gauze to cover the inserting portion of the syringes/ tubes/ cannulas to prevent leakage and slipping. Fix large leaks using suture, banding, or clumping. Small leaks are permissible.</li>
		<li>Suspend the heart in a plastic container.</li>
		<li>Connect 22-24 Fr soft plastic tubing to each cannula and insert the other end of the tube into the container filled with fixative.</li>
		<li>Circulate fixative through the right- and left-heart circuits using a high-flow pump set at approximately 100-300 mL/min for the right heart and 200-400 mL/min for the left heart to achieve approximately 20 mmHg in the right ventricle and 80 mmHg in the left ventricle, respectively.</li>
		<li>Maintain perfusion at 4 &#176;C for 24 h.</li>
		<li>Wash the heart with 0.01 mol/L PBS for 30 min with agitation four times.</li>
		<li>Store heart in 0.01 mol/L PBS/0.02% sodium azide at 4 &#176;C. 
		NOTE: The pressure-perfusion fixation is only effective for a fresh heart, not for a heart recovered from an embalmed cadaver.</li>
	</ol>
	</li>
	<li>Gross dissection
	<ol>
		<li>Perform progressive dissection with photographic recordings at each stage of dissection.</li>
		<li>To maintain clinical relevance, pay special attention to avoid distorting/deforming any structures to maintain the physiological morphology of the heart.</li>
		<li>Image target structures using clinically relevant orientation, such as right anterior oblique orientation.</li>
	</ol>
	</li>
	<li>Photography
	<ol>
		<li>Place the pressure-perfused and fixed heart on a tripod with a platform mounted with multiple prongs and the ability to rotate 360o.</li>
		<li>Photograph the heart using a digital single-lens reflex camera&#160;(Figure 5)24 while using multiple light-emitting diode light panels set on the C-Stands and wide black duvetyn background cloth.</li>
		<li>Photograph using the lens with a long focal length (200 mm) for a working distance of 4-6 ft to minimize distortion of the subject14.</li>
	</ol>
	</li>
	<li>Anaglyphs
	<ol>
		<li>To display anaglyphic images, reconstruct a pair of photographs or volume-rendered images from CT datasets with a 10&#176; difference in the rotation angle on the horizontal plane.</li>
		<li>Convert a set of these two-dimensional (2D) images, referred to as a stereogram, into anaglyphs using freeware16.</li>
		<li>To view an anaglyph, use red/cyan glasses.</li>
	</ol>
	</li>
	<li>Photogrammetry 
	NOTE: Photogrammetry is the applied science of generating a three-dimensional surface-rendered reconstruction from multiple two-dimensional photographs taken at varying angles17.
	<ol>
		<li>Suspend the sample on C-Stands or place it on the rotation table to obtain hundreds of multi-directional photographs with a smartphone.</li>
		<li>Generate the 3D model in FBX format using commercially available software.</li>
	</ol>
	</li>
	<li>CT scanning 
	NOTE: CT scanning may be performed after pressure perfusion and fixation and at any stage of dissection.
	<ol>
		<li>Suspend the heart sample from a bar placed across the top of the container. To prevent the heart from swinging during the scan, support the base of the heart with plastic prongs fixed at the bottom of the container. Thus, the air will serve as a negative contrast.</li>
		<li>Perform the CT scan using a commercially available multi-detector row CT scanner with the following parameters: tube voltage of 120 kV, tube current of 800-900 mA, and a gantry rotation of 280 ms. The dose length product is generally 500-1200 mGy.cm.</li>
		<li>Reconstruct axial image data using the following parameters: a section thickness, 0.6 mm; an incremental interval, 0.3 mm; a field of view, as small as possible (generally 100-200 mm); and a matrix, 512 &#215; 512.</li>
	</ol>
	</li>
	<li>Virtual dissection
	<ol>
		<li>Analyze the CT scan images using commercially available software to generate virtual dissection images. 
		NOTE: Virtual dissection is a modification of the volume-rendering process wherein the focus is shifted to the walls of the cardiac chambers and vessels18. In this process, manual thresholding virtually removes the enhanced chamber from the original datasets.</li>
		<li>Visualize the non-enhanced walls, septa, and valves with virtual dissection to produce images similar to gross dissection. Unlike gross dissection of the heart specimens, the cut planes during virtual dissection are practically unlimited. Almost any view can be recreated to visualize the structures of interest as needed.</li>
	</ol>
	</li>
	<li>3D printing
	<ol>
		<li>Open the compatible file of the heart sample in 3D printer software.</li>
		<li>Use the profile of 0.10 mm Fast DETAIL for the print Settings in the 3D printer and reduce the print speed to 20 mm/s. Enable Generate support material.</li>
		<li>Use the profile of TPU&#8203;&#160;filament for &#34;Filament Settings&#34; in the 3D printer.</li>
		<li>Use the profile of the Original Prusa MK4 Input Shaper 0.4 nozzle for &#34;Printer Settings&#34; in the printer.</li>
		<li>After slicing is completed, save the BGCODE file in a USB flash drive for 3D printing.</li>
		<li>Use the 1.75 mm TPU filament for 3D printing the human heart sample. Before 3D printing, dry the TPU filament for 6 h using a&#160;filament dryer.</li>
		<li>To reduce filament tension during 3D printing, place the filament spool on a spool holder with a built-in bearing to facilitate filament spool rotation. Perform 3D printing using a commercially available 3D printer with a textured powder-coated steel sheet.</li>
		<li>Carefully remove support materials when 3D printing is complete.</li>
	</ol>
	</li>
</ol>

