This work was funded by the National Institutes of Health (NIH) Award # R15CA208798 and in part by the National Science Foundation (NSF) Award # 1408007. Funding for the pulsed THz system was obtained through NSF/MRI Award # 1228958. We acknowledge the use of tissues procured by the National Disease Research Interchange (NDRI) with support from the NIH grant U42OD11158. We also acknowledge the collaboration with Oklahoma Animal Disease Diagnostic Laboratory at the Oklahoma State University for conducting the histopathology procedure on all the tissues handled in this work.

<ol>
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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=Terahertz+spectroscopy+for+the+assessment+of+burn+injuries+in+vivo.">Terahertz spectroscopy for the assessment of burn injuries in vivo.</a> Journal of Biomedical Optics. 18 (7), 077004 (2013).</li><li>Sy, 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=Terahertz+spectroscopy+of+liver+cirrhosis:+investigating+the+origin+of+contrast.">Terahertz spectroscopy of liver cirrhosis: investigating the origin of contrast.</a> Physics in Medicine and Biology. 55 (24), 7587-7596 (2010).</li><li>Yu, C., Fan, S., Sun, Y., Pickwell-Macpherson, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+potential+of+terahertz+imaging+for+cancer+diagnosis:+A+review+of+investigations+to+date.">The potential of terahertz imaging for cancer diagnosis: A review of investigations to date.</a> Quantitative Imaging in Medicine and Surgery. 2 (1), 33-45 (2012).</li><li>El-Shenawee, M., Vohra, N., Bowman, T., Bailey, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cancer+detection+in+excised+breast+tumors+using+terahertz+imaging+and+spectroscopy.">Cancer detection in excised breast tumors using terahertz imaging and spectroscopy.</a> Biomedical Spectroscopy and Imaging. 8 (1-2), 1-9 (2019).</li><li>Yamaguchi, 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=Brain+tumor+imaging+of+rat+fresh+tissue+using+terahertz+spectroscopy.">Brain tumor imaging of rat fresh tissue using terahertz spectroscopy.</a> Scientific Reports. 6 (30124), 1-6 (2016).</li><li>Rong, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Terahertz+in-line+digital+holography+of+human+hepatocellular+carcinoma+tissue.">Terahertz in-line digital holography of human hepatocellular carcinoma tissue.</a> Scientific Reports. 5 (8445), 1-6 (2015).</li><li>Park, J. Y., Choi, H. J., Nam, G., Cho, K., Son, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+Vivo+Dual-Modality+Terahertz+/+Magnetic+Resonance+Imaging+Using+Superparamagnetic+Iron+Oxide+Nanoparticles+as+a+Dual+Contrast+Agent.">In Vivo Dual-Modality Terahertz / Magnetic Resonance Imaging Using Superparamagnetic Iron Oxide Nanoparticles as a Dual Contrast Agent.</a> IEEE Transactions on Terahertz Science and Technology. 2 (1), 93-98 (2012).</li><li>Ji, Y. 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=Feasibility+of+terahertz+reflectometry+for+discrimination+of+human+early+gastric+cancers.">Feasibility of terahertz reflectometry for discrimination of human early gastric cancers.</a> Biomedical Optics Express. 6 (4), 1413-1421 (2015).</li><li>Bowman, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Phantom+Study+of+Terahertz+Spectroscopy+and+Imaging+of+Micro-+and+Nano-diamonds+and+Nano-onions+as+Contrast+Agents+for+Breast+Cancer.">A Phantom Study of Terahertz Spectroscopy and Imaging of Micro- and Nano-diamonds and Nano-onions as Contrast Agents for Breast Cancer.</a> Biomedical Physics and Engineering Express. 3 (5), 055001 (2017).</li><li>Chavez, T., Bowman, T., Wu, J., Bailey, K., El-Shenawee, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assessment+of+Terahertz+Imaging+for+Excised+Breast+Cancer+Tumors+with+Image+Morphing.">Assessment of Terahertz Imaging for Excised Breast Cancer Tumors with Image Morphing.</a> Journal of Infrared, Millimeter, and Terahertz Waves. 39 (12), 1283-1302 (2018).</li><li>Bowman, T. C., El-Shenawee, M., Campbell, L. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Terahertz+Imaging+of+Excised+Breast+Tumor+Tissue+on+Paraffin+Sections.">Terahertz Imaging of Excised Breast Tumor Tissue on Paraffin Sections.</a> IEEE Transactions on Antennas and Propagation. 63 (5), 2088-2097 (2015).</li><li>Bowman, T., El-Shenawee, M., Campbell, L. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Terahertz+transmission+vs+reflection+imaging+and+model-based+characterization+for+excised+breast+carcinomas.">Terahertz transmission vs reflection imaging and model-based characterization for excised breast carcinomas.</a> Biomedical Optics Express. 7 (9), 3756-3783 (2016).</li><li>Bowman, T., Wu, Y., Gauch, J., Campbell, L. K., El-Shenawee, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Terahertz+Imaging+of+Three-Dimensional+Dehydrated+Breast+Cancer+Tumors.">Terahertz Imaging of Three-Dimensional Dehydrated Breast Cancer Tumors.</a> Journal of Infrared, Millimeter, and Terahertz Waves. 38 (6), 766-786 (2017).</li><li>Bowman, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Pulsed+terahertz+imaging+of+breast+cancer+in+freshly+excised+murine+tumors.">Pulsed terahertz imaging of breast cancer in freshly excised murine tumors.</a> Journal of Biomedical Optics. 23 (2), 026004 (2018).</li><li>Bowman, T., Vohra, N., Bailey, K., El-Shenawee, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Terahertz+tomographic+imaging+of+freshly+excised+human+breast+tissues.">Terahertz tomographic imaging of freshly excised human breast tissues.</a> Journal of Medical Imaging. 6 (2), 023501 (2019).</li><li>Vohra, 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=Pulsed+Terahertz+Reflection+Imaging+of+Tumors+in+a+Spontaneous+Model+of+Breast+Cancer.">Pulsed Terahertz Reflection Imaging of Tumors in a Spontaneous Model of Breast Cancer.</a> Biomedical Physics and Engineering Express. 4 (6), 065025 (2018).</li><li>Jacobs, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Positive+margins:+the+challenge+continues+for+breast+surgeons.">Positive margins: the challenge continues for breast surgeons.</a> Annals of Surgical Oncology. 15 (5), 1271-1272 (2008).</li><li>Moran, M. 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=Society+of+Surgical+Oncology--American+Society+for+Radiation+Oncology+Consensus+Guideline+on+Margins+for+Breast-Conserving+Surgery+With+Whole-Breast+Irradiation+in+Stages+I+and+II+Invasive+Breast+Cancer.">Society of Surgical Oncology--American Society for Radiation Oncology Consensus Guideline on Margins for Breast-Conserving Surgery With Whole-Breast Irradiation in Stages I and II Invasive Breast Cancer.</a> International Journal of Radiation Oncology. 88 (3), 553-564 (2014).</li><li>Fitzgerald, A. 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=Terahertz+Pulsed+Imaging+of+human+breast+tumors.">Terahertz Pulsed Imaging of human breast tumors.</a> Radiology. 239 (2), 533-540 (2006).</li><li>Ashworth, P. C., 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=Terahertz+pulsed+spectroscopy+of+freshly+excised+human+breast+cancer.">Terahertz pulsed spectroscopy of freshly excised human breast cancer.</a> Optics Express. 17 (15), 12444-12454 (2009).</li><li>Doradla, P., Alavi, K., Joseph, C., Giles, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+colon+cancer+by+continuous-wave+terahertz+polarization+imaging+technique.">Detection of colon cancer by continuous-wave terahertz polarization imaging technique.</a> Journal of Biomedical Optics. 18 (9), 090504 (2013).</li><li>Reid, C. 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=Terahertz+pulsed+imaging+of+freshly+excised+human+colonic+tissues.">Terahertz pulsed imaging of freshly excised human colonic tissues.</a> Physics in Medicine and Biology. 56 (1), 4333-4353 (2011).</li><li>. Teraview.com Available from: <a target="_blank" href="https://teraview.com">https://teraview.com</a> (2019)</li><li>Orosco, R. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Positive+Surgical+Margins+in+the+10+Most+Common+Solid+Cancers.">Positive Surgical Margins in the 10 Most Common Solid Cancers.</a> Scientific Reports. 8 (1), 1-9 (2018).</li><li>Bowman, T., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Statistical+signal+processing+for+quantitative+assessment+of+pulsed+terahertz+imaging+of+human+breast+tumors.">Statistical signal processing for quantitative assessment of pulsed terahertz imaging of human breast tumors.</a> 2017 42nd International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz). , 1-2 (2017).</li><li>Gavdush, A. 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The authors declare that they have no conflict of interest.

