Proceedings of SPIE--the International Society for Optical Engineering最新文献

{"title":"Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures.","authors":"Shunxing Bao, Sichen Zhu, Vasantha L Kolachala, Lucas W Remedios, Yeonjoo Hwang, Yutong Sun, Ruining Deng, Can Cui, Rendong Zhang, Yike Li, Jia Li, Joseph T Roland, Qi Liu, Ken S Lau, Subra Kugathasan, Peng Qiu, Keith T Wilson, Lori A Coburn, Bennett A Landman, Yuankai Huo","doi":"10.1117/12.3006675","DOIUrl":"10.1117/12.3006675","url":null,"abstract":"<p><p>Crohn's disease (CD) is a chronic and relapsing inflammatory condition that affects segments of the gastrointestinal tract. CD activity is determined by histological findings, particularly the density of neutrophils observed on Hematoxylin and Eosin stains (H&E) imaging. However, understanding the broader morphometry and local cell arrangement beyond cell counting and tissue morphology remains challenging. To address this, we characterize six distinct cell types from H&E images and develop a novel approach for the local spatial signature of each cell. Specifically, we create a 10-cell neighborhood matrix, representing neighboring cell arrangements for each individual cell. Utilizing t-SNE for non-linear spatial projection in scatter-plot and Kernel Density Estimation contour-plot formats, our study examines patterns of differences in the cellular environment associated with the odds ratio of spatial patterns between active CD and control groups. This analysis is based on data collected at the two research institutes. The findings reveal heterogeneous nearest-neighbor patterns, signifying distinct tendencies of cell clustering, with a particular focus on the rectum region. These variations underscore the impact of data heterogeneity on cell spatial arrangements in CD patients. Moreover, the spatial distribution disparities between the two research sites highlight the significance of collaborative efforts among healthcare organizations. All research analysis pipeline tools are available at https://github.com/MASILab/cellNN.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12933 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11415268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302981","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cleaning and Harmonizing Medical Image Data for Reliable AI: Lessons Learned from Longitudinal Oral Cancer Natural History Study Data.","authors":"Zhiyun Xue, Tochi Oguguo, Kelly J Yu, Tseng-Cheng Chen, Chun-Hung Hua, Chung Jan Kang, Chih-Yen Chien, Ming-Hsui Tsai, Cheng-Ping Wang, Anil K Chaturvedi, Sameer Antani","doi":"10.1117/12.3005875","DOIUrl":"10.1117/12.3005875","url":null,"abstract":"<p><p>For deep learning-based machine learning, not only are large and sufficiently diverse data crucial but their good qualities are equally important. However, in real-world applications, it is very common that raw source data may contain incorrect, noisy, inconsistent, improperly formatted and sometimes missing elements, particularly, when the datasets are large and sourced from many sites. In this paper, we present our work towards preparing and making image data ready for the development of AI-driven approaches for studying various aspects of the natural history of oral cancer. Specifically, we focus on two aspects: 1) cleaning the image data; and 2) extracting the annotation information. Data cleaning includes removing duplicates, identifying missing data, correcting errors, standardizing data sets, and removing personal sensitive information, toward combining data sourced from different study sites. These steps are often collectively referred to as data harmonization. Annotation information extraction includes identifying crucial or valuable texts that are manually entered by clinical providers related to the image paths/names and standardizing of the texts of labels. Both are important for the successful deep learning algorithm development and data analyses. Specifically, we provide details on the data under consideration, describe the challenges and issues we observed that motivated our work, present specific approaches and methods that we used to clean and standardize the image data and extract labelling information. Further, we discuss the ways to increase efficiency of the process and the lessons learned. Research ideas on automating the process with ML-driven techniques are also presented and discussed. Our intent in reporting and discussing such work in detail is to help provide insights in automating or, minimally, increasing the efficiency of these critical yet often under-reported processes.