Comprehensive 3D Analysis of Human Hearts from Micro to Macro Scales

<ol>
	<li>Tawara, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Das+reizleitungssystem+des+s&#228;ugetierherzens.+Eine+anatomisch-histologische+studie+&#252;ber+das+atrioventrikularb&#252;ndel+und+die+purkinjeschen+f&#228;den.">Das reizleitungssystem des s&#228;ugetierherzens. Eine anatomisch-histologische studie &#252;ber das atrioventrikularb&#252;ndel und die purkinjeschen f&#228;den.</a> Jena: Gustav fischer. , (1906).</li><li>Stephenson, R. 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=High-resolution+3-dimensional+imaging+of+the+human+cardiac+conduction+system+from+microanatomy+to+mathematical+modeling.">High-resolution 3-dimensional imaging of the human cardiac conduction system from microanatomy to mathematical modeling.</a> Sci Rep. 7 (1), 7188 (2017).</li><li>Kawashima, T., Sato, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=First+in+situ+3D+visualization+of+the+human+cardiac+conduction+system+and+its+transformation+associated+with+heart+contour+and+inclination.">First in situ 3D visualization of the human cardiac conduction system and its transformation associated with heart contour and inclination.</a> Sci Rep. 11 (1), 8636 (2021).</li><li>Bojsen-Moller, F., Tranum-Jensen, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Whole-mount+demonstration+of+cholinesterase-containing+nerves+in+the+right+atrial+wall,+nodal+tissue,+and+atrioventricular+bundle+of+the+pig+heart.">Whole-mount demonstration of cholinesterase-containing nerves in the right atrial wall, nodal tissue, and atrioventricular bundle of the pig heart.</a> J Anat. 108, 375-386 (1971).</li><li>Zhao, Y., 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=Ganglionated+plexi+and+ligament+of+marshall+ablation+reduces+atrial+vulnerability+and+causes+stellate+ganglion+remodeling+in+ambulatory+dogs.">Ganglionated plexi and ligament of marshall ablation reduces atrial vulnerability and causes stellate ganglion remodeling in ambulatory dogs.</a> Heart Rhythm. 13 (10), 2083-2090 (2016).</li><li>Chung, W. 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=Ischemia-induced+ventricular+proarrhythmia+and+cardiovascular+autonomic+dysreflexia+after+cardioneuroablation.">Ischemia-induced ventricular proarrhythmia and cardiovascular autonomic dysreflexia after cardioneuroablation.</a> Heart Rhythm. 20 (11), 1534-1545 (2023).</li><li>Crick, S. J., Sheppard, M. N., Ho, S. Y., Gebstein, L., Anderson, 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=Anatomy+of+the+pig+heart:+Comparisons+with+normal+human+cardiac+structure.">Anatomy of the pig heart: Comparisons with normal human cardiac structure.</a> J Anat. 193, 105-119 (1998).</li><li>Saburkina, I., Pauziene, N., Solomon, O. I., Rysevaite-Kyguoliene, K., Pauza, D. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparative+gross+anatomy+of+epicardiac+ganglionated+nerve+plexi+on+the+human+and+sheep+cardiac+ventricles.">Comparative gross anatomy of epicardiac ganglionated nerve plexi on the human and sheep cardiac ventricles.</a> Anat Rec (Hoboken). 306 (9), 2302-2312 (2023).</li><li>Hoagland, D. T., Santos, W., Poelzing, S., Gourdie, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+role+of+the+gap+junction+perinexus+in+cardiac+conduction:+Potential+as+a+novel+anti-arrhythmic+drug+target.">The role of the gap junction perinexus in cardiac conduction: Potential as a novel anti-arrhythmic drug target.</a> Prog Biophys Mol Biol. 144, 41-50 (2019).</li><li>Aksu, T., Gopinathannair, R., Gupta, D., Pauza, D. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Intrinsic+cardiac+autonomic+nervous+system:+What+do+clinical+electrophysiologists+need+to+know+about+the+&amp;#34;heart+brain&amp;#34.">Intrinsic cardiac autonomic nervous system: What do clinical electrophysiologists need to know about the &amp;#34;heart brain&amp;#34.</a> J Cardiovasc Electrophysiol. 32 (6), 1737-1747 (2021).</li><li>Hanna, 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=Innervation+and+neuronal+control+of+the+mammalian+sinoatrial+node+a+comprehensive+atlas.">Innervation and neuronal control of the mammalian sinoatrial node a comprehensive atlas.</a> Circ Res. 128 (9), 1279-1296 (2021).</li><li>Rajendran, P. 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=Identification+of+peripheral+neural+circuits+that+regulate+heart+rate+using+optogenetic+and+viral+vector+strategies.">Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies.</a> Nature Communications. 10, 1944 (2019).</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>Mcalpine, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Heart+and+coronary+arteries:+An+anatomical+atlas+for+clinical+diagnosis,+radiological+investigation,+and+surgical+treatment.">Heart and coronary arteries: An anatomical atlas for clinical diagnosis, radiological investigation, and surgical treatment.</a> Springer-verlag. , (1975).</li><li>Mori, S., Shivkumar, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stereoscopic+three-dimensional+anatomy+of+the+heart:+Another+legacy+of+dr.+Wallace+a.+Mcalpine.">Stereoscopic three-dimensional anatomy of the heart: Another legacy of dr. Wallace a. Mcalpine.</a> Anat Sci Int. 96 (3), 485-488 (2021).</li><li>Izawa, Y., Nishii, T., Mori, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stereogram+of+the+living+heart,+lung,+and+adjacent+structures.">Stereogram of the living heart, lung, and adjacent structures.</a> Tomography. 8 (2), 824-841 (2022).</li><li>Sato, T., Hanna, P., Ajijola, O. A., Shivkumar, K., Mori, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Photogrammetry+of+perfusion-fixed+heart:+Innovative+approach+to+study+3-dimensional+cardiac+anatomy.">Photogrammetry of perfusion-fixed heart: Innovative approach to study 3-dimensional cardiac anatomy.</a> JACC Case Rep. 21, 101937 (2023).</li><li>Tretter, J. T., Gupta, S. K., Izawa, Y., Nishii, T., Mori, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Virtual+dissection:+Emerging+as+the+gold+standard+of+analyzing+living+heart+anatomy.">Virtual dissection: Emerging as the gold standard of analyzing living heart anatomy.</a> J Cardiovasc Dev Dis. 7 (3), 30 (2020).</li><li>Thomas, A. C., Davies, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+demonstration+of+cardiac+pathology+using+perfusion-fixation.">The demonstration of cardiac pathology using perfusion-fixation.</a> Histopathology. 9 (1), 5-19 (1985).</li><li>Glagov, S., Eckner, F. A., Lev, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Controlled+pressure+fixation+apparatus+for+hearts.">Controlled pressure fixation apparatus for hearts.</a> Arch Pathol. 76, 640-646 (1963).</li><li>Iaizzo, 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=The+visible+heart(r)+project+and+free-access+website+'atlas+of+human+cardiac+anatomy.">The visible heart(r) project and free-access website 'atlas of human cardiac anatomy.</a> Europace. 18, 163-172 (2016).</li><li>Yang, Y., Huang, H., Li, L., Yang, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiplex+immunohistochemistry+staining+for+paraffin-embedded+lung+cancer+tissue.">Multiplex immunohistochemistry staining for paraffin-embedded lung cancer tissue.</a> J Vis Exp. (201), e65850 (2023).</li><li>Tripathy, S., Das, S. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Strategies+for+organ+preservation:+Current+prospective+and+challenges.">Strategies for organ preservation: Current prospective and challenges.</a> Cell Biol Int. 47 (3), 520-538 (2023).</li><li>Mori, S., Shivkumar, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Atlas+of+cardiac+anatomy+(anatomical+basis+of+cardiac+interventions.+Vol.+1).">Atlas of cardiac anatomy (anatomical basis of cardiac interventions. Vol. 1).</a> Cardiotext. , (2022).</li><li>Crosado, B., 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=Phenoxyethanol-based+embalming+for+anatomy+teaching:+An+18+years'+experience+with+crosado+embalming+at+the+university+of+otago+in+new+zealand.">Phenoxyethanol-based embalming for anatomy teaching: An 18 years' experience with crosado embalming at the university of otago in new zealand.</a> Anat Sci Educ. 13 (6), 778-793 (2020).</li><li>Titmus, 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=A+workflow+for+the+creation+of+photorealistic+3d+cadaveric+models+using+photogrammetry.">A workflow for the creation of photorealistic 3d cadaveric models using photogrammetry.</a> J Anat. 243 (2), 319-333 (2023).</li><li>Silva, J. N. A., Southworth, M., Raptis, C., Silva, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Emerging+applications+of+virtual+reality+in+cardiovascular+medicine.">Emerging applications of virtual reality in cardiovascular medicine.</a> JACC Basic Transl Sci. 3 (3), 420-430 (2018).</li><li>Maresky, H. 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=Virtual+reality+and+cardiac+anatomy:+Exploring+immersive+three-dimensional+cardiac+imaging,+a+pilot+study+in+undergraduate+medical+anatomy+education.">Virtual reality and cardiac anatomy: Exploring immersive three-dimensional cardiac imaging, a pilot study in undergraduate medical anatomy education.</a> Clin Anat. 32 (2), 238-243 (2019).</li><li>Mori, S., Shivkumar, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Real+three-dimensional+cardiac+imaging+using+leading-edge+holographic+display.">Real three-dimensional cardiac imaging using leading-edge holographic display.</a> Clin Anat. 34 (6), 966-968 (2021).</li></ol>