Effective THz reflection imaging of fresh tissue is primarily dependent on two critical aspects: 1) the proper consideration of tissue handling (sections 2 and 4.15); and 2) the stage setup (primarily section 4.11). Insufficient drying of the tissue can result in increased reflection and inability to visualize regions due to high reflections of DMEM and other fluids. Meanwhile, poor tissue contact with the imaging window creates rings or spots of low reflection in the THz reflection image that obscure the results. Extra effort should be taken to ensure good tissue contact with the imaging window, including repositioning the tissue to obtain a better interface. For tissue characterization, additional considerations for the stage setup must be carefully implemented. Improper balancing of the stage by even a few microns can cause significant shifts in the calculated refractive index and absorption coefficient of the tissue. This can also be a result of applying too much pressure to the tissue when mounting it on the imaging window, which can cause bowing of the polystyrene plate. For accurate calculations, the reference signal selected for characterization must also be obtained from the same phase plane of the image to avoid artificial phase shift.
The primary area where the protocol can be modified is in the dielectric materials used to mount the tissue, such as quartz (sections 3.6&#8211;3.7) and polystyrene (starting in section 4.5). As long as the selected window materials are uniformly thick and of low enough absorption to have good signal interaction with the tumor, other materials can be substituted. Materials should be evaluated ahead of time to determine whether they provide an adequate phase plane. Alternatively, for systems where the imaging window will be fixed, a nonuniform window thickness can be addressed by characterizing the phase shift calculated from an empty window scan. There is also some room for modification in how the tissue is mounted for shipment to the pathologist. While tissue marking dyes are used here out of convention, the important aspect is to have a method in place that enables comparison between the THz imaging and the pathology. The primary troubleshooting concerns for the protocol will involve obtaining a good THz signal and establishing proper windowing, which will depend on the specific system being used.
A primary limitation of any fresh tissue handling technique is the time that the tissue is exposed to air. This protocol was designed such that the tissue could remain exposed for no more than 1 h to avoid decomposition prior to the pathology assessment. This is also reflected in the selection of the step size of the image. The THz system in this protocol can reach any step size from 50&#8211;500 &#181;m in 50 &#181;m increments, though the maximum spatial resolution of the system is around 80 &#181;m due to the spectral content of the THz signal. The 200 &#181;m step in the protocol provided sufficient detail while maintaining a reasonable scan time of ~30 min. Assessment of the tumor samples by our consulting pathologist determined that this amount of air exposure does not cause damage to the tissue in an observable way at the cellular level. However, materials such as gelatin can be used to provide clear THz imaging without excessive drying, and may be investigated for future updates to the protocol29. For efficient use of time, steps like purging the system with dry nitrogen and setting up the imaging or spectroscopy can be performed before the tissue is removed from the DMEM. This is also important for future intraoperative applications where the time taken for imaging is a key factor in implementing the THz imaging into the surgical workflow.
Using this protocol intraoperatively represents a potential significant decrease in the time to assess the surgical margins of the tumor from several days or weeks to few a minutes. This will be accomplished when the hardware of the THz system is improved to use THz cameras instead of stepper motor scanners in the future. At present the most similar method employed intraoperatively is specimen radiography, which takes transmission X-ray images of excised tumors for interpretation by a radiologist to determine whether there is cancer on the tissue surface. The described imaging protocol provides a means of direct imaging of the tissue surface. The protocol for the freshly excised breast cancer tumors can also be used for the characterization and imaging of any other type of freshly excised solid tumor8,9,10,11. While this manuscript focuses on imaging freshly excised breast tumors following the described protocol, THz imaging of the associated formalin-fixed paraffin-embedded tissue blocks has also been successfully validated with pathology14,15,16,17,19. Imaging protocols similar to the one proposed here could be developed for pathology support in analyzing embedded tissues as well.

