RECOMIA - a cloud-based platform for artificial intelligence research in nuclear medicine and radiology

Background: Artificial intelligence (AI) is about to transform medical imaging. The Research Consortium for Medical Image Analysis (RECOMIA), a not-for-profit organisation, has developed an online platform to facilitate collaboration between medical researchers and AI researchers. The aim is to minimise the time and effort researchers need to spend on technical aspects, such as transfer, display, and annotation of images, as well as legal aspects, such as de-identification. The purpose of this article is to present the RECOMIA platform and its AI-based tools for organ segmentation in computed tomography (CT), which can be used for extraction of standardised uptake values from the corresponding positron emission tomography (PET) image. Results: The RECOMIA platform includes modules for (1) local de-identification of medical images, (2) secure transfer of images to the cloud-based platform, (3) display functions available using a standard web browser, (4) tools for manual annotation of organs or pathology in the images, (5) deep learning-based tools for organ segmentation or other customised analyses, (6) tools for quantification of segmented volumes, and (7) an export function for the quantitative results. The AI-based tool for organ segmentation in CT currently handles 100 organs (77 bones and 23 soft tissue organs). The segmentation is based on two convolutional neural networks (CNNs): one network to handle organs with multiple similar instances, such as vertebrae and ribs, and one network for all other organs. The CNNs have been trained using CT studies from 339 patients. Experienced radiologists annotated organs in the CT studies. The performance of the segmentation tool, measured as mean Dice index on a manually annotated test set, with 10 representative organs, was 0.93 for all foreground voxels, and the mean Dice index over the organs were 0.86 (0.82 for the soft tissue organs and 0.90 for the bones). Conclusion: The paper presents a platform that provides deep learning-based tools that can perform basic organ segmentations in CT, which can then be used to automatically obtain the different measurement in the corresponding PET image. The RECOMIA platform is available on request at www.recomia.org for research purposes

AI Driven IoT Web-Based Application for Automatic Segmentation and Reconstruction of Abdominal Organs from Medical Images

Medical imaging technology has rapidly advanced in the last few decades, providing detailed images of the human body. The accurate analysis of these images and the segmentation of anatomical structures can produce significant morphological information, provide additional guidance toward subject stratification after diagnosis or before a clinical trial, and help predict a medical condition. Usually, medical scans are manually segmented by expert operators, such as radiologists and radiographers, which is complex, time-consuming and prone to inter-observer variability. A system that generates automatic, accurate quantitative organ segmentation on a large scale could deliver a clinical impact, supporting current investigations in subjects with medical conditions and aiding early diagnosis and treatment planning. This paper proposes a web-based application that automatically segments multiple abdominal organs and muscle, produces respective 3D reconstructions and extracts valuable biomarkers using a deep learning backend engine. Furthermore, it is possible to upload image data and access the medical image segmentation tool without installation using any device connected to the Internet. The final aim is to deliver a web- based image-processing service that clinical experts, researchers and users can seamlessly access through IoT devices without requiring knowledge of the underpinning technology

Cloud-Based Benchmarking of Medical Image Analysis

Medical imagin

TotalSegmentator: robust segmentation of 104 anatomical structures in CT images

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.Comment: Accepted at Radiology: Artificial Intelligenc

Towards Real-time Remote Processing of Laparoscopic Video

Laparoscopic surgery is a minimally invasive technique where surgeons insert a small video camera into the patient\u27s body to visualize internal organs and use small tools to perform these procedures. However, the benefit of small incisions has a disadvantage of limited visualization of subsurface tissues. Image-guided surgery (IGS) uses pre-operative and intra-operative images to map subsurface structures and can reduce the limitations of laparoscopic surgery. One particular laparoscopic system is the daVinci-si robotic surgical vision system. The video streams generate approximately 360 megabytes of data per second, demonstrating a trend toward increased data sizes in medicine, primarily due to higher-resolution video cameras and imaging equipment. Real-time processing this large stream of data on a bedside PC, single or dual node setup, may be challenging and a high-performance computing (HPC) environment is not typically available at the point of care. To process this data on remote HPC clusters at the typical 30 frames per second rate (fps), it is required that each 11.9 MB (1080p) video frame be processed by a server and returned within the time this frame is displayed or 1/30th of a second. The ability to acquire, process, and visualize data in real time is essential for the performance of complex tasks as well as minimizing risk to the patient. We have implemented and compared performance of compression, segmentation and registration algorithms on Clemson\u27s Palmetto supercomputer using dual Nvidia graphics processing units (GPUs) per node and compute unified device architecture (CUDA) programming model. We developed three separate applications that run simultaneously: video acquisition, image processing, and video display. The image processing application allows several algorithms to run simultaneously on different cluster nodes and transfer images through message passing interface (MPI). Our segmentation and registration algorithms resulted in an acceleration factor of around 2 and 8 times respectively. To achieve a higher frame rate, we also resized images and reduced the overall processing time. As a result, using high-speed network to access computing clusters with GPUs to implement these algorithms in parallel will improve surgical procedures by providing real-time medical image processing and laparoscopic data

Liver Segmentation and its Application to Hepatic Interventions

The thesis addresses the development of an intuitive and accurate liver segmentation approach, its integration into software prototypes for the planning of liver interventions, and research on liver regeneration. The developed liver segmentation approach is based on a combination of the live wire paradigm and shape-based interpolation. Extended with two correction modes and integrated into a user-friendly workflow, the method has been applied to more than 5000 data sets. The combination of the liver segmentation with image analysis of hepatic vessels and tumors allows for the computation of anatomical and functional remnant liver volumes. In several projects with clinical partners world-wide, the benefit of the computer-assisted planning was shown. New insights about the postoperative liver function and regeneration could be gained, and most recent investigations into the analysis of MRI data provide the option to further improve hepatic intervention planning

Enrichment of the NLST and NSCLC-Radiomics computed tomography collections with AI-derived annotations

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 their downstream analysis. Artificial intelligence-based annotation tools have been shown to achieve acceptable performance and thus 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 of computed tomography images of the chest, NSCLC-Radiomics, and 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 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 be used to aid in cancer imaging