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1.
Res Sq ; 2024 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-38746269

RESUMO

Rapid advances in medical imaging Artificial Intelligence (AI) offer unprecedented opportunities for automatic analysis and extraction of data from large imaging collections. Computational demands of such modern AI tools may be difficult to satisfy with the capabilities available on premises. Cloud computing offers the promise of economical access and extreme scalability. Few studies examine the price/performance tradeoffs of using the cloud, in particular for medical image analysis tasks. We investigate the use of cloud-provisioned compute resources for AI-based curation of the National Lung Screening Trial (NLST) Computed Tomography (CT) images available from the National Cancer Institute (NCI) Imaging Data Commons (IDC). We evaluated NCI Cancer Research Data Commons (CRDC) Cloud Resources - Terra (FireCloud) and Seven Bridges-Cancer Genomics Cloud (SB-CGC) platforms - to perform automatic image segmentation with TotalSegmentator and pyradiomics feature extraction for a large cohort containing >126,000 CT volumes from >26,000 patients. Utilizing >21,000 Virtual Machines (VMs) over the course of the computation we completed analysis in under 9 hours, as compared to the estimated 522 days that would be needed on a single workstation. The total cost of utilizing the cloud for this analysis was $1,011.05. Our contributions include: 1) an evaluation of the numerous tradeoffs towards optimizing the use of cloud resources for large-scale image analysis; 2) CloudSegmentator, an open source reproducible implementation of the developed workflows, which can be reused and extended; 3) practical recommendations for utilizing the cloud for large-scale medical image computing tasks. We also share the results of the analysis: the total of 9,565,554 segmentations of the anatomic structures and the accompanying radiomics features in IDC as of release v18.

2.
Clin Anat ; 2024 Mar 31.
Artigo em Inglês | MEDLINE | ID: mdl-38556919

RESUMO

TA2Viewer is an open-access, web-based application and database for browsing anatomical terms and associated medical information on a computer or mobile device (https://ta2viewer.openanatomy.org/). It incorporates the official digital version of the second edition of Terminologia Anatomica (TA2) as published by the Federative International Programme for Anatomical Terminology (FIPAT), and adopted by the International Federation of Associations of Anatomists (IFAA) and other associations. It provides a dynamic and interactive view of the Latin and English nomenclatures. The organizational hierarchy of the terminology can be navigated by using a scrollable, expandable, and collapsible structured listing. Interactive search includes the official TA2 terms, synonyms, and related terms. TA2Viewer also uses TA2 term information to provide convenient access to other online resources, including Google web and image searches, PubMed, and Radiopaedia. Using cross-references from Wikidata, which were provided by the Wikipedia community, TA2Viewer offers links to Wikipedia, UBERON, UMLS, FMA, MeSH, NeuroNames, the public domain 20th edition of Gray's Anatomy, and other data sources. In addition, it can optionally use unofficial synonyms from Wikidata to provide multilingual term searches in hundreds of languages. By leveraging TA2, TA2Viewer provides free access to a curated anatomical nomenclature and serves as an index of online anatomical knowledge.

3.
Front Psychiatry ; 15: 1337888, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38590789

RESUMO

Current views on immunity support the idea that immunity extends beyond defense functions and is tightly intertwined with several other fields of biology such as virology, microbiology, physiology and ecology. It is also critical for our understanding of autoimmunity and cancer, two topics of great biological relevance and for critical public health considerations such as disease prevention and treatment. Central to this review, the immune system is known to interact intimately with the nervous system and has been recently hypothesized to be involved not only in autonomic and limbic bio-behaviors but also in cognitive function. Herein we review the structural architecture of the brain network involved in immune response. Furthermore, we elaborate upon the implications of inflammatory processes affecting brain-immune interactions as reported recently in pathological conditions due to SARS-Cov-2 virus infection, namely in acute and post-acute COVID-19. Moreover, we discuss how current neuroimaging techniques combined with ad hoc clinical autopsies and histopathological analyses could critically affect the validity of clinical translation in studies of human brain-immune interactions using neuroimaging. Advances in our understanding of brain-immune interactions are expected to translate into novel therapeutic avenues in a vast array of domains including cancer, autoimmune diseases or viral infections such as in acute and post-acute or Long COVID-19.