Terahertz (THz) imaging and spectroscopy has been a rapidly growing area of research in the past decade. The continued development of more efficient and consistent THz emitters in the range of 0.1&#8211;4 THz has made their applications grow significantly1. One area where THz has shown promise and significant growth is the biomedical field2. THz radiation has been shown to be nonionizing and biologically safe at the power levels generally used to analyze fixed tissues3. As a result, THz imaging and spectroscopy has been used to classify and differentiate various tissue features such as water content to indicate burn damage and healing4, liver cirrhosis5, and cancer in excised tissues6,7. Cancer assessment in particular covers a broad range of potential clinical and surgical applications, and has been investigated for cancers of the brain8, liver9, ovaries10, gastrointestinal tract11, and breast7,12,13,14,15,16,17,18,19.
THz applications for breast cancer are primarily focused on supporting breast conserving surgery, or lumpectomy, via margin assessment. The objective of a lumpectomy is to remove the tumor and a small layer of surrounding healthy tissue, in contrast to full mastectomy, which removes the entire breast. The surgical margin of the excised tissue is then assessed via pathology once the sample has been fixed in formalin, sectioned, embedded in paraffin, and mounted in 4 &#181;m&#8211;5 &#181;m slices on microscope slides. This process can be time-consuming and requires a secondary surgical procedure at a later time if a positive margin is observed20. Current guidelines by the American Society of Radiation Oncology define this positive margin as having cancer cells contacting the surface-level margin ink21. THz imaging for high-absorption hydrated tissue is primarily limited to surface imaging with some varying penetration based on tissue type, which is sufficient for meeting the surgical needs of rapid margin assessment. A quick analysis of margin conditions during the surgical setting would greatly decrease surgical costs and follow-up procedure rate. To date, THz has proven effective in differentiating between cancer and healthy tissue in formalin-fixed, paraffin-embedded (FFPE) tissues, but additional investigation is needed to provide reliable detection of cancer in freshly excised tissues7.
This protocol details the steps for performing THz imaging and spectroscopy on freshly excised human tissue samples obtained from a biobank. THz applications built on freshly excised human breast cancer tissues have seldom been used in published research7,18,22,23, especially by research groups not integrated with a hospital. The use of freshly excised tissues is likewise rare for other cancer applications, with most non-breast human cancer examples being reported for colonic cancer24,25. One reason for this is that FFPE tissue blocks are far easier to access and handle than freshly excised tissue unless the THz system being used for the study is part of the surgical workflow. Similarly, most commercial laboratory THz systems are not prepared to handle fresh tissue, and those that do are still in the stages of using cell line growth or have only started to look at excised tissue from animal models. To apply THz to an intraoperative setting requires that imaging and characterization steps be developed for fresh tissue in advance so that the analysis does not interfere with the ability to perform standard pathology. For applications that are not inherently meant to be intraoperative, the characterization of fresh tissue is still a challenging step that must be addressed to work towards in vivo applications and differentiation.
The objective of this work is to provide a guideline for THz application for freshly excised tissue using a commercial THz system. The protocol was developed on a THz imaging and spectroscopy system26 for murine breast cancer tumors13,17,19 and was extended to human surgical tissue obtained from biobanks7,18. While the protocol was generated for breast cancer, the same concepts can be applied to similar THz imaging systems and other types of solid-tumor cancers that are treated with surgery where success depends on margin assessment27. Due to a fairly small amount of published THz results on freshly excised tissues, this is the first work to the authors&#8217; knowledge to focus on the protocol of fresh tissue handling for THz imaging and characterization.

