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1. Enhancing ground penetrating radar with augmented reality systems for underground utility management

   https://doi.org/10.1117/12.2561042  

   Childs, Joshua ; Orfeo, Dan ; Burns, Dylan ; Huston, Dryver ; Xia, Tian ( April 2020 , SPIE Proc Vol 11426-08, Virtual, Augmented, and Mixed Reality (XR) Technology for Multi-Domain Operations)

   Dennison, Mark S. (Ed.)

   Successful maintenance and development of underground infrastructures depends on the ability to access underground utilities efficiently. In general, obtaining accurate positions and conditions of subterranean utilities is not trivial due to inaccurate data records and occlusions that are common in densely populated urban areas. Limited access to underground resources poses challenges to underground utilities management. Ground penetrating radar (GPR) is an effective sensing tools widely used for underground sensing. Combining high accuracy GPR data and augmented reality (AR) poses enables accurate real time visualizations of the buried objects. Although GPR and AR collect and visualize high accuracy data, intensive computation is required. This work presents a novel GPR-AR system that decreases post-processing time significantly while maintaining a neutral format across GPR-AR data collection methods regardless of varying Internet or GPS connection strengths. The methods explored in this work to mitigate failures of previous systems include automated and georeferenced post processing, the classification of underground assets using artificial intelligence, and real time data collection path visualizations. This work also lays a foundation for the potential combinations of a 5G GPR-AR system in which the temporal gap between data collection and visualization can be alleviated. 

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2. Inside the ice shelf: using augmented reality to visualise 3D lidar and radar data of Antarctica

   https://doi.org/10.1111/phor.12298  

   Boghosian, Alexandra L. ; Pratt, Martin J. ; Becker, Maya K. ; Cordero, S. Isabel ; Dhakal, Tejendra ; Kingslake, Jonathan ; Locke, Caitlin D. ; Tinto, Kirsty J. ; Bell, Robin E. ( December 2019 , The Photogrammetric Record)

   From 2015 to 2017, theROSETTA‐Ice project comprehensively mapped Antarctica's Ross Ice Shelf using IcePod, a newly developed aerogeophysical platform. The campaign imaged the ice‐shelf surface with lidar and its internal structure with ice‐penetrating radar. TheROSETTA‐Ice data was combined with pre‐existing ice surface and bed topography digital elevation models to create the first augmented reality (AR) visualisation of the Antarctic Ice Sheet, using the Microsoft HoloLens. TheROSETTA‐Ice datasets support cross‐disciplinary science that aims to understand 4D processes, namely the change of 3D ice‐shelf structures over time. The work presented here usesARto visualise this dataset in 3D and highlights howARcan be simultaneously a useful research tool for interdisciplinary geoscience as well as an effective device for science communication education.

    

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3. Enabling human–infrastructure interfaces for inspection using augmented reality

   https://doi.org/10.1177/1475921720977017  

   Maharjan, D ; Agüero, M ; Mascarenas, D ; Fierro, R ; Moreu, F ( July 2021 , Structural Health Monitoring)

   Decaying infrastructure maintenance cost allocation depends heavily on accurate and safe inspection in the field. New tools to conduct inspections can assist in prioritizing investments in maintenance and repairs. The industrial revolution termed as “Industry 4.0” is based on the intelligence of machines working with humans in a collaborative workspace. Contrarily, infrastructure management has relied on the human for making day-to-day decisions. New emerging technologies can assist during infrastructure inspections, to quantify structural condition with more objective data. However, today’s owners agree in trusting the inspector’s decision in the field over data collected with sensors. If data collected in the field is accessible during the inspections, the inspector decisions can be improved with sensors. New research opportunities in the human–infrastructure interface would allow researchers to improve the human awareness of their surrounding environment during inspections. This article studies the role of Augmented Reality (AR) technology as a tool to increase human awareness of infrastructure in their inspection work. The domains of interest of this research include both infrastructure inspections (emphasis on the collection of data of structures to inform management decisions) and emergency management (focus on the data collection of the environment to inform human actions). This article describes the use of a head-mounted device to access real-time data and information during their field inspection. The authors leverage the use of low-cost smart sensors and QR code scanners integrated with Augmented Reality applications for augmented human interface with the physical environment. This article presents a novel interface architecture for developing Augmented Reality–enabled inspection to assist the inspector’s workflow in conducting infrastructure inspection works with two new applications and summarizes the results from various experiments. The main contributions of this work to computer-aided community are enabling inspectors to visualize data files from database and real-time data access using an Augmented Reality environment. 

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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 not 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. 

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5. Quill: A Declarative Approach for Accelerating Augmented Reality Application Development

   Codi Burley, Ritesh Sarkhel ( September 2022 , A Quarterly bulletin of the Computer Society of the IEEE Technical Committee on Data Engineering)

   Sudeepa Roy and Jun Yang (Ed.)

   Data we encounter in the real-world such as printed menus, business documents, and nutrition labels, are often ad-hoc. Valuable insights can be gathered from this data when combined with additional information. Recent advances in computer vision and augmented reality have made it possible to understand and enrich such data. Joining real-world data with remote data stores and surfacing those enhanced results in place, within an augmented reality interface can lead to better and more informed decision-making capabilities. However, building end-user applications that perform these joins with minimal human effort is not straightforward. It requires a diverse set of expertise, including machine learning, database systems, computer vision, and data visualization. To address this complexity, we present Quill – a framework to develop end-to-end applications that model augmented reality applications as a join between real- world data and remote data stores. Using an intuitive domain-specific language, Quill accelerates the development of end-user applications that join real-world data with remote data stores. Through experiments on applications from multiple different domains, we show that Quill not only expedites the process of development, but also allows developers to build applications that are more performant than those built using standard developer tools, thanks to the ability to optimize declarative specifications. We also perform a user-focused study to investigate how easy (or difficult) it is to use Quill for developing augmented reality applications than other existing tools. Our results show that Quill allows developers to build and deploy applications with a lower technical background than building the same application using existing developer tools. 

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