4.
J Thorac Dis ; 16(2): 1009-1020, 2024 Feb 29.
Artigo em Inglês | MEDLINE | ID: mdl-38505008

RESUMO

Background: The global coronavirus disease 2019 (COVID-19) pandemic has posed substantial challenges for healthcare systems, notably the increased demand for chest computed tomography (CT) scans, which lack automated analysis. Our study addresses this by utilizing artificial intelligence-supported automated computer analysis to investigate lung involvement distribution and extent in COVID-19 patients. Additionally, we explore the association between lung involvement and intensive care unit (ICU) admission, while also comparing computer analysis performance with expert radiologists' assessments. Methods: A total of 81 patients from an open-source COVID database with confirmed COVID-19 infection were included in the study. Three patients were excluded. Lung involvement was assessed in 78 patients using CT scans, and the extent of infiltration and collapse was quantified across various lung lobes and regions. The associations between lung involvement and ICU admission were analysed. Additionally, the computer analysis of COVID-19 involvement was compared against a human rating provided by radiological experts. Results: The results showed a higher degree of infiltration and collapse in the lower lobes compared to the upper lobes (P<0.05). No significant difference was detected in the COVID-19-related involvement of the left and right lower lobes. The right middle lobe demonstrated lower involvement compared to the right lower lobes (P<0.05). When examining the regions, significantly more COVID-19 involvement was found when comparing the posterior vs. the anterior halves and the lower vs. the upper half of the lungs. Patients, who required ICU admission during their treatment exhibited significantly higher COVID-19 involvement in their lung parenchyma according to computer analysis, compared to patients who remained in general wards. Patients with more than 40% COVID-19 involvement were almost exclusively treated in intensive care. A high correlation was observed between computer detection of COVID-19 affections and the rating by radiological experts. Conclusions: The findings suggest that the extent of lung involvement, particularly in the lower lobes, dorsal lungs, and lower half of the lungs, may be associated with the need for ICU admission in patients with COVID-19. Computer analysis showed a high correlation with expert rating, highlighting its potential utility in clinical settings for assessing lung involvement. This information may help guide clinical decision-making and resource allocation during ongoing or future pandemics. Further studies with larger sample sizes are warranted to validate these findings.

5.
Cancer Res ; 84(9): 1388-1395, 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38488507

RESUMO

Since 2014, the NCI has launched a series of data commons as part of the Cancer Research Data Commons (CRDC) ecosystem housing genomic, proteomic, imaging, and clinical data to support cancer research and promote data sharing of NCI-funded studies. This review describes each data commons (Genomic Data Commons, Proteomic Data Commons, Integrated Canine Data Commons, Cancer Data Service, Imaging Data Commons, and Clinical and Translational Data Commons), including their unique and shared features, accomplishments, and challenges. Also discussed is how the CRDC data commons implement Findable, Accessible, Interoperable, Reusable (FAIR) principles and promote data sharing in support of the new NIH Data Management and Sharing Policy. See related articles by Brady et al., p. 1384, Pot et al., p. 1396, and Kim et al., p. 1404.


Assuntos
Disseminação de Informação , National Cancer Institute (U.S.) , Neoplasias , Humanos , Estados Unidos , Neoplasias/metabolismo , Disseminação de Informação/métodos , Pesquisa Biomédica , Genômica/métodos , Animais , Proteômica/métodos
6.
Sci Data ; 11(1): 25, 2024 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-38177130

RESUMO

Public imaging datasets are critical for the development and evaluation of automated tools in cancer imaging. Unfortunately, many do not include annotations or image-derived features, complicating downstream analysis. Artificial intelligence-based annotation tools have been shown to achieve acceptable performance and can be used to automatically annotate large datasets. As part of the effort to enrich public data available within NCI Imaging Data Commons (IDC), here we introduce AI-generated annotations for two collections containing computed tomography images of the chest, NSCLC-Radiomics, and a subset of the National Lung Screening Trial. Using publicly available AI algorithms, we derived volumetric annotations of thoracic organs-at-risk, their corresponding radiomics features, and slice-level annotations of anatomical landmarks and regions. The resulting annotations are publicly available within IDC, where the DICOM format is used to harmonize the data and achieve FAIR (Findable, Accessible, Interoperable, Reusable) data principles. The annotations are accompanied by cloud-enabled notebooks demonstrating their use. This study reinforces the need for large, publicly accessible curated datasets and demonstrates how AI can aid in cancer imaging.