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12931 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11107840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141077451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Weakly-Supervised Detection of Bone Lesions in CT.","authors":"Tao Sheng, Tejas Sudharshan Mathai, Alexander Shieh, Ronald M Summers","doi":"10.1117/12.3008823","DOIUrl":"10.1117/12.3008823","url":null,"abstract":"<p><p>The skeletal region is one of the common sites of metastatic spread of cancer in the breast and prostate. CT is routinely used to measure the size of lesions in the bones. However, they can be difficult to spot due to the wide variations in their sizes, shapes, and appearances. Precise localization of such lesions would enable reliable tracking of interval changes (growth, shrinkage, or unchanged status). To that end, an automated technique to detect bone lesions is highly desirable. In this pilot work, we developed a pipeline to detect bone lesions (lytic, blastic, and mixed) in CT volumes via a proxy segmentation task. First, we used the bone lesions that were prospectively marked by radiologists in a few 2D slices of CT volumes and converted them into weak 3D segmentation masks. Then, we trained a 3D full-resolution nnUNet model using these weak 3D annotations to segment the lesions and thereby detected them. Our automated method detected bone lesions in CT with a precision of 96.7% and recall of 47.3% despite the use of incomplete and partial training data. To the best of our knowledge, we are the first to attempt the direct detection of bone lesions in CT via a proxy segmentation task.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12927 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11225794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141556147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatial Pathomics Toolkit for Quantitative Analysis of Podocyte Nuclei with Histology and Spatial Transcriptomics Data in Renal Pathology.","authors":"Jiayuan Chen, Yu Wang, Ruining Deng, Quan Liu, Can Cui, Tianyuan Yao, Yilin Liu, Jianyong Zhong, Agnes B Fogo, Haichun Yang, Shilin Zhao, Yuankai Huo","doi":"10.1117/12.3006318","DOIUrl":"10.1117/12.3006318","url":null,"abstract":"<p><p>Podocytes, specialized epithelial cells that envelop the glomerular capillaries, play a pivotal role in maintaining renal health. The current description and quantification of features on pathology slides are limited, prompting the need for innovative solutions to comprehensively assess diverse phenotypic attributes within Whole Slide Images (WSIs). In particular, understanding the morphological characteristics of podocytes, terminally differentiated glomerular epithelial cells, is crucial for studying glomerular injury. This paper introduces the Spatial Pathomics Toolkit (SPT) and applies it to podocyte pathomics. The SPT consists of three main components: (1) instance object segmentation, enabling precise identification of podocyte nuclei; (2) pathomics feature generation, extracting a comprehensive array of quantitative features from the identified nuclei; and (3) robust statistical analyses, facilitating a comprehensive exploration of spatial relationships between morphological and spatial transcriptomics features. The SPT successfully extracted and analyzed morphological and textural features from podocyte nuclei, revealing a multitude of podocyte morphomic features through statistical analysis. Additionally, we demonstrated the SPT's ability to unravel spatial information inherent to podocyte distribution, shedding light on spatial patterns associated with glomerular injury. By disseminating the SPT, our goal is to provide the research community with a powerful and user-friendly resource that advances cellular spatial pathomics in renal pathology. The toolkit's implementation and its complete source code are made openly accessible at the GitHub repository: https://github.com/hrlblab/spatial_pathomics.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12933 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12080590/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144082617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Learning-based Free-Water Correction using Single-shell Diffusion MRI.","authors":"Tianyuan Yao, Derek B Archer, Praitayini Kanakaraj, Nancy Newlin, Shunxing Bao, Daniel Moyer, Kurt Schilling, Bennett A Landman, Yuankai Huo","doi":"10.1117/12.3006901","DOIUrl":"10.1117/12.3006901","url":null,"abstract":"<p><p>Diffusion magnetic resonance imaging (dMRI) offers the ability to assess subvoxel brain microstructure through the extraction of biomarkers like fractional anisotropy, as well as to unveil brain connectivity by reconstructing white matter fiber trajectories. However, accurate analysis becomes challenging at the interface between cerebrospinal fluid and white matter, where the MRI signal originates from both the cerebrospinal fluid and the white matter partial volume. The presence of free water partial volume effects introduces a substantial bias in estimating diffusion properties, thereby limiting the clinical utility of DWI. Moreover, current mathematical models often lack applicability to single-shell acquisitions commonly encountered in clinical settings. Without appropriate regularization, direct model fitting becomes impractical. We propose a novel voxel-based deep learning method for mapping and correcting free-water partial volume contamination in DWI to address these limitations. This approach leverages data-driven techniques to reliably infer plausible free-water volumes across different diffusion MRI acquisition schemes, including single-shell acquisitions. Our evaluation demonstrates that the introduced methodology consistently produces more consistent and plausible results than previous approaches. By effectively mitigating the impact of free water partial volume effects, our approach enhances the accuracy and reliability of DWI analysis for single-shell dMRI, thereby expanding its applications in assessing brain microstructure and connectivity.