The present study demonstrates&#160;the comprehensive pipeline to analyze samples obtained from whole human hearts. Representative results show&#160;micro- to macroscale anatomical examinations carried out routinely for a single heart. As a&#160;human heart sample is extremely precious, a multi-scale approach is ideal and effective so as not to waste any parts of the sample by applying multiple&#160;protocols for various purposes, including discovery in scientific research, improvement of clinical procedures, and anatomi...

As function follows form, understanding the architecture of the heart is fundamental for appreciation of its physiology. Although numerous investigations have revealed cardiac anatomy from micro- to macroscales1,2,3, multiple questions remain unresolved, especially those related to human cardiac anatomy. This is in part because basic studies focusing on functional anatomy generally utilized animal hearts4,5,6, which are often distinct from human hearts1,7,8. Furthermore, each individual study, even those using human heart samples, tends to focus on very specific structures, which renders it difficult to apply the findings in the context of the whole heart. This is even more so if the focused structures are at micro- or mesoscales, such as the perinexus9 and ganglionated plexuses10.
In this context, systemic structural study of the human heart rejected for transplantation provides a unique and rare opportunity to obtain a comprehensive atlas of cardiac structures in focus across microscopic and macroscopic scales11. Microscopic examination protocols include tissue clearing (modified immunolabeling-enabled three-dimensional (3D) imaging of solvent-cleared organs, iDISCO+)12,13, and immunohistochemical staining. Mesoscopic examination protocols include stereoscopic dissection, macro photography, and micro-computed tomographic (CT) scanning. Macroscopic examination protocols include gross dissection14, photography (including anaglyphs and photogrammetry)15,16,17, CT, virtual dissection18, and 3D printing of the physically or virtually dissected or whole heart17. In preparation for&#160;macroscopic examination, pressure-perfusion fixation is&#160;performed to maintain the 3D architecture and physiologically relevant morphology of the heart14,19,20,21.&#160;The combined application of these techniques is unique and crucial to correlate distinct anatomic features in the context of the 3D architecture of the human heart.
As the opportunity to obtain a non-pathological human heart sample is extremely limited, a multi-scale approach described herein maximizes the use of the sample. By applying various procedures described below, representative results will illustrate to the reader how the findings can be utilized for multiple purposes, including discovery in scientific research11 (comprehensive analyses of cardiac innervation, distribution of ganglionated plexuses), improvement of clinical procedures (simulation for surgical and interventional approaches), and anatomical education (real 3D demonstration of cardiac anatomy).