Assuntos
Carcinoma Pulmonar de Células não Pequenas , Neoplasias Pulmonares , Humanos , Inteligência Artificial , Carcinoma Pulmonar de Células não Pequenas/diagnóstico por imagem , Pulmão/diagnóstico por imagem , Neoplasias Pulmonares/diagnóstico por imagem , Tomografia Computadorizada por Raios X
7.
bioRxiv ; 2024 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-38260369

RESUMO

The retinogeniculate visual pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus. Identification and visualization of the RGVP are important in studying the anatomy of the visual system and can inform the treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced imaging method that uniquely enables in vivo mapping of the 3D trajectory of the RGVP. Currently, identification of the RGVP from tractography data relies on expert (manual) selection of tractography streamlines, which is time-consuming, has high clinical and expert labor costs, and is affected by inter-observer variability. In this paper, we present a novel deep learning framework, DeepRGVP , to enable fast and accurate identification of the RGVP from dMRI tractography data. We design a novel microstructure-informed supervised contrastive learning method that leverages both streamline label and tissue microstructure information to determine positive and negative pairs. We propose a simple and successful streamline-level data augmentation method to address highly imbalanced training data, where the number of RGVP streamlines is much lower than that of non-RGVP streamlines. We perform comparisons with several state-of-the-art deep learning methods that were designed for tractography parcellation, and we show superior RGVP identification results using DeepRGVP. In addition, we demonstrate a good generalizability of DeepRGVP to dMRI tractography data from neurosurgical patients with pituitary tumors and we show DeepRGVP can successfully identify RGVPs despite the effect of lesions affecting the RGVPs. Overall, our study shows the high potential of using deep learning to automatically identify the RGVP.

9.
Comput Med Imaging Graph ; 111: 102312, 2024 01.
Artigo em Inglês | MEDLINE | ID: mdl-38141568

RESUMO

Accurate lymph node size estimation is critical for staging cancer patients, initial therapeutic management, and assessing response to therapy. Current standard practice for quantifying lymph node size is based on a variety of criteria that use uni-directional or bi-directional measurements. Segmentation in 3D can provide more accurate evaluations of the lymph node size. Fully convolutional neural networks (FCNs) have achieved state-of-the-art results in segmentation for numerous medical imaging applications, including lymph node segmentation. Adoption of deep learning segmentation models in clinical trials often faces numerous challenges. These include lack of pixel-level ground truth annotations for training, generalizability of the models on unseen test domains due to the heterogeneity of test cases and variation of imaging parameters. In this paper, we studied and evaluated the performance of lymph node segmentation models on a dataset that was completely independent of the one used to create the models. We analyzed the generalizability of the models in the face of a heterogeneous dataset and assessed the potential effects of different disease conditions and imaging parameters. Furthermore, we systematically compared fully-supervised and weakly-supervised methods in this context. We evaluated the proposed methods using an independent dataset comprising 806 mediastinal lymph nodes from 540 unique patients. The results show that performance achieved on the independent test set is comparable to that on the training set. Furthermore, neither the underlying disease nor the heterogeneous imaging parameters impacted the performance of the models. Finally, the results indicate that our weakly-supervised method attains 90%- 91% of the performance achieved by the fully supervised training.