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12926 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11394251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesizing High-Resolution Dual-Energy Radiographs from Coronary Artery Calcium CT Images.","authors":"Kian Shaker, Linxi Shi, Scott Hsieh, Akyl Swaby, Shiva Abbaszadeh, Adam S Wang","doi":"10.1117/12.3006250","DOIUrl":"10.1117/12.3006250","url":null,"abstract":"<p><p>Generating realistic radiographs from CT is mainly limited by the native spatial resolution of the latter. Here we present a general approach for synthesizing high-resolution digitally reconstructed radiographs (DRRs) from an arbitrary resolution CT volume. Our approach is based on an upsampling framework where tissues of interest are first segmented from the original CT volume and then upsampled individually to the desired voxelization (here ~1 mm → 0.2 mm). Next, we create high-resolution 2D tissue maps by cone-beam projection of individual tissues in the desired radiography direction. We demonstrate this approach on a coronary artery calcium (CAC) patient CT scan and show that our approach preserves individual tissue volumes, yet enhances the tissue interfaces, creating a sharper DRR without introducing artificial features. Lastly, we model a dual-layer detector to synthesize high-resolution dual-energy (DE) anteroposterior and lateral radiographs from the patient CT to visualize the CAC in 2D through material decomposition. On a general level, we envision that this approach is valuable for creating libraries of synthetic yet realistic radiographs from corresponding large CT datasets.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12925 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11529825/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142570572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PixelPrint: Generating Patient-Specific Phantoms for Spectral CT using Dual Filament 3D Printing.","authors":"Pouyan Pasyar, Jessica Im, Kai Mei, Leening Liu, Olivia Sandvold, Michael Geagan, Peter B Noël","doi":"10.1117/12.3006512","DOIUrl":"10.1117/12.3006512","url":null,"abstract":"<p><p>In recent years, the importance of spectral CT scanners in clinical settings has significantly increased, necessitating the development of phantoms with spectral capabilities. This study introduces a dual-filament 3D printing technique for the fabrication of multi-material phantoms suitable for spectral CT, focusing particularly on creating realistic phantoms with orthopedic implants to mimic metal artifacts. Previously, we developed PixelPrint for creating patient-specific lung phantoms that accurately replicate lung properties through precise attenuation profiles and textures. This research extends PixelPrint's utility by incorporating a dual-filament printing approach, which merges materials such as calcium-doped Polylactic Acid (PLA) and metal-doped PLA, to emulate both soft tissue and bone, as well as orthopedic implants. The PixelPrint dual-filament technique utilizes an interleaved approach for material usage, whereby alternating lines of calcium-doped and metal-doped PLA are laid down. The development of specialized filament extruders and deposition mechanisms in this study allows for controlled layering of materials. The effectiveness of this technique was evaluated using various phantom types, including one with a dual filament orthopedic implant and another based on a human knee CT scan with a medical implant. Spectral CT scanner results demonstrated a high degree of similarity between the phantoms and the original patient scans in terms of texture, density, and the creation of realistic metal artifacts. The PixelPrint technology's ability to produce multi-material, lifelike phantoms present new opportunities for evaluating and developing metal artifact reduction (MAR) algorithms and strategies.