This work has been partially supported by the National governments and the European Union through the ENIAC JU project DeNeCoR under grant agreement number 324257. The authors would like to thank Prof. Giovanni Magenes, Prof. Piero Tortoli and Dr. Giosu&#232; Caliano for their precious support, supervision, and insightful comments that made this work possible. We are also grateful to Prof. Egidio D'Angelo and his group (BCC Lab.), together with Fondazione Istituto Neurologico C. Mondino, for providing the motion tracking and MR instrumentation, and to Giancarlo Germani for MR acquisitions. Finally, we'd like to thank Dr. Nicoletta Caramia, Dr. Alessandro Dallai and Ms. Barbara Mauti for their valuable technical support and Mr. Walter Volpi for providing the bovine brain.

<ol>
	<li>Matrone, G., Savoia, A. S., Terenzi, M., Caliano, G., Quaglia, F., Magenes, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Volumetric+CMUT-Based+Ultrasound+Imaging+System+Simulator+With+Integrated+Reception+and+&#181;-Beamforming+Electronics+Models.">A Volumetric CMUT-Based Ultrasound Imaging System Simulator With Integrated Reception and &#181;-Beamforming Electronics Models.</a> IEEE Trans. Ultrason. Ferroelectr. Freq. Control. 61 (5), 792-804 (2014).</li><li>Pappalardo, M., Caliano, G., Savoia, A. S., Caronti, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Micromachined ultrasonic transducers. Piezoelectric and Acoustic Materials for Transducer Applications. , 453-478 (2008).</li><li>Oralkan, O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Capacitive+micromachined+ultrasonic+transducers:+Next-generation+arrays+for+acoustic+imaging?.">Capacitive micromachined ultrasonic transducers: Next-generation arrays for acoustic imaging?.</a> IEEE Trans. Ultrason. Ferroelectr. Freq. Control. 49 (11), 1596-1610 (2002).</li><li>Savoia, A., Caliano, G., Pappalardo, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+CMUT+probe+for+medical+ultrasonography:+From+microfabrication+to+system+integration.">A CMUT probe for medical ultrasonography: From microfabrication to system integration.</a> IEEE Trans. Ultrason. Ferroelectr. Freq. Control. 59 (6), 1127-1138 (2012).</li><li>Ramalli, A., Boni, E., Savoia, A. S., Tortoli, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Density-tapered+spiral+arrays+for+ultrasound+3-D+imaging.">Density-tapered spiral arrays for ultrasound 3-D imaging.</a> IEEE Trans. Ultrason. Ferroelectr. Freq. Control. 62 (8), 1580-1588 (2015).</li><li>Lazebnik, R. S., Lancaster, T. L., Breen, M. S., Lewin, J. S., Wilson, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Volume+registration+using+needle+paths+and+point+landmarks+for+evaluation+of+interventional+MRI+treatments.">Volume registration using needle paths and point landmarks for evaluation of interventional MRI treatments.</a> IEEE Trans. Med. Imag. 22 (5), 653-660 (2003).</li><li>Dawe, R. J., Bennett, D. A., Schneider, J. A., Vasireddi, S. K., Arfanakis, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Postmortem+MRI+of+human+brain+hemispheres:+T2+relaxation+times+during+formaldehyde+fixation.">Postmortem MRI of human brain hemispheres: T2 relaxation times during formaldehyde fixation.</a> Magn. Reson. Med. 61 (4), 810-818 (2009).</li><li>Chen, S. 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=An+anthropomorphic+polyvinyl+alcohol+brain+phantom+based+on+Colin27+for+use+in+multimodal+imaging.">An anthropomorphic polyvinyl alcohol brain phantom based on Colin27 for use in multimodal imaging.</a> Mag. Res. Phys. 39 (1), 554-561 (2012).</li><li>Farrer, A. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+and+evaluation+of+tissue-mimicking+gelatin+phantoms+for+use+with+MRgFUS.">Characterization and evaluation of tissue-mimicking gelatin phantoms for use with MRgFUS.</a> J. Ther. Ultrasound. 3 (9), (2015).</li><li>Choe, A. S., Gao, Y., Li, X., Compton, K. B., Stepniewska, I., Anderson, A. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Accuracy+of+image+registration+between+MRI+and+light+microscopy+in+the+ex+vivo+brain.">Accuracy of image registration between MRI and light microscopy in the ex vivo brain.</a> Magn. Reson. Imaging. 29 (5), 683-692 (2011).</li><li>Gobbi, D. G., Comeau, R. M., Peters, T. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrasound+probe+tracking+for+real-time+ultrasound/MRI+overlay+and+visualization+of+brain+shift.">Ultrasound probe tracking for real-time ultrasound/MRI overlay and visualization of brain shift.</a> Int. Conf. Med. Image Comput. Comput. Assist. Interv (MICCAI) n. 920, 927 (1999).</li><li>Ternifi, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ultrasound+measurements+of+brain+tissue+pulsatility+correlate+with+the+volume+of+MRI+white-matter+hyperintensity.">Ultrasound measurements of brain tissue pulsatility correlate with the volume of MRI white-matter hyperintensity.</a> J. Cereb. Blood Flow. Metab. 34 (6), 942-944 (2014).</li><li>Unsgaard, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Neuronavigation+by+Intraoperative+Three-dimensional+Ultrasound:+Initial+Experience+during+Brain+Tumor+Resection.">Neuronavigation by Intraoperative Three-dimensional Ultrasound: Initial Experience during Brain Tumor Resection.</a> Neurosurgery. 50 (4), 804-812 (2002).</li><li>Pfefferbaum, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Postmortem+MR+imaging+of+formalin-fixed+human+brain.">Postmortem MR imaging of formalin-fixed human brain.</a> NeuroImage. 21 (4), 1585-1595 (2004).</li><li>Schulz, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+strain+fields+in+human+brain+resulting+from+formalin+fixation.">Three-dimensional strain fields in human brain resulting from formalin fixation.</a> J. Neurosci. Meth. 202 (1), 17-27 (2011).</li><li>Ahrens, J., Geveci, B., Law, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ParaView:+An+End-User+Tool+for+Large+Data+Visualization.">ParaView: An End-User Tool for Large Data Visualization.</a> Visualization Handbook. , (2005).</li><li>Cloutier, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+multimodality+vascular+imaging+phantom+with+fiducial+markers+visible+in+DSA,+CTA,+MRA,+and+ultrasound.">A multimodality vascular imaging phantom with fiducial markers visible in DSA, CTA, MRA, and ultrasound.</a> Med. Phys. 31 (6), 1424-1433 (2004).</li><li>Boni, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+reconfigurable+and+programmable+FPGA-based+system+for+nonstandard+ultrasound+methods.">A reconfigurable and programmable FPGA-based system for nonstandard ultrasound methods.</a> IEEE Trans. Ultrason. Ferroelectr. Freq. Control. 59 (7), 1378-1385 (2012).</li><li>Bagolini, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PECVD+low+stress+silicon+nitride+analysis+and+optimization+for+the+fabrication+of+CMUT+devices.">PECVD low stress silicon nitride analysis and optimization for the fabrication of CMUT devices.</a> J. Micromech. Microeng. 25 (1), (2015).</li><li>Savoia, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Design+and+fabrication+of+a+cMUT+probe+for+ultrasound+imaging+of+fingerprints.">Design and fabrication of a cMUT probe for ultrasound imaging of fingerprints.</a> Proc. IEEE Int. Ultrasonics Symp. , 1877-1880 (2010).</li><li>Fenster, A., Downey, D. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Three-dimensional+ultrasound+imaging.">Three-dimensional ultrasound imaging.</a> Annu. Rev. Biomed. Eng. 2, 457-475 (2000).</li><li>Matrone, G., Ramalli, A., Savoia, A. S., Tortoli, P., Magenes, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High+Frame-Rate,+High+Resolution+Ultrasound+Imaging+with+Multi-Line+Transmission+and+Filtered-Delay+Multiply+And+Sum+Beamforming.">High Frame-Rate, High Resolution Ultrasound Imaging with Multi-Line Transmission and Filtered-Delay Multiply And Sum Beamforming.</a> IEEE Trans. Med. Imag. 36 (2), 478-486 (2017).</li><li>Matrone, G., Savoia, A. S., Caliano, G., Magenes, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Depth-of-field+enhancement+in+Filtered-Delay+Multiply+and+Sum+beamformed+images+using+Synthetic+Aperture+Focusing.">Depth-of-field enhancement in Filtered-Delay Multiply and Sum beamformed images using Synthetic Aperture Focusing.