Assuntos
Imageamento Tridimensional , Redes Neurais de Computação , Humanos , Imageamento Tridimensional/métodos , Tomografia Computadorizada por Raios X/métodos , Linfonodos/diagnóstico por imagem , Estadiamento de Neoplasias , Processamento de Imagem Assistida por Computador/métodos
10.
Front Digit Health ; 5: 1283726, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-38144260

RESUMO

This paper compares three finite element-based methods used in a physics-based non-rigid registration approach and reports on the progress made over the last 15 years. Large brain shifts caused by brain tumor removal affect registration accuracy by creating point and element outliers. A combination of approximation- and geometry-based point and element outlier rejection improves the rigid registration error by 2.5 mm and meets the real-time constraints (4 min). In addition, the paper raises several questions and presents two open problems for the robust estimation and improvement of registration error in the presence of outliers due to sparse, noisy, and incomplete data. It concludes with preliminary results on leveraging Quantum Computing, a promising new technology for computationally intensive problems like Feature Detection and Block Matching in addition to finite element solver; all three account for 75% of computing time in deformable registration.

11.
Radiographics ; 43(12): e230180, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37999984

RESUMO

The remarkable advances of artificial intelligence (AI) technology are revolutionizing established approaches to the acquisition, interpretation, and analysis of biomedical imaging data. Development, validation, and continuous refinement of AI tools requires easy access to large high-quality annotated datasets, which are both representative and diverse. The National Cancer Institute (NCI) Imaging Data Commons (IDC) hosts large and diverse publicly available cancer image data collections. By harmonizing all data based on industry standards and colocalizing it with analysis and exploration resources, the IDC aims to facilitate the development, validation, and clinical translation of AI tools and address the well-documented challenges of establishing reproducible and transparent AI processing pipelines. Balanced use of established commercial products with open-source solutions, interconnected by standard interfaces, provides value and performance, while preserving sufficient agility to address the evolving needs of the research community. Emphasis on the development of tools, use cases to demonstrate the utility of uniform data representation, and cloud-based analysis aim to ease adoption and help define best practices. Integration with other data in the broader NCI Cancer Research Data Commons infrastructure opens opportunities for multiomics studies incorporating imaging data to further empower the research community to accelerate breakthroughs in cancer detection, diagnosis, and treatment. Published under a CC BY 4.0 license.


Assuntos
Inteligência Artificial , Neoplasias , Estados Unidos , Humanos , National Cancer Institute (U.S.) , Reprodutibilidade dos Testes , Diagnóstico por Imagem , Multiômica , Neoplasias/diagnóstico por imagem
12.
Hum Brain Mapp ; 44(17): 6055-6073, 2023 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-37792280

RESUMO

The corticospinal tract (CST) is a critically important white matter fiber tract in the human brain that enables control of voluntary movements of the body. The CST exhibits a somatotopic organization, which means that the motor neurons that control specific body parts are arranged in order within the CST. Diffusion magnetic resonance imaging (MRI) tractography is increasingly used to study the anatomy of the CST. However, despite many advances in tractography algorithms over the past decade, modern, state-of-the-art methods still face challenges. In this study, we compare the performance of six widely used tractography methods for reconstructing the CST and its somatotopic organization. These methods include constrained spherical deconvolution (CSD) based probabilistic (iFOD1) and deterministic (SD-Stream) methods, unscented Kalman filter (UKF) tractography methods including multi-fiber (UKF2T) and single-fiber (UKF1T) models, the generalized q-sampling imaging (GQI) based deterministic tractography method, and the TractSeg method. We investigate CST somatotopy by dividing the CST into four subdivisions per hemisphere that originate in the leg, trunk, hand, and face areas of the primary motor cortex. A quantitative and visual comparison is performed using diffusion MRI data (N = 100 subjects) from the Human Connectome Project. Quantitative evaluations include the reconstruction rate of the eight anatomical subdivisions, the percentage of streamlines in each subdivision, and the coverage of the white matter-gray matter (WM-GM) interface. CST somatotopy is further evaluated by comparing the percentage of streamlines in each subdivision to the cortical volumes for the leg, trunk, hand, and face areas. Overall, UKF2T has the highest reconstruction rate and cortical coverage. It is the only method with a significant positive correlation between the percentage of streamlines in each subdivision and the volume of the corresponding motor cortex. However, our experimental results show that all compared tractography methods are biased toward generating many trunk streamlines (ranging from 35.10% to 71.66% of total streamlines across methods). Furthermore, the coverage of the WM-GM interface in the largest motor area (face) is generally low (under 40%) for all compared tractography methods. Different tractography methods give conflicting results regarding the percentage of streamlines in each subdivision and the volume of the corresponding motor cortex, indicating that there is generally no clear relationship, and that reconstruction of CST somatotopy is still a large challenge. Overall, we conclude that while current tractography methods have made progress toward the well-known challenge of improving the reconstruction of the lateral projections of the CST, the overall problem of performing a comprehensive CST reconstruction, including clinically important projections in the lateral (hand and face areas) and medial portions (leg area), remains an important challenge for diffusion MRI tractography.