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12925 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11148765/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141249242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterizing Low-cost Registration for Photographic Images to Computed Tomography.","authors":"Michael E Kim, Ho Hin Lee, Karthik Ramadass, Chenyu Gao, Katherine Van Schaik, Eric Tkaczyk, Jeffrey Spraggins, Daniel C Moyer, Bennett A Landman","doi":"10.1117/12.3005578","DOIUrl":"10.1117/12.3005578","url":null,"abstract":"<p><p>Mapping information from photographic images to volumetric medical imaging scans is essential for linking spaces with physical environments, such as in image-guided surgery. Current methods of accurate photographic image to computed tomography (CT) image mapping can be computationally intensive and/or require specialized hardware. For general purpose 3-D mapping of bulk specimens in histological processing, a cost-effective solution is necessary. Here, we compare the integration of a commercial 3-D camera and cell phone imaging with a surface registration pipeline. Using surgical implants and chuck-eye steak as phantom tests, we obtain 3-D CT reconstruction and sets of photographic images from two sources: Canfield Imaging's H1 camera and an iPhone 14 Pro. We perform surface reconstruction from the photographic images using commercial tools and open-source code for Neural Radiance Fields (NeRF) respectively. We complete surface registration of the reconstructed surfaces with the iterative closest point (ICP) method. Manually placed landmarks were identified at three locations on each of the surfaces. Registration of the Canfield surfaces for three objects yields landmark distance errors of 1.747, 3.932, and 1.692 mm, while registration of the respective iPhone camera surfaces yields errors of 1.222, 2.061, and 5.155 mm. Photographic imaging of an organ sample prior to tissue sectioning provides a low-cost alternative to establish correspondence between histological samples and 3-D anatomical samples.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12930 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Learning site-invariant features of connectomes to harmonize complex network measures.","authors":"Nancy R Newlin, Praitayini Kanakaraj, Thomas Li, Kimberly Pechman, Derek Archer, Angela Jefferson, Bennett Landman, Daniel Moyer","doi":"10.1117/12.3009645","DOIUrl":"10.1117/12.3009645","url":null,"abstract":"<p><p>Multi-site diffusion MRI data is often acquired on different scanners and with distinct protocols. Differences in hardware and acquisition result in data that contains site dependent information, which confounds connectome analyses aiming to combine such multi-site data. We propose a data-driven solution that isolates site-invariant information whilst maintaining relevant features of the connectome. We construct a latent space that is uncorrelated with the imaging site and highly correlated with patient age and a connectome summary measure. Here, we focus on network modularity. The proposed model is a conditional, variational autoencoder with three additional prediction tasks: one for patient age, and two for modularity trained exclusively on data from each site. This model enables us to 1) isolate site-invariant biological features, 2) learn site context, and 3) re-inject site context and project biological features to desired site domains. We tested these hypotheses by projecting 77 connectomes from two studies and protocols (Vanderbilt Memory and Aging Project (VMAP) and Biomarkers of Cognitive Decline Among Normal Individuals (BIOCARD) to a common site. We find that the resulting dataset of modularity has statistically similar means (p-value <0.05) across sites. In addition, we fit a linear model to the joint dataset and find that positive correlations between age and modularity were preserved.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12930 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11364372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FNPC-SAM: Uncertainty-Guided False Negative/Positive Control for SAM on Noisy Medical Images.","authors":"Xing Yao, Han Liu, Dewei Hu, Daiwei Lu, Ange Lou, Hao Li, Ruining Deng, Gabriel Arenas, Baris Oguz, Nadav Schwartz, Brett C Byram, Ipek Oguz","doi":"10.1117/12.3006867","DOIUrl":"10.1117/12.3006867","url":null,"abstract":"<p><p>The Segment Anything Model (SAM) is a recently developed all-range foundation model for image segmentation. It can use sparse manual prompts such as bounding boxes to generate pixel-level segmentation in natural images but struggles in medical images such as low-contrast, noisy ultrasound images. We propose a refined test-phase prompt augmentation technique designed to improve SAM's performance in medical image segmentation. The method couples multi-box prompt augmentation and an aleatoric uncertainty-based false-negative (FN) and false-positive (FP) correction (FNPC) strategy. We evaluate the method on two ultrasound datasets and show improvement in SAM's performance and robustness to inaccurate prompts, without the necessity for further training or tuning. Moreover, we present the Single-Slice-to-Volume (SS2V) method, enabling 3D pixel-level segmentation using only the bounding box annotation from a single 2D slice. Our results allow efficient use of SAM in even noisy, low-contrast medical images. The source code has been released at: https://github.com/MedICL-VU/FNPC-SAM.</p>","PeriodicalId":74505,"journal":{"name":"Proceedings of SPIE--the International Society for Optical Engineering","volume":"12926 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11182739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141422173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}