</a> Ultrasonics. 75, 216-225 (2017).</li><li>Boni, E., Cellai, A., Ramalli, A., Tortoli, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+high+performance+board+for+acquisition+of+64-channel+ultrasound+RF+data.">A high performance board for acquisition of 64-channel ultrasound RF data.</a> Proc. IEEE Int. Ultrasonics Symp. , 2067-2070 (2012).</li><li>Matrone, G., Savoia, A. S., Caliano, G., Magenes, 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+Delay+Multiply+and+Sum+beamforming+algorithm+in+medical+ultrasound+imaging.">The Delay Multiply and Sum beamforming algorithm in medical ultrasound imaging.</a> IEEE Trans. Med. Imag. 34, 940-949 (2015).</li><li>Savoia, A. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+lateral+resolution+and+contrast+in+ultrasound+imaging+using+a+sidelobe+masking+technique.">Improved lateral resolution and contrast in ultrasound imaging using a sidelobe masking technique.</a> Proc. IEEE Int. Ultrasonics Symp. , 1682-1685 (2014).</li><li>Gy&#246;ngy, G., Makra, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Experimental+validation+of+a+convolution-+based+ultrasound+image+formation+model+using+a+planar+arrangement+of+micrometer-scale+scatterers.">Experimental validation of a convolution- based ultrasound image formation model using a planar arrangement of micrometer-scale scatterers.</a> IEEE Trans. Ultrason. Ferroelectr. Freq. Control. 62 (6), 1211-1219 (2015).</li><li>Shapoori, K., Sadler, J., Wydra, A., Malyarenko, E. V., Sinclair, A. N., Maev, 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=An+Ultrasonic-Adaptive+Beamforming+Method+and+Its+Application+for+Trans-skull+Imaging+of+Certain+Types+of+Head+Injuries;+Part+I:+Transmission+Mode.">An Ultrasonic-Adaptive Beamforming Method and Its Application for Trans-skull Imaging of Certain Types of Head Injuries; Part I: Transmission Mode.</a> IEEE Trans. Biomed. Eng. 62 (5), 1253-1264 (2015).</li><li>Salles, S., Liebgott, H., Basset, O., Cachard, C., Vray, D., Lavarello, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Experimental+evaluation+of+spectral-based+quantitative+ultrasound+imaging+using+plane+wave+compounding.">Experimental evaluation of spectral-based quantitative ultrasound imaging using plane wave compounding.</a> IEEE Trans. Ultrason. Ferroelectr. Freq. Control. 61 (11), 1824-1834 (2014).</li><li>Alessandrini, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+New+Technique+for+the+Estimation+of+Cardiac+Motion+in+Echocardiography+Based+on+Transverse+Oscillations:+A+Preliminary+Evaluation+In+Silico+and+a+Feasibility+Demonstration+In+Vivo.">A New Technique for the Estimation of Cardiac Motion in Echocardiography Based on Transverse Oscillations: A Preliminary Evaluation In Silico and a Feasibility Demonstration In Vivo.</a> IEEE Trans. Med. Imag. 33 (5), 1148-1162 (2014).</li><li>Ramalli, A., Basset, O., Cachard, C., Boni, E., Tortoli, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Frequency-domain-based+strain+estimation+and+high-frame-rate+imaging+for+quasi-static+elastography.">Frequency-domain-based strain estimation and high-frame-rate imaging for quasi-static elastography.</a> IEEE Trans. Ultrason. Ferroelectr. Freq. Control. 59 (4), 817-824 (2012).</li><li>Markley, F. L., Cheng, Y., Crassidis, J. L., Oshman, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Averaging+quaternions.">Averaging quaternions.</a> J. Guid. Cont. Dyn. 30 (4), 1193-1197 (2007).</li><li>Dorst, L., Fontijne, D., Mann, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Geometric Algebra for Computer Science. An Object-oriented Approach to Geometry. , (2007).</li><li>Horn, B. K. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Closed-form+solution+of+absolute+orientation+using+unit+quaternions.">Closed-form solution of absolute orientation using unit quaternions.</a> J. Opt. Soc. Am. A. 4 (4), 629-642 (1987).</li></ol>