Assuntos
Neoplasias Encefálicas , Imagem de Tensor de Difusão , Humanos , Imagem de Tensor de Difusão/métodos , Tratos Piramidais/diagnóstico por imagem , Tratos Piramidais/patologia , Imagem de Difusão por Ressonância Magnética , Encéfalo/diagnóstico por imagem , Encéfalo/patologia , Neoplasias Encefálicas/cirurgia
13.
Comput Methods Programs Biomed ; 242: 107839, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37832430

RESUMO

BACKGROUND AND OBJECTIVES: Reproducibility is a major challenge in developing machine learning (ML)-based solutions in computational pathology (CompPath). The NCI Imaging Data Commons (IDC) provides >120 cancer image collections according to the FAIR principles and is designed to be used with cloud ML services. Here, we explore its potential to facilitate reproducibility in CompPath research. METHODS: Using the IDC, we implemented two experiments in which a representative ML-based method for classifying lung tumor tissue was trained and/or evaluated on different datasets. To assess reproducibility, the experiments were run multiple times with separate but identically configured instances of common ML services. RESULTS: The results of different runs of the same experiment were reproducible to a large extent. However, we observed occasional, small variations in AUC values, indicating a practical limit to reproducibility. CONCLUSIONS: We conclude that the IDC facilitates approaching the reproducibility limit of CompPath research (i) by enabling researchers to reuse exactly the same datasets and (ii) by integrating with cloud ML services so that experiments can be run in identically configured computing environments.


Assuntos
Neoplasias Pulmonares , Software , Humanos , Reprodutibilidade dos Testes , Computação em Nuvem , Diagnóstico por Imagem , Neoplasias Pulmonares/diagnóstico por imagem
14.
J Psychiatr Res ; 167: 10-15, 2023 Sep 30.
Artigo em Inglês | MEDLINE | ID: mdl-37804756

RESUMO

A common symptom of the neuropsychiatric Post-Acute COVID-19 syndrome (neuro-PACS) is the so called 'brain fog'. Patients describe the brain fog as problems with attention, memory and mental fatigue. Brain fog is experienced by 9-55% of people for months after having contracted SARS-CoV-2 virus. Several theories have been proposed to explain PACS's brain fog, including a neuroinflammatory hypothesis, but the hypothesis remains to be proven. Here, we examined inflammatory and immunological blood profile in a cohort of patients with PACS to investigate the association between executive functions and blood inflammatory markers. Executive function was assessed by the Trail Making Test (TMT) Part A and Part B, as well as the Barkley Deficits in Executive Functioning Scale (BDEFS), in 71 patients (36 men), average age of 40 years (range: 15-82, SD: 15.7). Impairment in executive functioning (BDEFS scores and TMT B scores) correlated with increased levels of Interleukin-6 (IL-6), fibrinogen and ferritin. Moreover, elevated levels of Il-6, fibrinogen, ferritin, tumor necrosis factor-alpha and C-reactive protein have been observed in PACS. These findings demonstrate that PACS is characterized by the presence of an immuno-inflammatory process, which is associated with diminished executive functioning. Here, we argue in favour of a shift from the non-descriptive definition of 'mental fog' to a characterization of a subtype of PACS, associated with alteration in executive functioning. Implication for clinical settings and prevention are discussed.

