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1. 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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2. DeepOrganNet: On-the-Fly Reconstruction and Visualization of 3D / 4D Lung Models from Single-View Projections by Deep Deformation Network

   Wang, Yifan ; Zhong, Zichun ; Hua, Jing ( January 2020 , IEEE transactions on visualization and computer graphics)

   This paper introduces a deep neural network based method, i.e., DeepOrganNet, to generate and visualize fully high-fidelity 3D / 4D organ geometric models from single-view medical images with complicated background in real time. Traditional 3D / 4D medical image reconstruction requires near hundreds of projections, which cost insufferable computational time and deliver undesirable high imaging / radiation dose to human subjects. Moreover, it always needs further notorious processes to segment or extract the accurate 3D organ models subsequently. The computational time and imaging dose can be reduced by decreasing the number of projections, but the reconstructed image quality is degraded accordingly. To our knowledge, there is no method directly and explicitly reconstructing multiple 3D organ meshes from a single 2D medical grayscale image on the fly. Given single-view 2D medical images, e.g., 3D / 4D-CT projections or X-ray images, our end-to-end DeepOrganNet framework can efficiently and effectively reconstruct 3D / 4D lung models with a variety of geometric shapes by learning the smooth deformation fields from multiple templates based on a trivariate tensor-product deformation technique, leveraging an informative latent descriptor extracted from input 2D images. The proposed method can guarantee to generate high-quality and high-fidelity manifold meshes for 3D / 4D lung models; while, all current deep learning based approaches on the shape reconstruction from a single image cannot. The major contributions of this work are to accurately reconstruct the 3D organ shapes from 2D single-view projection, significantly improve the procedure time to allow on-the-fly visualization, and dramatically reduce the imaging dose for human subjects. Experimental results are evaluated and compared with the traditional reconstruction method and the state-of-the-art in deep learning, by using extensive 3D and 4D examples, including both synthetic phantom and real patient datasets. The efficiency of the proposed method shows that it only needs several milliseconds to generate organ meshes with 10K vertices, which has great potential to be used in real-time image guided radiation therapy (IGRT). 

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3. Mimicking non-ideal instrument behavior for hologram processing using neural style translation

   https://doi.org/10.1364/OE.486741  

   Schreck, John S. ; Hayman, Matthew ; Gantos, Gabrielle ; Bansemer, Aaron ; Gagne, David John ( May 2023 , Optics Express)

   Holographic cloud probes provide unprecedented information on cloud particle density, size and position. Each laser shot captures particles within a large volume, where images can be computationally refocused to determine particle size and location. However, processing these holograms with standard methods or machine learning (ML) models requires considerable computational resources, time and occasional human intervention. ML models are trained on simulated holograms obtained from the physical model of the probe since real holograms have no absolute truth labels. Using another processing method to produce labels would be subject to errors that the ML model would subsequently inherit. Models perform well on real holograms only when image corruption is performed on the simulated images during training, thereby mimicking non-ideal conditions in the actual probe. Optimizing image corruption requires a cumbersome manual labeling effort. Here we demonstrate the application of the neural style translation approach to the simulated holograms. With a pre-trained convolutional neural network, the simulated holograms are “stylized” to resemble the real ones obtained from the probe, while at the same time preserving the simulated image “content” (e.g. the particle locations and sizes). With an ML model trained to predict particle locations and shapes on the stylized data sets, we observed comparable performance on both simulated and real holograms, obviating the need to perform manual labeling. The described approach is not specific to holograms and could be applied in other domains for capturing noise and imperfections in observational instruments to make simulated data more like real world observations.

    

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4. High frequency beam oscillation keyhole dynamics in laser melting revealed by in-situ x-ray imaging

   https://doi.org/10.1038/s43246-023-00332-z  

   Wu, Ziheng ; Tang, Guannan ; Clark, Samuel J. ; Meshkov, Andrey ; Roychowdhury, Subhrajit ; Gould, Benjamin ; Ostroverkhov, Victor ; Adcock, Thomas ; Duclos, Steven J. ; Fezzaa, Kamel ; et al ( December 2023 , Communications Materials)

   Abstract The metal additive manufacturing industry is actively developing instruments and strategies to enable higher productivity, optimal build quality, and controllable as-built microstructure. A beam controlling technique, laser oscillation has shown potential in all these aspects in laser welding; however, few attempts have been made to understand the underlying physics of the oscillating keyholes/melt pools which are the prerequisites for these strategies to become a useful tool for laser-based additive manufacturing processes. Here, to address this gap, we utilized a synchrotron-based X-ray operando technique to image the dynamic keyhole oscillation in Ti-6Al-4V using a miniature powder bed fusion setup. We found good agreement between the experimental observations and simulations performed with a validated Lattice Boltzmann multiphysics model. The study revealed the continuous and periodic fluctuations in the characteristic keyhole parameters that are unique to the oscillating laser beam processing and responsible for the chevron pattern formation at solidification. In particular, despite the intrinsic longer-range fluctuation, the oscillating technique displayed potential for reducing keyhole instability, mitigating porosity formation, and altering surface topology. These insights on the oscillating keyhole dynamics can be useful for the future development and application of this technique. 