The authors declare they have no competing financial interests.

Several works have been presented in the literature describing techniques that are similar or related to the protocol presented. These techniques are also based on the use of realistic targets, including fixed animal or cadaver brains, but they are mainly conceived for testing of digital registration methods of various sorts.
The protocol described here, however, has the specific purpose of testing US probes in different configurations in the early stages of development and, due to this, it fu...

<table border="0" cellpadding="0" cellspacing="0" width="925">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">ULA-OP</td>
			<td style="width:167px;">University of Florence</td>
			<td style="width:104px;">N/A</td>
			<td style="width:415px;">Ultrasound imaging research system</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">3D imaging piezeoelectric probe</td>
			<td style="width:167px;">Esaote s.p.a.</td>
			<td style="width:104px;">9600195000</td>
			<td>Mechanically-swept 3D ultrasound probe, model BL-433</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Linear-array piezoelectric probe</td>
			<td style="width:167px;">Esaote s.p.a.</td>
			<td style="width:104px;">122001100</td>
			<td>Ultrasound linear array probe, model LA-533</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">CMUT probe</td>
			<td style="width:167px;">University Roma Tre</td>
			<td style="width:104px;">N/A</td>
			<td>Ultrasound linear array probe based on CMUT technology</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">MAGNETOM Skyra 3T MR scanner</td>
			<td style="width:167px;">Siemens Healthcare</td>
			<td style="width:104px;">N/A</td>
			<td>MR scanner</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Head coil</td>
			<td style="width:167px;">Siemens Healthcare</td>
			<td style="width:104px;">N/A</td>
			<td>32-channel head coil for MR imaging</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">NDI Polaris Vicra</td>
			<td style="width:167px;">NDI Medical</td>
			<td style="width:104px;">8700335001</td>
			<td>Optical motion tracking system</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Pointer tool</td>
			<td style="width:167px;">NDI Medical</td>
			<td style="width:104px;">8700340</td>
			<td>Passive pointer tool with 4 reflecting markers</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Clamp-equipped tool</td>
			<td style="width:167px;">NDI Medical</td>
			<td style="width:104px;">8700399</td>
			<td>Rigid body with 4 reflecting markers and a clamp to be connected to the US probe handle</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Bovine brain</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Brain of an adult bovine, from food suppliers</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Formalin solution</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>10% buffered formalin solution for bovine brain fixation - CAUTION, formalin is a toxic chemical substance and must be handled with care; specific regulations may also apply (see for instance US OSHA Standard 1910.1048 App A)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Plastic container for anatomical parts</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Cilindrical plastic container with lid</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Glass spheres</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>3mm diameter spheres of Flint glass</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Agar</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>30 g, for phantom preparation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Glycerine</td>
			<td style="width:167px;">AEFFE Farmaceutici</td>
			<td style="width:104px;">A908005248</td>
			<td>100 g, for phantom preparation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Distilled water</td>
			<td style="width:167px;">Solbat Gaysol</td>
			<td style="width:104px;">8027391000015</td>
			<td>870 g, for phantom preparation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Beaker</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Beaker used for the diluition of glycerine and agar in distilled water</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Lysoform</td>
			<td style="width:167px;">Lever</td>
			<td style="width:104px;">8000680500014</td>
			<td>A benzalkonium chloride and water solution was used for the agar phantom preservation</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Polystyrene mannequin head</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Polyestirene model which was cutted and used to design the configuration of spheres&#39;patterns</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Green tissue marking dye for histology</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Colour used to mark the glass spheres&#39; positions on the bovine brain surface</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Yellow enamel</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Enamel used to colour the glass spheres implanted in the agar phantom</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Water tank</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>50x50x30 cm plastic tank filled degassed water up to a 15cm height&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Mechanical arm</td>
			<td style="width:167px;">Esaote s.p.a.</td>
			<td style="width:104px;">N/A</td>
			<td>Mechanical arm clamped to the water tank border and used to held the probe in fixed positions</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Plate of synthetic resin</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Plate used as a support for the bovine brain positioning in the water tank</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Sewing threads</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Sewing thread segments used to immobilize the brain on the resin plate</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Adhesive tape</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Adhesive tape used to fix the sewing thread extremities onto the resin plate</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Plastic food container</td>
			<td style="width:167px;">N/A</td>
			<td style="width:104px;">N/A</td>
			<td>Sealed food container used for the agar phantom</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Notebook</td>
			<td style="width:167px;">Lenovo</td>
			<td style="width:104px;">Z50-70</td>
			<td>Lenovo&#160; Z50-70, Intel(R) Core i7-4510U @ 2.0 GHz, 8 GB RAM</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Workstation</td>
			<td style="width:167px;">Dell Inc.</td>
			<td style="width:104px;">T5810</td>
			<td>Intel(R) Xeon(R) CPU E3-1240v3 @ 3.40 GHz, 16 GB RAM</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Matlab</td>
			<td style="width:167px;">The MathWorks</td>
			<td style="width:104px;">R2013a</td>
			<td>Software tool, used for space transformation computation and 3D reconstruction from image planes</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">Paraview</td>
			<td style="width:167px;">Kitware Inc.</td>
			<td style="width:104px;">v. 4.4.1</td>
			<td>Open-source software for 3D image processing and visualization</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">NDI Toolbox - ToolTracker Utility</td>
			<td style="width:167px;">NDI Medical</td>
			<td style="width:104px;">v. 4.007.007</td>
			<td>Software for marker position visualization and tracking in the NDI Polaris Vicra measurement volume</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">C++ data-logging software</td>
			<td style="width:167px;">NDI Medical</td>
			<td style="width:104px;">v. 4.007.007</td>
			<td>Software for marker position recording on a text log file</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:240px;">ULA-OP software&#160;</td>
			<td style="width:167px;">University of Florence</td>
			<td style="width:104px;">N/A</td>
			<td>Software for real-time display and control of the ULA-OP system</td>
		</tr>
	</tbody>
</table>

an experimental protocol for assessing the performance of new ultrasound probes based on cmut technology in application to brain imaging