<table>
	<tbody>
		<tr>
			<td>70% isopropyl alcohol</td>
			<td>VWR</td>
			<td>89108-162</td>
			<td>Contains 70% USP grade isopropanol and 30% USP grade deionized water</td>
		</tr>
		<tr>
			<td>Alconox powder detergent</td>
			<td>VWR</td>
			<td>21835-032</td>
			<td>Concentrated detergent to remove organic contaminants from glass, metal, stainless steel, porcelain, ceramic, plastic, rubber, and fiberglass</td>
		</tr>
		<tr>
			<td>Bio Hazard Bags</td>
			<td>Fisher Scientific</td>
			<td>19-033-712</td>
			<td>Justrite FM-Approved Biohazard Waste Container Replacement Bags</td>
		</tr>
		<tr>
			<td>Cardboard holder</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Scrap cardboard to keep tissue imaging face intact when immersed in formalin</td>
		</tr>
		<tr>
			<td>Centrifuge Tubes</td>
			<td>VWR</td>
			<td>10026-078</td>
			<td>Centrifuge Tubes with Flat Caps, Conical-Bottom, Polypropylene, Sterile, Standard Line</td>
		</tr>
		<tr>
			<td>Cotton Swabs</td>
			<td>Walmart</td>
			<td>551398298</td>
			<td>Q-tips Original Cotton Swabs used to dye the tissue</td>
		</tr>
		<tr>
			<td>Ethyl Alcohol</td>
			<td>VWR</td>
			<td>71002-426</td>
			<td>KOPTECH Pure (undenatured) anhydrous (200 proof/100%) ethyl alcohol</td>
		</tr>
		<tr>
			<td>Eye protection goggles</td>
			<td>VWR</td>
			<td>89130-918</td>
			<td>Kimberly-clark professional safety glasses</td>
		</tr>
		<tr>
			<td>Face Mask</td>
			<td>VWR</td>
			<td>95041-774</td>
			<td>DUKAL Corporation surgical masks</td>
		</tr>
		<tr>
			<td>Filter paper</td>
			<td>Sigma Aldrich</td>
			<td>Z240087</td>
			<td>Whatman grade 1 cellulose filters</td>
		</tr>
		<tr>
			<td>Formalin solution</td>
			<td>Sigma Aldrich</td>
			<td>HT501128-4L</td>
			<td>10% neutral buffered formalin</td>
		</tr>
		<tr>
			<td>Human freshly excised tumors (Infilterating Ductal Carcinoma (IDC))</td>
			<td>National Disease Research Interchange (NDRI biobank</td>
			<td>N/A</td>
			<td>A protocol is signed with the NDRI for the type of tumors required</td>
		</tr>
		<tr>
			<td>IRADECON Bleach solution</td>
			<td>VWR</td>
			<td>89234-816</td>
			<td>Pre-diluted Sodium Hypochlorite Bleach solution</td>
		</tr>
		<tr>
			<td>KIMTECH SCIENCE wipes</td>
			<td>VWR</td>
			<td>21905-026</td>
			<td>Kimberly-clark professional Kim wipes</td>
		</tr>
		<tr>
			<td>Laboratory Coat</td>
			<td>VWR</td>
			<td>10141-342</td>
			<td>This catalog number is for medium size coat</td>
		</tr>
		<tr>
			<td>Laboratory tweezers/Forceps</td>
			<td>VWR</td>
			<td>82027-388</td>
			<td>Any laboratory tweezers can be used as long as it does not damage the tissue</td>
		</tr>
		<tr>
			<td>Liquid sample holder (two quartz windows with a 0.1 mm teflon spacer)</td>
			<td>TeraView, Ltd</td>
			<td>N/A</td>
			<td>1&#34; diameter, and 0.1452&#34; thick quartz windows</td>
		</tr>
		<tr>
			<td>Nitrile hand gloves</td>
			<td>VWR</td>
			<td>82026-426</td>
			<td>This catalog number is for medium size gloves</td>
		</tr>
		<tr>
			<td>Nitrogen cylinder</td>
			<td>Airgas</td>
			<td>NI UHP300</td>
			<td>NITROGEN UHP GR 5.0 SIZE 300</td>
		</tr>
		<tr>
			<td>Paper towel</td>
			<td>VWR</td>
			<td>14222-321</td>
			<td>11 x 8.78&#34; Sheets, 1 Ply</td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>VWR</td>
			<td>52858-076</td>
			<td>Flexible thermoplastic. Rolled, waterproof sheet interwound with paper to prevent self-adhesion.</td>
		</tr>
		<tr>
			<td>Petri Dish</td>
			<td>VWR</td>
			<td>470210-568</td>
			<td>VWR Petri Dish, Slippable, Mono Plate (undivided bottom)</td>
		</tr>
		<tr>
			<td>Polystyrene Plate</td>
			<td>Home Depot</td>
			<td>1S11143A</td>
			<td>~ 10 x 10 cm square piece cut from a 11&#34; x 14&#34; x 0.05&#34; Non-glare styrene sheet</td>
		</tr>
		<tr>
			<td>ScanAcquire Software</td>
			<td>TeraView, Ltd</td>
			<td>N/A</td>
			<td>System Software for THz reflection imaging measurements</td>
		</tr>
		<tr>
			<td>Stainless steel low-profile blade (#4689)</td>
			<td>VWR</td>
			<td>25608-964</td>
			<td>Tissue-Tek Accu-Edge Disposable Microtome Blades</td>
		</tr>
		<tr>
			<td>Stainless steel metal tray</td>
			<td>Quick Medical</td>
			<td>10F</td>
			<td>Polar Ware Stainless Steel Medical Instrument Trays</td>
		</tr>
		<tr>
			<td>Tissue Marking Dyes</td>
			<td>Ted Pella, Inc</td>
			<td>Yellow Dye #27213-1 
			Red Dye #27213-2 
			Blue Dye #27213-4</td>
			<td>Used to orient excised tissue samples 
			sent to the histopathology laboratory</td>
		</tr>
		<tr>
			<td>TPS Spectra 3000</td>
			<td>TeraView, Ltd</td>
			<td>N/A</td>
			<td>THz imaging and spectroscopy system</td>
		</tr>
		<tr>
			<td>TPS Spectra Software</td>
			<td>TeraView, Ltd</td>
			<td>N/A</td>
			<td>System Software for THz transmission spectroscopy measurements</td>
		</tr>
	</tbody>
</table>

terahertz imaging and characterization protocol for freshly excised breast cancer tumors

This manuscript presents a protocol to handle, characterize, and image freshly excised human breast tumors using pulsed terahertz imaging and spectroscopy techniques. The protocol involves terahertz transmission mode at normal incidence and terahertz reflection mode at an oblique angle of 30&#176;. The collected experimental data represent time domain pulses of the electric field. The terahertz electric field signal transmitted through a fixed point on the excised tissue is processed, through an analytical model, to extract the refractive index and absorption coefficient of the tissue. Utilizing a stepper motor scanner, the terahertz emitted pulse is reflected from each pixel on the tumor providing a planar image of different tissue regions. The image can be presented in time or frequency domain. Furthermore, the extracted data of the refractive index and absorption coefficient at each pixel are utilized to provide a tomographic terahertz image of the tumor. The protocol demonstrates clear differentiation between cancerous and healthy tissues. On the other hand, not adhering to the protocol can result in noisy or inaccurate images due to the presence of air bubbles and fluid remains on the tumor surface. The protocol provides a method for surgical margins assessment of breast tumors.