15.
ArXiv ; 2023 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-37731651

RESUMO

Current neurosurgical procedures utilize medical images of various modalities to enable the precise location of tumors and critical brain structures to plan accurate brain tumor resection. The difficulty of using preoperative images during the surgery is caused by the intra-operative deformation of the brain tissue (brain shift), which introduces discrepancies concerning the preoperative configuration. Intra-operative imaging allows tracking such deformations but cannot fully substitute for the quality of the pre-operative data. Dynamic Data Driven Deformable Non-Rigid Registration (D4NRR) is a complex and time-consuming image processing operation that allows the dynamic adjustment of the pre-operative image data to account for intra-operative brain shift during the surgery. This paper summarizes the computational aspects of a specific adaptive numerical approximation method and its variations for registering brain MRIs. It outlines its evolution over the last 15 years and identifies new directions for the computational aspects of the technique.

16.
Res Sq ; 2023 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-37333197

RESUMO

Background: The aim of the current study was to investigate the distribution and extent of lung involvement in patients with COVID-19 with AI-supported, automated computer analysis and to assess the relationship between lung involvement and the need for intensive care unit (ICU) admission. A secondary aim was to compare the performance of computer analysis with the judgment of radiological experts. Methods: A total of 81 patients from an open-source COVID database with confirmed COVID-19 infection were included in the study. Three patients were excluded. Lung involvement was assessed in 78 patients using computed tomography (CT) scans, and the extent of infiltration and collapse was quantified across various lung lobes and regions. The associations between lung involvement and ICU admission were analyzed. Additionally, the computer analysis of COVID-19 involvement was compared against a human rating provided by radiological experts. Results: The results showed a higher degree of infiltration and collapse in the lower lobes compared to the upper lobes (p < 0.05) No significant difference was detected in the COVID-19-related involvement of the left and right lower lobes. The right middle lobe demonstrated lower involvement compared to the right lower lobes (p < 0.05). When examining the regions, significantly more COVID-19 involvement was found when comparing the posterior vs. the anterior halves of the lungs and the lower vs. the upper half of the lungs. Patients, who required ICU admission during their treatment exhibited significantly higher COVID-19 involvement in their lung parenchyma according to computer analysis, compared to patients who remained in general wards. Patients with more than 40% COVID-19 involvement were almost exclusively treated in intensive care. A high correlation was observed between computer detection of COVID-19 affections and expert rating by radiological experts. Conclusion: The findings suggest that the extent of lung involvement, particularly in the lower lobes, dorsal lungs, and lower half of the lungs, may be associated with the need for ICU admission in patients with COVID-19. Computer analysis showed a high correlation with expert rating, highlighting its potential utility in clinical settings for assessing lung involvement. This information may help guide clinical decision-making and resource allocation during ongoing or future pandemics. Further studies with larger sample sizes are warranted to validate these findings.

17.
IEEE Trans Biomed Eng ; 70(12): 3436-3448, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37339047

RESUMO

Ultrasound-compatible phantoms are used to develop novel US-based systems and train simulated medical interventions. The price difference between lab-made and commercially available ultrasound-compatible phantoms lead to the publication of many papers categorized as low-cost in the literature. The aim of this review was to improve the phantom selection process by summarizing the pertinent literature. We compiled papers on US-compatible spine, prostate, vascular, breast, kidney, and li ver phantoms. We reviewed papers for cost and accessibility, providing an overview of the materials, construction time, shelf life, needle insertion limits, and manufacturing and evaluation methods. This information was summarized by anatomy. The clinical application associated with each phantom was also reported for those interested in a particular intervention. Techniques and common practices for building low-cost phantoms were provided. Overall, this article aims to summarize a breadth of ultrasound-compatible phantom research to enable informed phantom methods selection.


Assuntos
Mama , Próstata , Masculino , Humanos , Ultrassonografia , Mama/diagnóstico por imagem , Próstata/diagnóstico por imagem , Coluna Vertebral , Imagens de Fantasmas
18.
Int J Comput Assist Radiol Surg ; 18(10): 1925-1940, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37004646