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1x Phosphate buffered saline</td>
			<td>Sigma-Aldrich</td>
			<td>P3813</td>
			<td></td>
		</tr>
		<tr>
			<td>3D Viewer</td>
			<td>Microsoft</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>647 AffiniPure Donkey Anti-Rabbit IgG</td>
			<td>Jackson ImmunoResearch Laboratories</td>
			<td>711-605-152</td>
			<td></td>
		</tr>
		<tr>
			<td>647 AffiniPure Donkey Anti-Sheep IgG</td>
			<td>Jackson ImmunoResearch Laboratories</td>
			<td>713-605-147</td>
			<td></td>
		</tr>
		<tr>
			<td>AF Micro-NIKKOR 200 mm f/4D IF-ED lens</td>
			<td>Nikon</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Actin, &#945;-Smooth Muscle - Cy3 antibody</td>
			<td>Sigma-Aldrich</td>
			<td>C6198</td>
			<td></td>
		</tr>
		<tr>
			<td>Antigen Retrieval Buffer (100x EDTA Buffer, pH 8.0)</td>
			<td>Abcam</td>
			<td>ab93680</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-PGP9.5 (protein gene product 9.5)</td>
			<td>Abcam</td>
			<td>ab108986</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-TH (tyrosine hydrox ylase)</td>
			<td>Abcam</td>
			<td>ab1542</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-VAChT (vesicular acetylcholine transporter)</td>
			<td>Synaptic Systems</td>
			<td>139 103</td>
			<td></td>
		</tr>
		<tr>
			<td>Benzyl ether</td>
			<td>Sigma-Aldrich</td>
			<td>108014</td>
			<td></td>
		</tr>
		<tr>
			<td>Bovine serum albumin</td>
			<td>Sigma-Aldrich</td>
			<td>A4503-10G</td>
			<td></td>
		</tr>
		<tr>
			<td>Cheetah 3D printer filament (95A), 1.75 mm</td>
			<td>NinjaTek</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Coverslip, 22 mm x 30mm, No. 1.5</td>
			<td>VWR</td>
			<td>48393 151</td>
			<td></td>
		</tr>
		<tr>
			<td>Cy3 AffiniPure Donkey Anti-Rabbit IgG</td>
			<td>Jackson ImmunoResearch Laboratories</td>
			<td>711-165-152</td>
			<td></td>
		</tr>
		<tr>
			<td>Dichloromethane</td>
			<td>Sigma-Aldrich</td>
			<td>270997-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxide</td>
			<td>Sigma-Aldrich</td>
			<td>D8418-500ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol, 100%</td>
			<td>Decon laboratories</td>
			<td>2701</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Sigma-Aldrich</td>
			<td>G7126-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>GNEXT PET/CT</td>
			<td>SOFIE Biosciences</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Heparin sodium salt from porcine intestinal mucosa</td>
			<td>Sigma-Aldrich</td>
			<td>H3149-50KU</td>
			<td></td>
		</tr>
		<tr>
			<td>Histodenz</td>
			<td>Sigma-Aldrich</td>
			<td>D2158-100G</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrogen peroxide solution</td>
			<td>Sigma-Aldrich</td>
			<td>H1009-500ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Imaging software</td>
			<td>Zeiss</td>
			<td>ZEN (black edition)</td>
			<td></td>
		</tr>
		<tr>
			<td>Imaging software</td>
			<td>Oxford Instruments</td>
			<td>Imaris 10</td>
			<td></td>
		</tr>
		<tr>
			<td>iSpacer</td>
			<td>Sunjin Labs</td>
			<td>iSpacer 3mm</td>
			<td></td>
		</tr>
		<tr>
			<td>KIRI Engine</td>
			<td>KIRI Innovation</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Laser scanning confocal microscope</td>
			<td>Zeiss</td>
			<td>LSM 880</td>
			<td></td>
		</tr>
		<tr>
			<td>LEAD-2 - Vertical &#38; Multi-channels Peristaltic Pump</td>
			<td>LONGER</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Lightview XL&#160;</td>
			<td>Brightech</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Methanol (Certified ACS)</td>
			<td>Fischer Scientific</td>
			<td>A412-4</td>
			<td></td>
		</tr>
		<tr>
			<td>Nikon D850</td>
			<td>Nikon</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>NinjaTek NinjaFlex TPU @MK4</td>
			<td>NinjaTek</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Normal donkey serum</td>
			<td>Jackson ImmunoResearch Laboratories</td>
			<td>017-000-121</td>
			<td></td>
		</tr>
		<tr>
			<td>Original Prusa MK4 3D printer</td>
			<td>Prusa Research</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>PAP pen</td>
			<td>Abcam</td>
			<td>ab2601</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde, 32%</td>
			<td>Electron Microscopy Sciences</td>
			<td>15714-S</td>
			<td></td>
		</tr>
		<tr>
			<td>Polycam</td>
			<td>Polycam</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Primary antibody</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>PrusaSlicer 2.7.1</td>
			<td>Prusa Research</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>SARA-Engine</td>
			<td>pita4 mobile LLC</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Scaniverse</td>
			<td>Niantic</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Secondary antibody</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>SlowFade Gold Antiface Mountant</td>
			<td>Invitrogen</td>
			<td>S36936</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium azide, 5% (w/v)</td>
			<td>Ricca Chemical Company</td>
			<td>7144.8-32</td>
			<td></td>
		</tr>
		<tr>
			<td>SOMATOM Definition AS</td>
			<td>Siemens Healthcare</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Standard Field Surgi-Spec Telescopes,&#160;</td>
			<td>Designs for Vision</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Stereomicroscope System SZ61</td>
			<td>OLYMPUS</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>StereoPhoto Maker</td>
			<td>Free ware developed by Masuji Suto</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Superfrost Plus Microscope Slides, Precleaned</td>
			<td>Fisher Scientific</td>
			<td>12-550-15</td>
			<td></td>
		</tr>
		<tr>
			<td>Triton X-100</td>
			<td>Sigma-Aldrich</td>
			<td>T8787-50ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Sigma-Aldrich</td>
			<td>P9416-100ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene</td>
			<td>Sigma-Aldrich</td>
			<td>534056-4L</td>
			<td></td>
		</tr>
		<tr>
			<td>Ziostation2</td>
			<td>Ziosoft, AMIN</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