The possibility to perform an early and repeatable assessment of imaging performance is fundamental in the design and development process of new ultrasound (US) probes. Particularly, a more realistic analysis with application-specific imaging targets can be extremely valuable to assess the expected performance of US probes in their potential clinical field of application.
The experimental protocol presented in this work was purposely designed to provide an application-specific assessment procedure for newly-developed US probe prototypes based on Capacitive Micromachined Ultrasonic Transducer (CMUT) technology in relation to brain imaging.
The protocol combines the use of a bovine brain fixed in formalin as the imaging target, which ensures both realism and repeatability of the described procedures, and of neuronavigation techniques borrowed from neurosurgery. The US probe is in fact connected to a motion tracking system which acquires position data and enables the superposition of US images to reference Magnetic Resonance (MR) images of the brain. This provides a means for human experts to perform a visual qualitative assessment of the US probe imaging performance and to compare acquisitions made with different probes. Moreover, the protocol relies on the use of a complete and open research and development system for US image acquisition, i.e. the Ultrasound Advanced Open Platform (ULA-OP) scanner.
The manuscript describes in detail the instruments and procedures involved in the protocol, in particular for&#160;the calibration, image acquisition and registration of US and MR images. The obtained results prove the effectiveness of the overall protocol presented, which is entirely open (within the limits of the instrumentation involved), repeatable, and covers the entire set of acquisition and processing activities for US images.

The main result achieved via the described protocol is the experimental validation of an effective and repeatable assessment procedure for the 2D and 3D imaging capabilities of US probe prototypes based on CMUT technology, in the prospective application to brain imaging. After implementing all the described protocol steps, an expert can then apply the visualization software functions (e.g. free orientation slicing, subset extraction, volume interpolation, etc.) to compar...

Watch this Scientific Journal Video about An Experimental Protocol for Assessing the Performance of New Ultrasound Probes Based on CMUT Technology in Application to Brain Imaging at JoVE.com

An Experimental Protocol for Assessing the Performance of New Ultrasound Probes Based on CMUT Technology in Application to Brain Imaging

The development of new ultrasound (US) probes based on Capacitive Micromachined Ultrasonic Transducer (CMUT) technology requires an early realistic assessment of imaging capabilities. We describe a repeatable experimental protocol for US image acquisition and comparison with magnetic resonance images, using an ex vivo bovine brain as an imaging target.

The possibility to perform an early and repeatable assessment of imaging performance is fundamental in the design and development process of new ...

an-experimental-protocol-for-assessing-performance-new-ultrasound

Research

Education

JoVE Core

JoVE Journal

Electrical Engineering

Bioengineering

Unit 1

Diagrams and Signal Flow Graphs

SCIENTISTS IN ACTION

10.3K Views.  University of Pavia. The development of new ultrasound (US) probes based on Capacitive Micromachined Ultrasonic Transducer (CMUT) technology requires an early realistic assessment of imaging capabilities. We describe a repeatable experimental protocol for US image acquisition and comparison with magnetic resonance images, using an ex vivo bovine brain as an imaging target.

Video: An Experimental Protocol for Assessing the Performance of New Ultrasound Probes Based on CMUT Technology in Application to Brain Imaging

High-throughput, Automated Extraction of DNA and RNA from Clinical Samples using TruTip Technology on Common Liquid Handling Robots

TruTip is a simple nucleic acid extraction technology whereby a porous, monolithic binding matrix is inserted into a pipette tip. The geometry of the monolith can be adapted for specific pipette tips ranging in volume from 1.0 to 5.0 ml. The large porosity of the monolith enables viscous or complex samples to readily pass through it with minimal fluidic backpressure. Bi-directional flow maximizes residence time between the monolith and sample, and enables large sample volumes to be processed within a single TruTip. The fundamental steps, irrespective of sample volume or TruTip geometry, include cell lysis, nucleic acid binding to the inner pores of the TruTip monolith, washing away unbound sample components and lysis buffers, and eluting purified and concentrated nucleic acids into an appropriate buffer. The attributes and adaptability of TruTip are demonstrated in three automated clinical sample processing protocols using an Eppendorf epMotion 5070, Hamilton STAR and STARplus liquid handling robots, including RNA isolation from nasopharyngeal aspirate, genomic DNA isolation from whole blood, and fetal DNA extraction and enrichment from large volumes of maternal plasma (respectively).

TruTip is a simple nucleic acid extraction technology whereby a porous, monolithic binding matrix is inserted into a pipette tip. Consequently, the sample preparation format is compatible with most liquid handling instruments, and can be used for many medium to high-throughput clinical applications and sample types.

TruTip is a simple nucleic acid extraction  technology whereby a porous, monolithic binding matrix is inserted into a  pipette tip. The geometry of the ...