RESUMO

PURPOSE: Brain shift that occurs during neurosurgery disturbs the brain's anatomy. Prediction of the brain shift is essential for accurate localisation of the surgical target. Biomechanical models have been envisaged as a possible tool for such predictions. In this study, we created a framework to automate the workflow for predicting intra-operative brain deformations. METHODS: We created our framework by uniquely combining our meshless total Lagrangian explicit dynamics (MTLED) algorithm for computing soft tissue deformations, open-source software libraries and built-in functions within 3D Slicer, an open-source software package widely used for medical research. Our framework generates the biomechanical brain model from the pre-operative MRI, computes brain deformation using MTLED and outputs results in the form of predicted warped intra-operative MRI. RESULTS: Our framework is used to solve three different neurosurgical brain shift scenarios: craniotomy, tumour resection and electrode placement. We evaluated our framework using nine patients. The average time to construct a patient-specific brain biomechanical model was 3 min, and that to compute deformations ranged from 13 to 23 min. We performed a qualitative evaluation by comparing our predicted intra-operative MRI with the actual intra-operative MRI. For quantitative evaluation, we computed Hausdorff distances between predicted and actual intra-operative ventricle surfaces. For patients with craniotomy and tumour resection, approximately 95% of the nodes on the ventricle surfaces are within two times the original in-plane resolution of the actual surface determined from the intra-operative MRI. CONCLUSION: Our framework provides a broader application of existing solution methods not only in research but also in clinics. We successfully demonstrated the application of our framework by predicting intra-operative deformations in nine patients undergoing neurosurgical procedures.


Assuntos
Neoplasias Encefálicas , Encéfalo , Humanos , Encéfalo/diagnóstico por imagem , Encéfalo/cirurgia , Encéfalo/patologia , Neoplasias Encefálicas/diagnóstico por imagem , Neoplasias Encefálicas/cirurgia , Neoplasias Encefálicas/patologia , Imageamento por Ressonância Magnética/métodos , Procedimentos Neurocirúrgicos , Craniotomia
19.
Nat Commun ; 14(1): 1572, 2023 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-36949078

RESUMO

The exchange of large and complex slide microscopy imaging data in biomedical research and pathology practice is impeded by a lack of data standardization and interoperability, which is detrimental to the reproducibility of scientific findings and clinical integration of technological innovations. We introduce Slim, an open-source, web-based slide microscopy viewer that implements the internationally accepted Digital Imaging and Communications in Medicine (DICOM) standard to achieve interoperability with a multitude of existing medical imaging systems. We showcase the capabilities of Slim as the slide microscopy viewer of the NCI Imaging Data Commons and demonstrate how the viewer enables interactive visualization of traditional brightfield microscopy and highly-multiplexed immunofluorescence microscopy images from The Cancer Genome Atlas and Human Tissue Atlas Network, respectively, using standard DICOMweb services. We further show how Slim enables the collection of standardized image annotations for the development or validation of machine learning models and the visual interpretation of model inference results in the form of segmentation masks, spatial heat maps, or image-derived measurements.


Assuntos
Ciência de Dados , Microscopia , Humanos , Microscopia/métodos , Reprodutibilidade dos Testes
20.
Clin Anat ; 36(4): 641-650, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-36648069

RESUMO

Acupuncture point names written in Chinese Han characters often provide clinically useful information in both their literal and figurative meanings about location and therapeutic use. The World Health Organization (WHO) standard acupuncture nomenclature includes these names in Han characters in an unusual array that includes both "original" forms and, in parentheses, simplified forms. Construction of a multilingual table of acupuncture point names during development of a database revealed that the assumption that the "original" form in the WHO nomenclature was the traditional Chinese character was frequently false. The Han character forms in the pdf of the 2009 reprint of WHO Standard Acupuncture Point Locations were carefully compared with Han characters used in traditional and simplified Chinese, Japanese and Korean writing systems. This work utilized three online tools: UnicodePlus, Unihan Database Lookup, and Wiktionary. Only 48% of the "original" character forms were traditional Chinese characters. The Unicode number was correct in 99%, but in most cases the East Asian font used was not a traditional Chinese one. The issue about Han character forms was also found in all earlier versions of the WHO standard acupuncture nomenclature. Other detected problems included the use of wrong characters for an "original" character form in one name and for a simplified character form in another name. The WHO standard acupuncture nomenclature should be revised with a focus on accuracy in the usage of Han characters.


Assuntos
Pontos de Acupuntura , Idioma , Humanos , Terapia por Acupuntura , Multilinguismo , Terminologia como Assunto
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