pipeline for multi-scale three-dimensional anatomic study of the human heart

Detailed study of non-failing human hearts rejected for transplantation provides a unique opportunity to perform structural analyses across microscopic and macroscopic scales. These techniques include tissue clearing (modified immunolabeling-enabled three-dimensional (3D) imaging of solvent-cleared organs) and immunohistochemical staining. Mesoscopic examination procedures include stereoscopic dissection and micro-computed tomographic (CT) scanning. Macroscopic examination procedures include gross dissection, photography (including anaglyphs and photogrammetry), CT, and 3D printing of the physically or virtually dissected or whole heart. Before macroscopic examination, pressure-perfusion fixation may be performed to maintain the 3D architecture and physiologically relevant morphology of the heart. The application of these techniques in combination to study the human heart is unique and crucial in understanding the relationship between distinct anatomic features such as coronary vasculature and myocardial innervation in the context of the 3D architecture of the heart. This protocol describes the methodologies in detail and includes representative results&#160;to illustrate progress in the research of human cardiac anatomy.

Microscale examinations 
Applying tissue clearing allows imaging of larger volumes of tissue in 3D using confocal microscopy. In the heart, ganglia containing cardiac neurons and the neural patterning of myocardial innervation can be visualized (Figure 2). Figure 3 shows a confocal image of the human left ventricle myocardium immunostained for nerves and smooth muscle cells. Blood vessels are noted to traverse the myocardium, and numerous n...

Author Spotlight: Advancing Human Cardiac Anatomy Through Multi-Scale Analysis of Hearts

This protocol presents a comprehensive pipeline to analyze samples obtained from human hearts that span the microscopic and macroscopic scales.

Pipeline for Multi-Scale Three-Dimensional Anatomic Study of the Human Heart

Detailed study of non-failing human hearts rejected for transplantation provides a unique opportunity to perform structural analyses across microscopic ...

Knowing cardiac anatomy is fundamental to understanding cardiac physiology. Studies of functional anatomy have spanned the micro to macro scales, but have largely used animal hearts. Systematic study of donor human hearts rejected for transplantation provides a unique opportunity to develop a comprehensive atlas that spans the microscopic to macroscopic scales.Through study of the human heart across different scales, we've demonstrated the exquisite innervation of the heart, identified cardiac anatomic structures to improve surgical and interventional approaches, and developed resources for anatomic education. The advantage of studying the human heart across different scales is that the detailed study of microscopic structures may be placed in the context of gross anatomy. The use of pressure profusion fixation maintains the physiologically relevant morphology of the heart.

pipeline-for-multi-scale-three-dimensional-anatomic-study-human

Microsoft Bing

Research

JoVE Journal

Biology

251 Views.  David Geffen School of Medicine at UCLA. Knowing cardiac anatomy is fundamental to understanding cardiac physiology. Studies of functional anatomy have spanned the micro to macro scales, but have largely used animal hearts. Systematic study of donor human hearts rejected for transplantation provides a unique opportunity to develop a comprehensive atlas that spans the microscopic to macroscopic scales.Through study of the human heart across different scales, we've demonstrated the exquisite innervation of the heart, identified...

Video: Author Spotlight: Advancing Human Cardiac Anatomy Through Multi-Scale Analysis of Hearts

Testing Visual Sensitivity to the Speed and Direction of Motion in Lizards

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of the visual system provide more empirical evidence for functional applications. Investigation into the sensory system provides information about the sensory capacity, learning and memory ability, and establishes known baseline behaviour in which to gauge deviations (Burghardt, 1977). However, unlike mammalian or avian systems, testing for learning and memory in a reptile species is difficult. Furthermore, using an operant paradigm as a psychophysical measure of sensory ability is likewise as difficult. Historically, reptilian species have responded poorly to conditioning trials because of issues related to motivation, physiology, metabolism, and basic biological characteristics. Here, I demonstrate an operant paradigm used a novel model lizard species, the Jacky dragon (Amphibolurus muricatus) and describe how to test peripheral sensitivity to salient speed and motion characteristics. This method uses an innovative approach to assessing learning and sensory capacity in lizards. I employ the use of random-dot kinematograms (RDKs) to measure sensitivity to speed, and manipulate the level of signal strength by changing the proportion of dots moving in a coherent direction. RDKs do not represent a biologically meaningful stimulus, engages the visual system, and is a classic psychophysical tool used to measure sensitivity in humans and other animals. Here, RDKs are displayed to lizards using three video playback systems. Lizards are to select the direction (left or right) in which they perceive dots to be moving. Selection of the appropriate direction is reinforced by biologically important prey stimuli, simulated by computer-animated invertebrates.

Testing visual sensitivity in lizards using an operant conditioning paradigm that employs video playback of random-dot kinematograms and computer-generated invertebrates.

Testing visual sensitivity in any species provides basic information regarding behaviour, evolution, and ecology. However, testing specific features of ...

Computer-Generated Animal Model Stimuli

Communication between animals is diverse and complex. Animals may communicate using auditory, seismic, chemosensory, electrical, or visual signals. In particular, understanding the constraints on visual signal design for communication has been of great interest. Traditional methods for investigating animal interactions have used basic observational techniques, staged encounters, or physical manipulation of morphology. Less intrusive methods have tried to simulate conspecifics using crude playback tools, such as mirrors, still images, or models. As technology has become more advanced, video playback has emerged as another tool in which to examine visual communication (Rosenthal, 2000). However, to move one step further, the application of computer-animation now allows researchers to specifically isolate critical components necessary to elicit social responses from conspecifics, and manipulate these features to control interactions. Here, I provide detail on how to create an animation using the Jacky dragon as a model, but this process may be adaptable for other species. In building the animation, I elected to use Lightwave  3D to alter object morphology, add texture, install bones, and provide comparable weight shading that prevents exaggerated movement. The animation is then matched to select motor patterns to replicate critical movement features. Finally, the sequence must rendered into an individual clip for presentation. Although there are other adaptable techniques, this particular method had been demonstrated to be effective in eliciting both conspicuous and social responses in staged interactions.