3D Orbital Tracking in a Modified Two-photon Microscope: An Application to the Tracking of Intracellular Vesicles

The objective of this video protocol is to discuss how to perform and analyze a three-dimensional fluorescent orbital particle tracking experiment using a modified two-photon microscope1. As opposed to conventional approaches (raster scan or wide field based on a stack of frames), the 3D orbital tracking allows to localize and follow with a high spatial (10 nm accuracy) and temporal resolution (50 Hz frequency response) the 3D displacement of a moving fluorescent particle on length-scales of hundreds of microns2. The method is based on a feedback algorithm that controls the hardware of a two-photon laser scanning microscope in order to perform a circular orbit around the object to be tracked: the feedback mechanism will maintain the fluorescent object in the center by controlling the displacement of the scanning beam3-5. To demonstrate the advantages of this technique, we followed a fast moving organelle, the lysosome, within a living cell6,7. Cells were plated according to standard protocols, and stained using a commercially lysosome dye. We discuss briefly the hardware configuration and in more detail the control software, to perform a 3D orbital tracking experiment inside living cells. We discuss in detail the parameters required in order to control the scanning microscope and enable the motion of the beam in a closed orbit around the particle. We conclude by demonstrating how this method can be effectively used to track the fast motion of a labeled lysosome along microtubules in 3D within a live cell. Lysosomes can move with speeds in the range of 0.4-0.5 &#181;m/sec, typically displaying a directed motion along the microtubule network8.

In this video protocol we track - at high speed and in three dimensions - fluorescently labeled lysosomes within living cells, using the orbital tracking method in a modified two-photon microscope.

The objective of this video protocol is to discuss how to perform and analyze a three-dimensional fluorescent orbital particle tracking experiment using a ...

In Situ Mapping of the Mechanical Properties of Biofilms by Particle-tracking Microrheology

Bacterial cells are able to form surface-attached biofilm communities known as biofilms by encasing themselves in extracellular polymeric substances (EPS). The EPS serves as a physical and protective scaffold that houses the bacterial cells and consists of a variety of materials that includes proteins, exopolysaccharides and DNA. The composition of the EPS may change, which remodels the mechanic properties of the biofilm to further develop or support alternative biofilm structures, such as streamers, as a response to environmental cues. Despite this, there are little quantitative descriptions on how EPS components contribute to the mechanical properties and function of biofilms. Rheology, the study of the flow of matter, is of particular relevance to biofilms as many biofilms grow in flow conditions and are constantly exposed to shear stress. It also provides measurement and insight on the spreading of the biofilm on a surface. Here, particle-tracking microrheology is used to examine the viscoelasticity and effective crosslinking roles of different matrix components in various parts of the biofilm during development. This approach allows researchers to measure mechanic properties of biofilms at the micro-scale, which might provide useful information for controlling and engineering biofilms.

In Situ Mapping of the Mechanical Properties of Biofilms by Particle-tracking Microrheology

Particle-tracking microrheology investigates the viscoelasticity of materials. Here, the technique is used to determine the viscoelasticity, creep compliance and effective crosslinking roles of different matrix components of a bacterial biofilm. The matrix consists of polymeric substances secreted by the bacteria and its components determine biofilm structure and mechanical properties.

Bacterial cells are able to form surface-attached biofilm communities known as biofilms by encasing themselves in extracellular polymeric substances ...

An Experimental and Finite Element Protocol to Investigate the Transport of Neutral and Charged Solutes across Articular Cartilage

Osteoarthritis (OA) is a debilitating disease that is associated with degeneration of articular cartilage and subchondral bone. Degeneration of articular cartilage impairs its load-bearing function substantially as it experiences tremendous chemical degradation, i.e. proteoglycan loss and collagen fibril disruption. One promising way to investigate chemical damage mechanisms during OA is to expose the cartilage specimens to an external solute and monitor the diffusion of the molecules. The degree of cartilage damage (i.e. concentration and configuration of essential macromolecules) is associated with collisional energy loss of external solutes while moving across articular cartilage creates different diffusion characteristics compared to healthy cartilage. In this study, we introduce a protocol, which consists of several steps and is based on previously developed experimental micro-Computed Tomography (micro-CT) and finite element modeling. The transport of charged and uncharged iodinated molecules is first recorded using micro-CT, which is followed by applying biphasic-solute and multiphasic finite element models to obtain diffusion coefficients and fixed charge densities across cartilage zones.

We propose a protocol to investigate the transport of charged and uncharged molecules across articular cartilage with the aid of recently developed experimental and numerical methods.

Osteoarthritis (OA) is a debilitating disease that is associated with degeneration of articular cartilage and subchondral bone. Degeneration of articular ...