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5. Facile Functionalization of Graphene to Tune Response of Printed Electrochemical Sensors to Neurotransmitters

   https://doi.org/10.1149/MA2023-01532651mtgabs  

   Kammarchedu, Vinay ; Butler, Derrick ; Khamsi, Pouya Soltan ; Ebrahimi, Aida ( August 2023 , ECS Meeting Abstracts)

   Neurotransmitters are small molecules involved in neuronal signaling and can also serve as stress biomarkers.¹Their abnormal levels have been also proposed to be indicative of several neurological diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington disease, among others. Hence, measuring their levels is highly important for early diagnosis, therapy, and disease prognosis. In this work, we investigate facile functionalization methods to tune and enhance sensitivity of printed graphene sensors to neurotransmitters. Sensors based on direct laser scribing and screen-printed graphene ink are studied. These printing methods offer ease of prototyping and scalable fabrication at low cost.

   The effect of functionalization of laser induced graphene (LIG) by electrodeposition and solution-based deposition of TMDs (molybdenum disulfide²and tungsten disulfide) and metal nanoparticles is studied. For different processing methods, electrochemical characteristics (such as electrochemically active surface area: ECSA and heterogenous electron transfer rate: k⁰) are extracted and correlated to surface chemistry and defect density obtained respectively using X-ray photoelectron spectroscopy (XPS) and Raman spectroscopy. These functionalization methods are observed to directly impact the sensitivity and limit of detection (LOD) of the graphene sensors for the studied neurotransmitters. For example, as compared to bare LIG, it is observed that electrodeposition of MoS₂on LIG improves ECSA by 3 times and k⁰by 1.5 times.³Electrodeposition of MoS₂also significantly reduces LOD of serotonin and dopamine in saliva, enabling detection of their physiologically relevant concentrations (in pM-nM range). In addition, chemical treatment of LIG sensors is carried out in the form of acetic acid treatment. Acetic acid treatment has been shown previously to improve C-C bonds improving the conductivity of LIG sensors.⁴In our work, in particular, acetic acid treatment leads to larger improvement of LOD of norepinephrine compared to MoS₂electrodeposition.

   In addition, we investigate the effect of plasma treatment to tune the sensor response by modifying the defect density and chemistry. For example, we find that oxygen plasma treatment of screen-printed graphene ink greatly improves LOD of norepinephrine up to three orders of magnitude, which may be attributed to the increased defects and oxygen functional groups on the surface as evident by XPS measurements. Defects are known to play a key role in enhancing the sensitivity of 2D materials to surface interactions, and have been explored in tuning/enhancing the sensor sensitivity.⁵Building on our previous work,³we apply a custom machine learning-based data processing method to further improve that sensitivity and LOD, and also to automatically benchmark different molecule-material pairs.

   Future work includes expanding the plasma chemistry and conditions, studying the effect of precursor mixture in laser-induced solution-based functionalization, and understanding the interplay between molecule-material system. Work is also underway to improve the machine learning model by using nonlinear learning models such as neural networks to improve the sensor sensitivity, selectivity, and robustness.

   References

   A. J. Steckl, P. Ray, (2018), doi:10.1021/acssensors.8b00726.

   Y. Lei, D. Butler, M. C. Lucking, F. Zhang, T. Xia, K. Fujisawa, T. Granzier-Nakajima, R. Cruz-Silva, M. Endo, H. Terrones, M. Terrones, A. Ebrahimi,Sci. Adv.6, 4250–4257 (2020).

   V. Kammarchedu, D. Butler, A. Ebrahimi,Anal. Chim. Acta.1232, 340447 (2022).

   H. Yoon, J. Nah, H. Kim, S. Ko, M. Sharifuzzaman, S. C. Barman, X. Xuan, J. Kim, J. Y. Park,Sensors Actuators B Chem.311, 127866 (2020).

   T. Wu, A. Alharbi, R. Kiani, D. Shahrjerdi,Adv. Mater.31, 1–12 (2019).

    

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