Computer-generated stimuli using the Jacky dragon as a model.

Communication between animals is diverse and complex. Animals may communicate using auditory, seismic, chemosensory, electrical, or visual signals. In ...

Microfabrication of Chip-sized Scaffolds for Three-dimensional Cell cultivation

Using microfabrication technologies is a prerequisite to create scaffolds of reproducible geometry and constant quality for three-dimensional cell cultivation. These technologies offer a wide spectrum of advantages not only for manufacturing but also for different applications. The size and shape of formed cell clusters can be influenced by the exact and reproducible architecture of the microfabricated scaffold and, therefore, the diffusion path length of nutrients and gases can be controlled.1 This is unquestionably a useful tool to prevent apoptosis and necrosis of cells due to an insufficient nutrient and gas supply or removal of cellular metabolites.
Our polymer chip, called CellChip, has the outer dimensions of 2 x 2 cm with a central microstructured area. This area is subdivided into an array of up to 1156 microcontainers with a typical dimension of 300 m edge length for the cubic design (cp- or cf-chip) or of 300 m diameter and depth for the round design (r-chip).2
So far, hot embossing or micro injection moulding (in combination with subsequent laborious machining of the parts) was used for the fabrication of the microstructured chips. Basically, micro injection moulding is one of the only polymer based replication techniques that, up to now, is capable for mass production of polymer microstructures.3 However, both techniques have certain unwanted limitations due to the processing of a viscous polymer melt with the generation of very thin walls or integrated through holes. In case of the CellChip, thin bottom layers are necessary to perforate the polymer and provide small pores of defined size to supply cells with culture medium e.g. by microfluidic perfusion of the containers.
In order to overcome these limitations and to reduce the manufacturing costs we have developed a new microtechnical approach on the basis of a down-scaled thermoforming process. For the manufacturing of highly porous and thin walled polymer chips, we use a combination of heavy ion irradiation, microthermoforming and track etching. In this so called "SMART" process (Substrate Modification And Replication by Thermoforming) thin polymer films are irradiated with energetic heavy projectiles of several hundred MeV introducing so-called "latent tracks" Subsequently, the film in a rubber elastic state is formed into three dimensional parts without modifying or annealing the tracks. After the forming process, selective chemical etching finally converts the tracks into cylindrical pores of adjustable diameter.

We present two processes for the microfabrication of porous polymer chips for three-dimensional cell cultivation. The first one is hot embossing combined with a solvent vapour welding process. The second one uses a recently developed microthermoforming process combined with ion track technology leading to a significant simplification of manufacture.

Using microfabrication technologies is a prerequisite to create scaffolds of reproducible geometry and constant quality for three-dimensional cell ...

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, into close spatial proximity 2-6. Deciphering the relationship between chromosome organization and genome activity will aid in understanding genomic processes, like transcription and replication. However, little is known about how chromosomes fold. Microscopy is unable to distinguish large numbers of loci simultaneously or at high resolution. To date, the detection of chromosomal interactions using chromosome conformation capture (3C) and its subsequent adaptations required the choice of a set of target loci, making genome-wide studies impossible 7-10.
We developed Hi-C, an extension of 3C that is capable of identifying long range interactions in an unbiased, genome-wide fashion. In Hi-C, cells are fixed with formaldehyde, causing interacting loci to be bound to one another by means of covalent DNA-protein cross-links. When the DNA is subsequently fragmented with a restriction enzyme, these loci remain linked. A biotinylated residue is incorporated as the 5' overhangs are filled in. Next, blunt-end ligation is performed under dilute conditions that favor ligation events between cross-linked DNA fragments. This results in a genome-wide library of ligation products, corresponding to pairs of fragments that were originally in close proximity to each other in the nucleus. Each ligation product is marked with biotin at the site of the junction. The library is sheared, and the junctions are pulled-down with streptavidin beads. The purified junctions can subsequently be analyzed using a high-throughput sequencer, resulting in a catalog of interacting fragments.
Direct analysis of the resulting contact matrix reveals numerous features of genomic organization, such as the presence of chromosome territories and the preferential association of small gene-rich chromosomes. Correlation analysis can be applied to the contact matrix, demonstrating that the human genome is segregated into two compartments: a less densely packed compartment containing open, accessible, and active chromatin and a more dense compartment containing closed, inaccessible, and inactive chromatin regions. Finally, ensemble analysis of the contact matrix, coupled with theoretical derivations and computational simulations, revealed that at the megabase scale Hi-C reveals features consistent with a fractal globule conformation.

The Hi-C method allows unbiased, genome-wide identification of chromatin interactions (1). Hi-C couples proximity ligation and massively parallel sequencing. The resulting data can be used to study genomic architecture at multiple scales: initial results identified features such as chromosome territories, segregation of open and closed chromatin, and chromatin structure at the megabase scale.

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, ...

Quantification of &gamma;H2AX Foci in Response to Ionising Radiation

DNA double-strand breaks (DSBs), which are induced by either endogenous metabolic processes or by exogenous sources, are one of the most critical DNA lesions with respect to survival and preservation of genomic integrity. An early response to the induction of DSBs is phosphorylation of the H2A histone variant, H2AX, at the serine-139 residue, in the highly conserved C-terminal SQEY motif, forming &gamma;H2AX1. Following induction of DSBs, H2AX is rapidly phosphorylated by the phosphatidyl-inosito 3-kinase (PIKK) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR)2. Typically, only a few base-pairs (bp) are implicated in a DSB, however, there is significant signal amplification, given the importance of chromatin modifications in DNA damage signalling and repair. Phosphorylation of H2AX mediated predominantly by ATM spreads to adjacent areas of chromatin, affecting approximately 0.03% of total cellular H2AX per DSB2,3. This corresponds to phosphorylation of approximately 2000 H2AX molecules spanning ~2 Mbp regions of chromatin surrounding the site of the DSB and results in the formation of discrete &gamma;H2AX foci which can be easily visualized and quantitated by immunofluorescence microscopy2. The loss of &gamma;H2AX at DSB reflects repair, however, there is some controversy as to what defines complete repair of DSBs; it has been proposed that rejoining of both strands of DNA is adequate however, it has also been suggested that re-instatement of the original chromatin state of compaction is necessary4-8. The disappearence of &gamma;H2AX involves at least in part, dephosphorylation by phosphatases, phosphatase 2A and phosphatase 4C5,6. Further, removal of &gamma;H2AX by redistribution involving histone exchange with H2A.Z has been implicated7,8. Importantly, the quantitative analysis of &gamma;H2AX foci has led to a wide range of applications in medical and nuclear research. Here, we demonstrate the most commonly used immunofluorescence method for evaluation of initial DNA damage by detection and quantitation of &gamma;H2AX foci in &gamma;-irradiated adherent human keratinocytes9.