A High-performance Compact Photoacoustic Tomography System for In Vivo Small-animal Brain Imaging

In vivo small-animal imaging has an important role to play in preclinical studies. Photoacoustic tomography (PAT) is an emerging hybrid imaging modality that shows great potential for both preclinical and clinical applications. Conventional optical parametric oscillator-based PAT (OPO-PAT) systems are bulky and expensive and cannot provide high-speed imaging. Recently, pulsed-laser diodes (PLDs) have been successfully demonstrated as an alternative excitation source for PAT. Pulsed-laser diode PAT (PLD-PAT) has been successfully demonstrated for high-speed imaging on photoacoustic phantoms and biological tissues. This work provides a visualized experimental protocol for in vivo brain imaging using PLD-PAT. The protocol includes the compact PLD-PAT system configuration and its description, animal preparation for brain imaging, and a typical experimental procedure for 2D cross-sectional rat brain imaging. The PLD-PAT system is compact and cost-effective and can provide high-speed, high-quality imaging. Brain images collected in vivo at various scan speeds are presented.

A High-performance Compact Photoacoustic Tomography System for In Vivo Small-animal Brain Imaging

A compact pulsed-laser diode-based photoacoustic tomography (PLD-PAT) system for high-speed in vivo brain imaging in small animals is demonstrated.

In vivo small-animal imaging has an important role to play in preclinical studies. Photoacoustic tomography (PAT) is an emerging hybrid imaging modality ...

Fabrication and Validation of an Organ-on-chip System with Integrated Electrodes to Directly Quantify Transendothelial Electrical Resistance

Organs-on-chips, in vitro models involving the culture of (human) tissues inside microfluidic devices, are rapidly emerging and promise to provide useful research tools for studying human health and disease. To characterize the barrier function of cell layers cultured inside organ-on-chip devices, often transendothelial or transepithelial electrical resistance (TEER) is measured. To this end, electrodes are usually integrated into the chip by micromachining methods to provide more stable measurements than is achieved with manual insertion of electrodes into the inlets of the chip. However, these electrodes frequently hamper visual inspection of the studied cell layer or require expensive cleanroom processes for fabrication. To overcome these limitations, the device described here contains four easily integrated electrodes that are placed and fixed outside of the culture area, making visual inspection possible. Using these four electrodes the resistance of six measurement paths can be quantified, from which the TEER can be directly isolated, independent of the resistance of culture medium-filled microchannels. The blood-brain barrier was replicated in this device and its TEER was monitored to show the device applicability. This chip, the integrated electrodes and the TEER determination method are generally applicable in organs-on-chips, both to mimic other organs or to be incorporated into existing organ-on-chip systems.

This publication describes the fabrication of an organ-on-chip device with integrated electrodes for direct quantification of transendothelial electrical resistance (TEER). For validation, the blood-brain barrier was mimicked inside this microfluidic device and its barrier function was monitored. The presented methods for electrode integration and direct TEER quantification are generally applicable.

Organs-on-chips, in vitro models involving the culture of (human) tissues inside microfluidic devices, are rapidly emerging and promise to provide useful ...

A Novel Surgical Technique As a Foundation for In Vivo Partial Liver Engineering in Rat

Organ engineering is a novel strategy to generate liver organ substitutes that can potentially be used in transplantation. Recently, in vivo liver engineering, including in vivo organ decellularization followed by repopulation, has emerged as a promising approach over ex vivo liver engineering. However, postoperative survival was not achieved. The aim of this study is to develop a novel surgical technique of in vivo selective liver lobe perfusion in rats as a prerequisite for in vivo liver engineering. We generate a circuit bypass only through the left lateral lobe. Then, the left lateral lobe is perfused with heparinized saline. The experiment is performed with 4 groups (n = 3 rats per group) based on different perfusion times of 20 min, 2 h, 3 h, and 4 h. Survival, as well as the macroscopically visible change of color and the histologically determined absence of blood cells in the portal triad and the sinusoids, is taken as an indicator for a successful model establishment. After selective perfusion of the left lateral lobe, we observe that the left lateral lobe, indeed, turned from red to faint yellow. In a histological assessment, no blood cells are visible in the branch of the portal vein, the central vein, and the sinusoids. The left lateral lobe turns red after reopening the blocked vessels. 12/12 rats survived the procedure for more than one week. We are the first to report a surgical model for in vivo single liver lobe perfusion with a long survival period of more than one week. In contrast to the previously published report, the most important advantage of the technique presented here is that perfusion of 70% of the liver is maintained throughout the whole procedure. The establishment of this technique provides a foundation for in vivo partial liver engineering in rats, including decellularization and recellularization.

A Novel Surgical Technique As a Foundation for In Vivo Partial Liver Engineering in Rat

We establish a novel surgical technique for an in vivo single liver lobe perfusion model in rat as a prerequisite for further studying in vivo partial liver engineering in the future.

