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1. Exploring the Feasibility of a Thermoacoustic Metastructure for Energy Harvesting and Noise Mitigation

   Biswas, Samarjith ; Manimala, James M. ( December 2022 , Proceedings of meetings on acoustics)

   The thermoacoustic effect provides a means to convert acoustic energy to heat and vice versa without the need for moving parts. This could enable the realization of mechanically-robust, noise mitigating energy harvesters via the development of thermoacoustic metastructures using additive and hybrid fabrication processes and materials. The mechanical, thermal and geometric properties of the porous stack that forms a set of acoustic waveguides in thermoacoustic metastructures are key to their performance. In this proof-ofconcept study, firstly, various ceramic and polymeric stack designs are evaluated using a custom-built thermoacoustic test rig. Influence of stack parameters such as material, length, location, porosity and pore geometry are correlated to simulations using DeltaEC, a software tool based on Rott’s linear approximation. Preliminary results also show a reduction in sound pressure level of around 5.28 dB across the thermoacoustic metastructure at resonance (117.5 Hz). An acousto-thermo-electric transduction scheme is employed to harvest useable electrical power using the best performing stack. Steady-state peak voltage generated was 33 mV for a temperature difference of about 30 degree Celsius across the stack at resonance. Further investigations are underway to establish structure-performance relationships by extracting scaling laws for power-to-volume ratio and frequency-thermal gradient dependencies.
2. Quiet power: Exploring the feasibility of a noise-mitigating, thermoacoustic energy harvester

   https://doi.org/10.1121/10.0011025  

   Biswas, Samarjith ; Manimala, James M. ( April 2022 , The Journal of the Acoustical Society of America)

   The thermoacoustic effect provides a means to convert acoustic energy to heat and vice versa without the need for moving parts. This enables the realization of mechanically robust, noise mitigating energy harvesters, although there are limitations to the power-to-volume ratio achievable. The mechanical, thermal, and geometric properties of the porous stack that forms a set of acoustic waveguides in thermoacoustic devices are key to its performance. In this feasibility study, first, various 4-in. diameter ceramic and polymeric stack designs are evaluated using a custom-built thermoacoustic test rig. Influence of stack parameters such as material, length, location, porosity, and pore geometry are correlated to simulations using DeltaEC, a software tool based on Rott’s linear approximation. An acousto-thermo-electric transduction scheme is employed to harvest useable electrical power using the best performing stack. Steady-state peak voltage generated was 33.5 mV for a temperature difference of 34 °C between thehot and cold sides of the stack at an acoustic excitation frequency of 117.5 Hz. Further investigations are underway to establish structure-performance relationships by extracting scaling laws for power-to-volume ratio and frequency-thermal gradient dependencies.
3. Standoff and Point Detection of Thin Polymer Layers Using Microcantilever Photothermal Spectroscopy

   https://doi.org/10.1149/1945-7111/ac5657  

   Zhao, Yaoli ; Chakraborty, Patatri ; Stavinski, Nicholas ; Velarde, Luis ; Maheshkar, Vaishali ; Dantu, Karthik ; Phani, Arindam ; Kim, Seonghwan ; Thundat, Thomas ( March 2022 , Journal of The Electrochemical Society)

   Standoff detection based on optical spectroscopy is an attractive method for identifying materials at a distance with very high molecular selectivity. Standoff spectroscopy can be exploited in demanding practical applications such as sorting plastics for recycling. Here, we demonstrate selective and sensitive standoff detection of polymer films using bi-material cantilever-based photothermal spectroscopy. We demonstrate that the selectivity of the technique is sufficient to discriminate various polymers. We also demonstrate in situ, point detection of thin layers of polymers deposited on bi-material cantilevers using photothermal spectroscopy. Comparison of the standoff spectra with those obtained by point detection, FTIR, and FTIR-ATR show relative broadening of peaks. Exposure of polymers to UV radiation (365 nm) reveal that the spectral peaks do not change with exposure time, but results in peak broadening with an overall increase in the background cantilever response. The sensitivity of the technique can be further improved by optimizing the thermal sensitivity of the bi-material cantilever and by increasing the number of photons impinging on the cantilever.
4. The Temple University Digital Pathology Corpus: The Breast Tissue Subset

   https://doi.org/10.1109/SPMB52430.2021.9672275  

   Wevodau, Z. ; Doshna, B. ; Jhala, N. ; Akhtar, I. ; Obeid, I. ; Picone, J. ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do notmore »have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA.« less
5. Influence of thermal diffusion on the spatial resolution of photothermal microscopy

   https://doi.org/10.1117/12.2607795  

   Brown, Brendan S. ; Hartland, Gregory V. ( March 2022 , Proc. SPIE 11990, Nanoscale and Quantum Materials: From Synthesis and Laser Processing to Applications)

   Kabashin, Andrei V. ; Farsari, Maria ; Mahjouri-Samani, Masoud (Ed.)

   Photothermal microscopy is a powerful method for investigating biological systems and solid state materials. Using a modulated pump to excite the sample, a continuous probe beam monitors the change in the refractive index of the sample due to the modulated heating. These experiments are typically performed at high frequencies to reduce the 1/f noise, achieving a higher signal to noise ratio. In this paper, we explore how the resolution and sensitivity of the photothermal experiments change when the modulation frequency is brought down below 100kHz. In the instance that the pump and probe are cofocused at the sample, the resolution is determined by the size of the pump beam. On the other hand, when a widefield pump is used, significant broadening occurs for frequencies under 20kHz. This broadening is attributed to thermal diffusion. However, the amount of broadening is less than that expected from the thermal diffusion length, which is about 1.7μm at 10kHz for nanoparticles in glycerol. We also explore the situation where the point spread functions of the pump and probe beams are smaller than the particle size as well as how the penetration depth depends on the properties of the pump and probe beams.