Quantification of &amp;#947;H2AX Foci in Response to Ionising Radiation

Quantification of DNA double-strand streaks using &gamma;H2AX formation as a molecular marker has become an invaluable tool in radiation biology. Here we demonstrate the use of an immunofluorescence assay for quantification of &gamma;H2AX foci after exposure of cells to radiation.

DNA double-strand breaks (DSBs), which are induced by either endogenous metabolic processes or by exogenous sources, are one of the most critical DNA ...

Evaluation of the Spatial Distribution of &gamma;H2AX following Ionizing Radiation

An early molecular response to DNA double-strand breaks (DSBs) is phosphorylation of the Ser-139 residue within the terminal SQEY motif of the histone H2AX1,2. This phosphorylation of H2AX is mediated by the phosphatidyl-inosito 3-kinase (PI3K) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR)3. The phosphorylated form of H2AX, referred to as &gamma;H2AX, spreads to adjacent regions of chromatin from the site of the DSB, forming discrete foci, which are easily visualized by immunofluorecence microscopy3. Analysis and quantitation of &gamma;H2AX foci has been widely used to evaluate DSB formation and repair, particularly in response to ionizing radiation and for evaluating the efficacy of various radiation modifying compounds and cytotoxic compounds4.
Given the exquisite specificity and sensitivity of this de novo marker of DSBs, it has provided new insights into the processes of DNA damage and repair in the context of chromatin. For example, in radiation biology the central paradigm is that the nuclear DNA is the critical target with respect to radiation sensitivity. Indeed, the general consensus in the field has largely been to view chromatin as a homogeneous template for DNA damage and repair. However, with the use of &gamma;H2AX as molecular marker of DSBs, a disparity in &gamma;-irradiation-induced &gamma;H2AX foci formation in euchromatin and heterochromatin has been observed5-7. Recently, we used a panel of antibodies to either mono-, di- or tri- methylated histone H3 at lysine 9 (H3K9me1, H3K9me2, H3K9me3) which are epigenetic imprints of constitutive heterochromatin and transcriptional silencing and lysine 4 (H3K4me1, H3K4me2, H3K4me3), which are tightly correlated actively transcribing euchromatic regions, to investigate the spatial distribution of &gamma;H2AX following ionizing radiation8. In accordance with the prevailing ideas regarding chromatin biology, our findings indicated a close correlation between &gamma;H2AX formation and active transcription9. Here we demonstrate our immunofluorescence method for detection and quantitation of &gamma;H2AX foci in non-adherent cells, with a particular focus on co-localization with other epigenetic markers, image analysis and 3D-modeling.

Evaluation of the Spatial Distribution of &amp;#947;H2AX following Ionizing Radiation

Microscopic analysis of &gamma;H2AX foci, which form following the phosphorylation of H2AX at Ser-139 in response to DNA double-strand breaks, has become an invaluable tool in radiation biology. Here we used an antibody to mono-methylated histone H3 at lysine 4 as an epigenetic marker of actively transcribing euchromatin, to evaluate the spatial distribution of radiation-induced &gamma;H2AX formation within the nucleus.

An early molecular response to DNA double-strand breaks (DSBs) is phosphorylation of the Ser-139 residue within the terminal SQEY motif of the histone ...

An Analytical Tool that Quantifies Cellular Morphology Changes from Three-dimensional Fluorescence Images

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for inclusion and exclusion of data points, and computer-aided pattern recognition to support the interpretation and findings of the analysis. It has become increasingly important to be able to measure fluorescence images constructed from three-dimensional (3D) datasets in order to be able to capture the complexity of cellular dynamics and understand the basis of cellular plasticity within biological systems. Sophisticated microscopy instruments have permitted the visualization of 3D fluorescence images through the acquisition of multispectral fluorescence images and powerful analytical software that reconstructs the images from confocal stacks that then provide a 3D representation of the collected 2D images. Advanced design-based stereology methods have progressed from the approximation and assumptions of the original model-based stereology1 even in complex tissue sections2. Despite these scientific advances in microscopy, a need remains for an automated analytic method that fully exploits the intrinsic 3D data to allow for the analysis and quantification of the complex changes in cell morphology, protein localization and receptor trafficking. 
Current techniques available to quantify fluorescence images include Meta-Morph (Molecular Devices, Sunnyvale, CA) and Image J (NIH) which provide manual analysis. Imaris (Andor Technology, Belfast, Northern Ireland) software provides the feature MeasurementPro, which allows the manual creation of measurement points that can be placed in a volume image or drawn on a series of 2D slices to create a 3D object. This method is useful for single-click point measurements to measure a line distance between two objects or to create a polygon that encloses a region of interest, but it is difficult to apply to complex cellular network structures. Filament Tracer (Andor) allows automatic detection of the 3D neuronal filament-like however, this module has been developed to measure defined structures such as neurons, which are comprised of dendrites, axons and spines (tree-like structure). This module has been ingeniously utilized to make morphological measurements to non-neuronal cells3, however, the output data provide information of an extended cellular network by using a software that depends on a defined cell shape rather than being an amorphous-shaped cellular model. To overcome the issue of analyzing amorphous-shaped cells and making the software more suitable to a biological application, Imaris developed Imaris Cell. This was a scientific project with the Eidgen&ouml;ssische Technische Hochschule, which has been developed to calculate the relationship between cells and organelles. While the software enables the detection of biological constraints, by forcing one nucleus per cell and using cell membranes to segment cells, it cannot be utilized to analyze fluorescence data that are not continuous because ideally it builds cell surface without void spaces. To our knowledge, at present no user-modifiable automated approach that provides morphometric information from 3D fluorescence images has been developed that achieves cellular spatial information of an undefined shape (Figure 1). 
We have developed an analytical platform using the Imaris core software module and Imaris XT interfaced to MATLAB (Mat Works, Inc.). These tools allow the 3D measurement of cells without a pre-defined shape and with inconsistent fluorescence network components. Furthermore, this method will allow researchers who have extended expertise in biological systems, but not familiarity to computer applications, to perform quantification of morphological changes in cell dynamics.