The THz imaging results18 obtained following the abovementioned protocol of human breast cancer tumor specimen #ND14139 received from the biobank are presented in Figure 9. According to the pathology report, the #ND14139 tumor was a I/II grade infiltrating ductal carcinoma (IDC) obtained from a 49-year-old woman via a left breast lumpectomy surgery procedure. The photograph of the tumor is shown in Figure 9A, the pathology image in Figure 9B, and the THz power spectra image obtained using equation (1) in the protocol is shown in Figure 9C. The assessment of the pathology image was done by our consulting pathologist at Oklahoma State University. Upon correlating the THz image with the pathology image, it was clear that the cancer region (i.e., the red color region in Figure 9C) showed higher reflection than the fat region (i.e., the blue color region in Figure 9C). The blue circle close to the center of the cancer region in Figure 9C was due to the presence of an air bubble beneath the tumor during the imaging process.
Tomographic images based on the electrical properties of the tumor obtained using the above discussed model for each pixel (2,477 pixels in total) are also presented. The tomographic images based on the absorption coefficient (cm-1) data (&#945;- images) and refractive index (n- image) data of the tumor obtained at frequency 0.5 THz and 1.0 THz are shown in Figure 9D, 9E, 9F, and 9G, respectively. As the frequency increased, the calculated absorption coefficient (cm-1) values for the cancer and fat pixels increased, with cancer pixels showing higher values than fat at both frequencies. In contrast, the refractive index of both tissues decreased as the frequency increased. It should be noted that the measured phase became subject to micrometer-scale variations in the imaging stage leveling, polystyrene plate thickness, and stepper motor jitter as the frequency increased. For example, the horizontal lines observed in Figure 9E and 9G were due to the small phase shift introduced by the stepper motors during the scanning process, which was not observed at lower frequencies.
<img alt="Figure 9" class="xfigimg" src="/files/ftp_upload/61007/61007fig09.jpg" /> 
Figure 9: Analysis of breast cancer tumor #ND14139 using THz imaging technique.&#160;(A) Photograph of the tumor. (B) Low power pathology image of the tumor. (C) THz power spectra image over the frequency range 0.5 THz&#8211;1.0 THz. (D) THz tomographic absorption coefficient image obtained at 0.5 THz. This image was constructed using the extracted absorption coefficient data at each pixel from the raw reflection imaging data of the tumor. (E) Absorption coefficient image obtained at 1.0 THz. (F) Refractive index image (n- image) obtained at 0.5 THz. This image was constructed using the extracted refractive index data at each pixel from the raw reflection imaging data of the tumor. (G) Refractive index image (n- image) obtained at 1.0 THz. Figure republished from T. Bowman et al.18 with permission from SPIE. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/61007/61007fig09large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
The THz results discussed in Figure 9 were obtained by successfully following the described protocol. Insufficient handling of the tissue can lead to misleading imaging results. For example, the THz imaging results in Figure 10 for human breast cancer tumor #ND10405 show the effects of insufficient drying. Excess DMEM solution in the tissue dominated the THz power spectra image of the tumor in Figure 10B28 with high reflection that did not correlate to the pathology image shown in Figure 10A28. This led to a false positive result, suggesting a larger presence of cancer in the tumor. DMEM showed a similarly high refractive index and absorption coefficient to water, as seen in Figure 10C19 and 10D19, so it is highly recommended to dry the tumor properly before imaging.
<img alt="Figure 10" class="xfigimg" src="/files/ftp_upload/61007/61007fig10.jpg" /> 
Figure 10: The effect on tumor imaging taken out of the DMEM solution without drying using filter paper.&#160;(A) Low power pathology image of the tumor #ND10405. (B) THz power spectra image of tumor #ND10405 over the frequency range 0.5 THz&#8211;1.0 THz. (C) The transmission refractive index plot for DMEM, PBS, and water ranging from 0.15 THz&#8211;3.5 THz. (D) The transmission absorption coefficient (cm&#8211;1) plot for DMEM, PBS, and water ranging from 0.15 THz&#8211;3.5 THz. Figure 10A, 10B are republished from T. Bowman et al.28 with permission from IEEE and Figure 10C, Figure 10D are republished from N. Vohra et al.19 with permission from IOP Publishing, Ltd. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/61007/61007fig10large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Another example of insufficient adherence to the protocol is shown for tumor #ND11713 in Figure 11. In this case, the air bubbles between the polystyrene plate and the tumor were not removed when the tumor was placed on the plate for the imaging procedure. This resulted in several spots of low reflection across the THz image in Figure 11B, which prevented accurate comparison to the pathology in Figure 11A. Thus, if any air bubbles are observed after placing the tumor on the plate, press it with the tweezers or lift the tumor and gently roll it onto the polystyrene until air gaps are removed.
<img alt="Figure 11" class="xfigimg" src="/files/ftp_upload/61007/61007fig11.jpg" /> 
Figure 11: The artifacts in the THz image caused by the presence of air bubbles between the polystyrene plate and tumor.&#160;(A) Low power pathology image of tumor #ND11713. (B) THz power spectra image of tumor #ND11713 over the frequency range from 0.5&#8211;1.0 THz. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/61007/61007fig11large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Transmission spectroscopy results18 for the same sample (# ND14139) are presented in Figure 12. Tumor sections were taken from points <img alt="Icon 1" src="/files/ftp_upload/61007/61007icon01.jpg" /> and <img alt="Icon 1" src="/files/ftp_upload/61007/61007icon02.jpg" /> in Figure 12A and characterized following the protocol. Both selected points were taken from the cancer tissue region in the tumor according to the pathology image in Figure 12B. The extracted absorption coefficient and refractive index for both tumor sections are presented in Figure 12C,D. Both points showed good agreement for the whole frequency range. The black curve from 0.15&#8211;2 THz in Figure 12C and Figure 12D represents data obtained from the literature23 to compare the results obtained in our work.
<img alt="Figure 12" class="xfigimg" src="/files/ftp_upload/61007/61007fig12.jpg" /> 
Figure 12: The characterization of breast cancer tumor #ND14139 using THz transmission spectroscopy.&#160;(A) The photograph of the tumor with two selected points marked <img alt="Icon 1" src="/files/ftp_upload/61007/61007icon01.jpg" /> and <img alt="Icon 1" src="/files/ftp_upload/61007/61007icon02.jpg" /> from where the 0.5 mm thick sections of the tumor were cut for the transmission spectroscopy measurements. (B) Low power pathology image of the tumor. (C) The transmission absorption coefficient (cm&#8211;1) plot ranging from 0.15&#8211;3.5 THz at points <img alt="Icon 1" src="/files/ftp_upload/61007/61007icon01.jpg" /> and <img alt="Icon 1" src="/files/ftp_upload/61007/61007icon02.jpg" />. (D) The transmission refractive index plot ranging from 0.15&#8211;3.5 THz at points <img alt="Icon 1" src="/files/ftp_upload/61007/61007icon01.jpg" /> and <img alt="Icon 1" src="/files/ftp_upload/61007/61007icon02.jpg" />. Figure republished from T. Bowman et al.18 with permission from SPIE. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/61007/61007fig12large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Terahertz Imaging and Characterization Protocol for Freshly Excised Breast Cancer Tumors at JoVE.com

Terahertz Imaging and Characterization Protocol for Freshly Excised Breast Cancer Tumors

Freshly excised human breast cancer tumors are characterized with terahertz spectroscopy and imaging following fresh tissue handling protocols. Tissue positioning is taken into consideration to enable effective characterization while providing analysis in a timely manner for future intraoperative applications.