Organ engineering is a novel strategy to generate liver organ substitutes that can potentially be used in transplantation. Recently, in vivo liver ...

A New Ex Vivo Model for the Evaluation of Endoscopic Submucosal Injection Material Performance

Increasing the performance of submucosal injection materials (SIMs) is important for endoscopic therapy of early gastrointestinal cancer. It is essential to establish an ex vivo model that can evaluate SIM performance accurately, for developing high-performance SIMs. In our previous study, we developed a new ex vivo model that can be used to evaluate the performance of various SIMs in detail by applying constant tension to the specimen&#39;s ends. We also confirmed that the proposed new ex vivo model allows accurate submucosal elevation height (SEH) measurement under uniform conditions and detailed comparisons of the performances of various types of SIMs. Here, we describe the new ex vivo model and explain the detailed setup methodology of this model. Since all parts of the new model were easy to obtain, the setup of the new model could be completed quickly. SEH of various SIMs could be measured more accurately by using the new model. The critical factor that determines SIM performance can be identified using the new model. SIM development speed will drastically increase after the factor has been identified.

A New Ex Vivo Model for the Evaluation of Endoscopic Submucosal Injection Material Performance

We developed a new ex vivo model that applies constant tension to the porcine gastric specimen. This development made it possible to evaluate the performance (the height and duration of the submucosal elevation) of various SIMs accurately.&#160; The detailed setup methodology of this new model is explained.

Increasing the performance of submucosal injection materials (SIMs) is important for endoscopic therapy of early gastrointestinal cancer. It is essential ...

An Open Source Technology Platform to Manufacture Hydrogel-Based 3D Culture Models in an Automated and Standardized Fashion

Current mixing steps of viscous materials rely on repetitive and time-consuming tasks which are performed mainly manually in a low throughput mode. These issues represent drawbacks in workflows that can ultimately result in irreproducibility of research findings. Manual-based workflows are further limiting the advancement and widespread adoption of viscous materials, such as hydrogels used for biomedical applications. These challenges can be overcome by using automated workflows with standardized mixing processes to increase reproducibility. In this study, we present step-by-step instructions to use an open source protocol designer, to operate an open source workstation, and to identify reproducible mixtures. Specifically, the open source protocol designer guides the user through the experimental parameter selection and generates a ready-to-use protocol code to operate the workstation. This workstation is optimized for pipetting of viscous materials to enable automated and highly reliable handling by the integration of temperature docks for thermoresponsive materials, positive displacement pipettes for viscous materials, and an optional tip touch dock to remove excess material from the pipette tip. The validation and verification of mixtures are performed by a fast and inexpensive absorbance measurement of Orange G. This protocol presents results to obtain 80% (v/v) glycerol mixtures, a dilution series for gelatin methacryloyl (GelMA), and double network hydrogels of 5% (w/v) GelMA and 2% (w/v) alginate. A troubleshooting guide is included to support users with protocol adoption. The described workflow can be broadly applied to a number of viscous materials to generate user-defined concentrations in an automated fashion.

This protocol serves as a comprehensive tutorial for standardized and reproducible mixing of viscous materials with a novel open source automation technology. Detailed instructions are provided on the operation of a newly developed open source workstation, the usage of an open source protocol designer, and the validation and verification to identify reproducible mixtures.

Current mixing steps of viscous materials rely on repetitive and time-consuming tasks which are performed mainly manually in a low throughput mode. These ...

Patient-Specific Polyvinyl Alcohol Phantom Fabrication with Ultrasound and X-Ray Contrast for Brain Tumor Surgery Planning

Phantoms are essential tools for clinical training, surgical planning and the development of novel medical devices. However, it is challenging to create anatomically accurate head phantoms with realistic brain imaging properties because standard fabrication methods are not optimized to replicate any patient-specific anatomical detail and 3D printing materials are not optimized for imaging properties. In order to test and validate a novel navigation system for use during brain tumor surgery, an anatomically accurate phantom with realistic imaging and mechanical properties was required. Therefore, a phantom was developed using real patient data as input and 3D printing of molds to fabricate a patient-specific head phantom comprising the skull, brain and tumor with both ultrasound and X-ray contrast. The phantom also had mechanical properties that allowed the phantom tissue to be manipulated in a similar manner to how human brain tissue is handled during surgery. The phantom was successfully tested during a surgical simulation in a virtual operating room.
The phantom fabrication method uses commercially available materials and is easy to reproduce. The 3D printing files can be readily shared, and the technique can be adapted to encompass many different types of tumor.

This protocol describes the fabrication of a patient specific skull, brain and tumor phantom. It uses 3D printing to create molds, and polyvinyl alcohol (PVA-c) is used as the tissue mimicking material.

Phantoms are essential tools for clinical training, surgical planning and the development of novel medical devices. However, it is challenging to create ...