We developed a software platform that utilizes Imaris Neuroscience, ImarisXT and MATLAB to measure the changes in morphology of an undefined shape taken from three-dimensional confocal fluorescence of single cells. This novel approach can be used to quantify changes in cell shape following receptor activation and therefore represents a possible additional tool for drug discovery.

The most common software analysis tools available for measuring fluorescence images are for two-dimensional (2D) data that rely on manual settings for ...

FRET Imaging in Three-dimensional Hydrogels

Imaging of F&#246;rster resonance energy transfer (FRET)&#160;is a powerful tool for examining cell biology in real-time. Studies utilizing FRET commonly employ two-dimensional (2D) culture, which does not mimic the three-dimensional (3D) cellular microenvironment. A method to perform quenched emission FRET imaging using conventional widefield epifluorescence microscopy of cells within a 3D hydrogel environment is presented. Here an analysis method for ratiometric FRET probes that yields linear ratios over the probe activation range is described. Measurement of intracellular cyclic adenosine monophosphate (cAMP) levels is demonstrated in chondrocytes under forskolin stimulation using a probe for EPAC1 activation (ICUE1) and the ability to detect differences in cAMP signaling dependent on hydrogel material type, herein a photocrosslinking hydrogel (PC-gel, polyethylene glycol dimethacrylate) and a thermoresponsive hydrogel (TR-gel). Compared with 2D FRET methods, this method requires little additional work. Laboratories already utilizing FRET imaging in 2D can easily adopt this method to perform cellular studies in a 3D microenvironment. It can further be applied to high throughput drug screening in engineered 3D microtissues. Additionally, it is compatible with other forms of FRET imaging, such as anisotropy measurement and fluorescence lifetime imaging (FLIM), and with advanced microscopy platforms using confocal, pulsed, or modulated illumination.

F&#246;rster resonance energy transfer (FRET) imaging is a powerful tool for real-time cell biology studies. Here a method for FRET imaging cells in physiologic three-dimensional (3D) hydrogel microenvironments using conventional epifluorescence microscopy is presented. An analysis for ratiometric FRET probes that yields linear ratios over the activation range is described.

Imaging of F&#246;rster resonance energy transfer (FRET)&#160;is a powerful tool for examining cell biology in real-time. Studies utilizing FRET commonly ...

Adipo-Clear: A Tissue Clearing Method for Three-Dimensional Imaging of Adipose Tissue

Adipose tissue plays a central role in energy homeostasis and thermoregulation. It is composed of different types of adipocytes, as well as adipocyte precursors, immune cells, fibroblasts, blood vessels, and nerve projections. Although the molecular control of cell type specification and how these cells interact have been increasingly delineated, a more comprehensive understanding of these adipose-resident cells can be achieved by visualizing their distribution and architecture throughout the whole tissue. Existing immunohistochemistry and immunofluorescence approaches to analyze adipose histology rely on thin paraffin-embedded sections. However, thin sections capture only a small portion of tissue; as a result, the conclusions can be biased by what portion of tissue is analyzed. We have therefore developed an adipose tissue clearing technique, Adipo-Clear, to permit comprehensive three-dimensional visualization of molecular and cellular patterns in whole adipose tissues. Adipo-Clear was adapted from iDISCO/iDISCO+, with specific modifications made to completely remove the lipid stored in the tissue while preserving native tissue morphology. In combination with light-sheet fluorescence microscopy, we demonstrate here the use of the Adipo-Clear method to obtain high-resolution volumetric images&#160;of an entire adipose tissue.

Due to the high lipid content, adipose tissue has been challenging to visualize using traditional histological methods. Adipo-Clear is a tissue clearing technique that allows robust labeling and high-resolution volumetric fluorescent imaging of adipose tissue. Here, we describe the methods for sample preparation, pretreatment, staining, clearing, and mounting for imaging.

Adipose tissue plays a central role in energy homeostasis and thermoregulation. It is composed of different types of adipocytes, as well as adipocyte ...

Intrathoracic Injection for the Study of Adult Zebrafish Heart

The adult zebrafish heart provides a powerful model in cardiac regeneration research. Although the strength of this system is based on transgenic approaches, a rapid delivery of exogenous factors provides a complementary technique in functional studies. Here, we present a method that relies on administration of a few microliters of solution into the pericardial cavity without causing myocardial damage. Intrathoracic (IT) injections can efficiently deliver proteins and chemical compounds directly onto the heart surface. The injected substances diffuse through the epicardium into the underlying cardiac tissues. Compared to intraperitoneal (IP) injections, the main advantage of intrathoracic injections is the focal administration of the tested factors on the target organ. The delivery of molecules directly into the pericardium is a suitable strategy for studies of cardiac preconditioning and regeneration in adult zebrafish.

This method relies on the injection of 0.5&#8722;3 &#956;L of solution into the thorax of adult zebrafish. The procedure efficiently delivers proteins and chemical compounds into the proximity of the zebrafish heart without damaging the organ. The approach is suitable for testing effects of exogenous factors on various tissues of the heart.