This manuscript presents a protocol to handle, characterize, and image freshly excised human breast tumors using pulsed terahertz imaging and spectroscopy ...

terahertz-imaging-characterization-protocol-for-freshly-excised

Nanyang Technological University

Research

JoVE Journal

Engineering

10.7K Views.  University of Arkansas. Freshly excised human breast cancer tumors are characterized with terahertz spectroscopy and imaging following fresh tissue handling protocols. Tissue positioning is taken into consideration to enable effective characterization while providing analysis in a timely manner for future intraoperative applications.

Video: Terahertz Imaging and Characterization Protocol for Freshly Excised Breast Cancer Tumors

Terahertz Microfluidic Sensing Using a Parallel-plate Waveguide Sensor

Refractive index (RI) sensing is a powerful noninvasive and label-free sensing technique for the identification, detection and monitoring of microfluidic samples with a wide range of possible sensor designs such as interferometers and resonators 1,2. Most of the existing RI sensing applications focus on biological materials in aqueous solutions in visible and IR frequencies, such as DNA hybridization and genome sequencing. At terahertz frequencies, applications include quality control, monitoring of industrial processes and sensing and detection applications involving nonpolar materials.
Several potential designs for refractive index sensors in the terahertz regime exist, including photonic crystal waveguides 3, asymmetric split-ring resonators 4, and photonic band gap structures integrated into parallel-plate waveguides 5. Many of these designs are based on optical resonators such as rings or cavities. The resonant frequencies of these structures are dependent on the refractive index of the material in or around the resonator. By monitoring the shifts in resonant frequency the refractive index of a sample can be accurately measured and this in turn can be used to identify a material, monitor contamination or dilution, etc.
The sensor design we use here is based on a simple parallel-plate waveguide 6,7. A rectangular groove machined into one face acts as a resonant cavity (Figures 1 and 2). When terahertz radiation is coupled into the waveguide and propagates in the lowest-order transverse-electric (TE1) mode, the result is a single strong resonant feature with a tunable resonant frequency that is dependent on the geometry of the groove 6,8. This groove can be filled with nonpolar liquid microfluidic samples which cause a shift in the observed resonant frequency that depends on the amount of liquid in the groove and its refractive index 9.
Our technique has an advantage over other terahertz techniques in its simplicity, both in fabrication and implementation, since the procedure can be accomplished with standard laboratory equipment without the need for a clean room or any special fabrication or experimental techniques. It can also be easily expanded to multichannel operation by the incorporation of multiple grooves 10. In this video we will describe our complete experimental procedure, from the design of the sensor to the data analysis and determination of the sample refractive index.

The procedure for implementing a refractive index sensor for terahertz frequencies based on a grooved parallel-plate waveguide geometry is described here. The method yields a measurement of the refractive index of a small volume of liquid through monitoring of the shift in the resonant frequency of the waveguide structure

Refractive index (RI) sensing is a powerful noninvasive and label-free sensing technique for the identification, detection and monitoring of microfluidic ...

Design, Fabrication, and Experimental Characterization of Plasmonic Photoconductive Terahertz Emitters

In this video article we present a detailed demonstration of a highly efficient method for generating terahertz waves. Our technique is based on photoconduction, which has been one of the most commonly used techniques for terahertz generation 1-8. Terahertz generation in a photoconductive emitter is achieved by pumping an ultrafast photoconductor with a pulsed or heterodyned laser illumination. The induced photocurrent, which follows the envelope of the pump laser, is routed to a terahertz radiating antenna connected to the photoconductor contact electrodes to generate terahertz radiation. Although the quantum efficiency of a photoconductive emitter can theoretically reach 100%, the relatively long transport path lengths of photo-generated carriers to the contact electrodes of conventional photoconductors have severely limited their quantum efficiency. Additionally, the carrier screening effect and thermal breakdown strictly limit the maximum output power of conventional photoconductive terahertz sources. To address the quantum efficiency limitations of conventional photoconductive terahertz emitters, we have developed a new photoconductive emitter concept which incorporates a plasmonic contact electrode configuration to offer high quantum-efficiency and ultrafast operation simultaneously. By using nano-scale plasmonic contact electrodes, we significantly reduce the average photo-generated carrier transport path to photoconductor contact electrodes compared to conventional photoconductors 9. Our method also allows increasing photoconductor active area without a considerable increase in the capacitive loading to the antenna, boosting the maximum terahertz radiation power by preventing the carrier screening effect and thermal breakdown at high optical pump powers. By incorporating plasmonic contact electrodes, we demonstrate enhancing the optical-to-terahertz power conversion efficiency of a conventional photoconductive terahertz emitter by a factor of 50 10.

We describe methods for the design, fabrication, and experimental characterization of plasmonic photoconductive emitters, which offer two orders of magnitude higher terahertz power levels compared to conventional photoconductive emitters.

In this video article we present a detailed demonstration of a highly efficient method for generating terahertz waves. Our technique is based on ...

Electron Channeling Contrast Imaging for Rapid III-V Heteroepitaxial Characterization

Misfit dislocations in heteroepitaxial layers of GaP grown on Si(001) substrates are characterized through use of electron channeling contrast imaging (ECCI) in a scanning electron microscope (SEM). ECCI allows for imaging of defects and crystallographic features under specific diffraction conditions, similar to that possible via plan-view transmission electron microscopy (PV-TEM). A particular advantage of the ECCI technique is that it requires little to no sample preparation, and indeed can use large area, as-produced samples, making it a considerably higher throughput characterization method than TEM. Similar to TEM, different diffraction conditions can be obtained with ECCI by tilting and rotating the sample in the SEM. This capability enables the selective imaging of specific defects, such as misfit dislocations at the GaP/Si interface, with high contrast levels, which are determined by the standard invisibility criteria. An example application of this technique is described wherein ECCI imaging is used to determine the critical thickness for dislocation nucleation for GaP-on-Si by imaging a range of samples with various GaP epilayer thicknesses. Examples of ECCI micrographs of additional defect types, including threading dislocations and a stacking fault, are provided as demonstration of its broad, TEM-like applicability. Ultimately, the combination of TEM-like capabilities &#8211; high spatial resolution and richness of microstructural data &#8211; with the convenience and speed of SEM, position ECCI as a powerful tool for the rapid characterization of crystalline materials.

The use of electron channeling contrast imaging in a scanning electron microscope to characterize defects in III-V/Si heteroexpitaxial thin films is described. This method yields similar results to plan-view transmission electron microscopy, but in significantly less time due to lack of required sample preparation.

Misfit dislocations in heteroepitaxial layers of GaP grown on Si(001) substrates are characterized through use of electron channeling contrast imaging ...

Use of a Multi-compartment Dynamic Single Enzyme Phantom for Studies of Hyperpolarized Magnetic Resonance Agents

Imaging of hyperpolarized substrates by magnetic resonance shows great clinical promise for assessment of critical biochemical processes in real time. Due to fundamental constraints imposed by the hyperpolarized state, exotic imaging and reconstruction techniques are commonly used. A practical system for characterization of dynamic, multi-spectral imaging methods is critically needed. Such a system must reproducibly recapitulate the relevant chemical dynamics of normal and pathological tissues. The most widely utilized substrate to date is hyperpolarized [1-13C]-pyruvate for assessment of cancer metabolism. We describe an enzyme-based phantom system that mediates the conversion of pyruvate to lactate. The reaction is initiated by injection of the hyperpolarized agent into multiple chambers within the phantom, each of which contains varying concentrations of reagents that control the reaction rate. Multiple compartments are necessary to ensure that imaging sequences faithfully capture the spatial and metabolic heterogeneity of tissue. This system will aid the development and validation of advanced imaging strategies by providing chemical dynamics that are not available from conventional phantoms, as well as control and reproducibility that is not possible in vivo.

A multi-compartment dynamic phantom is used to simulate some biology of interest for metabolic studies using hyperpolarized magnet resonance agents.

Imaging of hyperpolarized substrates by magnetic resonance shows great clinical promise for assessment of critical biochemical processes in real time. Due ...

Compact Lens-less Digital Holographic Microscope for MEMS Inspection and Characterization

A micro-electro-mechanical-system (MEMS) is a widely used component in many industries, including energy, biotechnology, medical, communications, and automotive. However, effective inspection and characterization metrology systems are needed to ensure the functional reliability of MEMS. This study presents a system based on digital holography as a tool for MEMS metrology. Digital holography has gained increasing attention in the past 20 years. With the fast development and decreasing cost of sensor arrays, resolution of such systems has increased broadening potential applications. Thus, it has attracted attention from both research and industry sides as a potential reliable tool for industrial metrology. Indeed, by recording the interference pattern between an object beam (which contains sample height information) and a reference beam on a CCD camera, one can retrieve the quantitative phase information of an object. However, most of digital holographic systems are bulky and thus not easy to implement on industry production lines. The novelty of the system presented is that it is lens-less and thus very compact. In this study, it is shown that the Compact Digital Holographic Microscope (CDHM) can be used to evaluate several characteristics typically consider as criteria in MEMS inspections. The surface profiles of MEMS in both static and dynamic conditions are presented. Comparison with AFM is investigated to validate the accuracy of the CDHM.

We present a compact reflection digital holographic system (CDHM) for inspection and characterization of MEMS devices. A lens-less design using a diverging input wave providing natural geometrical magnification is demonstrated. Both static and dynamic studies are presented.

A micro-electro-mechanical-system (MEMS) is a widely used component in many industries, including energy, biotechnology, medical, communications, and ...

Data Acquisition Protocol for Determining Embedded Sensitivity Functions

The effectiveness of many structural health monitoring techniques depends on the placement of sensors and the location of input forces. Algorithms for determining optimal sensor and forcing locations typically require data, either simulated or measured, from the damaged structure. Embedded sensitivity functions provide an approach for determining the best available sensor location to detect damage with only data from the healthy structure. In this video and manuscript, the data acquisition procedure and best practices for determining the embedded sensitivity functions of a structure is presented. The frequency response functions used in the calculation of the embedded sensitivity functions are acquired using modal impact testing. Data is acquired and representative results are shown for a residential scale wind turbine blade. Strategies for evaluating the quality of the data being acquired are provided during the demonstration of the data acquisition process.

The data acquisition procedure for determining embedded sensitivity functions is described. Data is acquired and representative results are shown for a residential scale wind turbine blade.

The effectiveness of many structural health monitoring techniques depends on the placement of sensors and the location of input forces. Algorithms for ...

Protocol of Electrochemical Test and Characterization of Aprotic Li-O2 Battery

We demonstrate a method for electrochemical testing of an aprotic Li-O2 battery. An aprotic Li-O2 battery is made of a Li-metal anode, an aprotic electrolyte, and an O2-breathing cathode. The aprotic electrolyte is a solution of lithium salt with aprotic solvent; and porous carbon is commonly used as the cathode substrate. To improve the performance, an electrocatalyst is deposited onto the porous carbon substrate by certain deposition methods, such as atomic layer deposition (ALD) and wet-chemistry reaction. The as-prepared cathode materials are characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray absorption near edge structure (XANES). A Swagelok-type cell, sealed in a glass chamber filled with pure O2, is used for the electrochemical test on a battery test system. The cells are tested under either capacity-controlled mode or voltage controlled mode. The reaction products are investigated by electron microscopy, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, and Raman spectroscopy to study the possible pathway of oxygen reduction reaction (ORR) and oxygen evolution reaction (OER). This protocol demonstrates a systematic and efficient arrangement of routine tests of the aprotic Li-O2 battery, including the electrochemical test and characterization of battery materials.

Protocol of Electrochemical Test and Characterization of Aprotic Li-O2 Battery

A protocol for the electrochemical testing of an aprotic Li-O2 battery with the preparation of electrodes and electrolytes and an introduction of the frequently used methods of characterization is presented here.

We demonstrate a method for electrochemical testing of an aprotic Li-O2 battery. An aprotic Li-O2 battery is made of a Li-metal anode, an aprotic ...

Fabrication of Nanopillar-Based Split Ring Resonators for Displacement Current Mediated Resonances in Terahertz Metamaterials

Terahertz (THz) split ring resonator (SRR) metamaterials (MMs) has been studied for gas, chemical, and biomolecular sensing applications because the SRR is not affected by environmental characteristics such as the temperature and pressure surrounding the resonator. Electromagnetic radiation in THz frequencies is biocompatible, which is a critical condition especially for the application of the biomolecular sensing. However, the quality factor (Q-factor) and frequency responses of traditional thin-film based split ring resonator (SRR) MMs are very low, which limits their sensitivities and selectivity as sensors. In this work, novel nanopillar-based SRR MMs, utilizing displacement current, are designed to enhance the Q-factor up to 450, which is around 45 times higher than that of traditional thin-film-based MMs. In addition to the enhanced Q-factor, the nanopillar-based MMs induce a larger frequency shifts (17 times compared to the shift obtained by the traditional thin-film based MMs). Because of the significantly enhanced Q-factors and frequency shifts as well as the property of biocompatible radiation, the THz nanopillar-based SRR are ideal MMs for the development of biomolecular sensors with high sensitivity and selectivity without inducing damage or distortion to biomaterials. A novel fabrication process has been demonstrated to build the nanopillar-based SRRs for displacement current mediated THz MMs. A two-step gold (Au) electroplating process and an atomic layer deposition (ALD) process are used to create sub-10 nm scale gaps between Au nanopillars. Since the ALD process is a conformal coating process, a uniform aluminum oxide (Al2O3) layer with nanometer-scale thickness can be achieved. By sequentially electroplating another Au thin film to fill the spaces between Al2O3 and Au, a close-packed Au-Al2O3-Au structure with nano-scale Al2O3 gaps can be fabricated. The size of the nano-gaps can be well defined by precisely controlling the deposition cycles of the ALD process, which has an accuracy of 0.1 nm.

A protocol for the design and fabrication of a novel nanopillar-based split ring resonator (SRR) is presented.

Terahertz (THz) split ring resonator (SRR) metamaterials (MMs) has been studied for gas, chemical, and biomolecular sensing applications because the SRR ...

Design and Characterization Methodology for Efficient Wide Range Tunable MEMS Filters

Here, we demonstrate the advantages of the laser Doppler vibrometer (LDV) over conventional techniques (the network analyzer), as well as the techniques to create an application-based microelectromechanical systems (MEMS) filter and how to use it efficiently (i.e., tuning the tuning-capability and avoiding both failure and stiction). LDV enables crucial measurements that are impossible with the network analyzer, such as higher mode detection (highly sensitive biosensor application) and resonance measurement for very small devices (fast prototyping). Accordingly, LDV was used to characterize the frequency tuning range and resonance frequency at different modes of the MEMS filters built for this study. This wide range frequency tuning mechanism is based simply on Joule heating from the embedded heaters and relatively high thermal stress with respect to the temperature of a fixed-fixed beam. However, we demonstrate that another limitation of this method is the resulting high thermal stress, which can burn the devices. Further improvement was achieved and shown for the first time in this study, such that the tuning capability was increased by 32% through an increase in the applied DC bias voltage (25 V to 35 V) between the two adjacent beams. This important finding eliminates the need for the extra Joule heating at the wider frequency tuning range. Another possible failure is through stiction and requirement of structure optimization: We propose a simple and easy technique of low frequency square wave signal application that can successfully separate the beams and eliminates the need for the more sophisticated and complicated methods given in the literature. The above findings necessitate a design methodology, and so we also provide an application-based design.

A protocol for a fixed-fixed beam design using a laser Doppler vibrometer (LDV), including the measurement of frequency tuning, modification of tuning capability, and avoidance of device failure and stiction, is presented. The superiority of the LDV method over the network analyzer is demonstrated due to its higher mode capability.

Here, we demonstrate the advantages of the laser Doppler vibrometer (LDV) over conventional techniques (the network analyzer), as well as the techniques ...

Guidelines and Experience Using Imaging Biomarker Explorer (IBEX) for Radiomics

Imaging Biomarker Explorer (IBEX) is an open-source tool for medical imaging radiomics work. The purpose of this paper is to describe how to use IBEX's graphical user interface (GUI) and to demonstrate how IBEX calculated features have been used in clinical studies. IBEX allows for the import of DICOM images with DICOM radiation therapy structure files or Pinnacle files. Once the images are imported, IBEX has tools within the Data Selection GUI to manipulate the viewing of the images, measure voxel values and distances, and create and edit contours. IBEX comes with 27 preprocessing and 132 feature choices to design feature sets. Each preprocessing and feature category has parameters that can be altered. The output from IBEX is a spreadsheet that contains: 1) each feature from the feature set calculated for each contour in a data set, 2) image information about each contour in a data set, and 3) a summary of the preprocessing and features used with their selected parameters. Features calculated from IBEX have been used in studies to test the variability of features under different imaging conditions and in survival models to improve current clinical models.

Guidelines and Experience Using Imaging Biomarker Explorer IBEX for Radiomics

We describe IBEX, an open-source tool designed for medical imaging radiomics studies, and how to use this tool. In addition, some published works that have used IBEX for uncertainty analysis and model building are showcased.

Imaging Biomarker Explorer (IBEX) is an open-source tool for medical imaging radiomics work. The purpose of this paper is to describe how to use IBEX's ...