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Early detection of the adenocarcinoma cancer in colon tissue by means of explainable deep learning, by classifying histological images and providing visual explainability on model prediction. Considering that in recent years, deep learning techniques have emerged as powerful techniques in medical image analysis, offering unprecedented accuracy and efficiency, in this paper we propose a method to automatically detect the presence of cancerous cells in colon tissue images. Various deep learning architectures are considered, with the aim of considering the best one in terms of quantitative and qualitative results. As a matter of fact, we consider qualitative results by taking into account the so-called prediction explainability, by providing a way to highlight on the tissue images the areas that from the model point of view are related to the presence of colon cancer. The experimental analysis, performed on 10,000 colon issue images, showed the effectiveness of the proposed method by obtaining an accuracy equal to 0.99. The experimental analysis shows that the proposed method can be successfully exploited for colon cancer detection and localisation from tissue images. [ABSTRACT FROM AUTHOR]

In recent years, the growth spurt of medical imaging data has led to the development of various machine learning algorithms for various healthcare applications. The MedMNISTv2 dataset, a comprehensive benchmark for 2D biomedical image classification, encompasses diverse medical imaging modalities such as Fundus Camera, Breast Ultrasound, Colon Pathology, Blood Cell Microscope etc. Highly accurate classifications performed on these datasets is crucial for identification of various diseases and determining the course of treatment. This research paper presents a comprehensive analysis of four subsets within the MedMNISTv2 dataset: BloodMNIST, BreastMNIST, PathMNIST and RetinaMNIST. Each of these selected datasets is of diverse data modalities and comes with various sample sizes, and have been selected to analyze the efficiency of the model against diverse data modalities. The study explores the idea of assessing the Vision Transformer Model's ability to capture intricate patterns and features crucial for these medical image classification and thereby transcend the benchmark metrics substantially. The methodology includes pre-processing the input images which is followed by training the ViT-base-patch16-224 model on the mentioned datasets. The performance of the model is assessed using key metrices and by comparing the classification accuracies achieved with the benchmark accuracies. With the assistance of ViT, the new benchmarks achieved for BloodMNIST, BreastMNIST, PathMNIST and RetinaMNIST are 97.90%, 90.38%, 94.62% and 57%, respectively. The study highlights the promise of Vision transformer models in medical image analysis, preparing the way for their adoption and further exploration in healthcare applications, aiming to enhance diagnostic accuracy and assist medical professionals in clinical decision-making. [ABSTRACT FROM AUTHOR]

Federated learning(FL) is a new kind of Artificial Intelligence(AI) aimed at data privacy preservation that builds on decentralizing the training data for the deep learning model. This new technique of data security and privacy sheds light on many critical domains with highly sensitive data, including medical image analysis. Developing a strong, scalable, and precise deep learning model has proven to count on a variety of high-quality data from different centers. However, data holders may not willing to share their data considering the restriction of privacy. In this paper, we approach this challenge with a federated learning paradigm. Specifically, we present a case study on the whole slide image classification problem. At each local client center, a multiple-instance learning classifier is developed to conduct whole slide image classification. We introduce a privacy-preserving federated learning framework based on hyper-network to update the global model. Hyper-network is deployed at the global center that produces the weights of the local network conditioned on its input. In this way, hyper-networks can simultaneously learn a family of the local client networks. Instead of communicating raw data with the local client, only model parameters injected with noise are transferred between the local client and the global model. By using a large scale of whole slide images with only slide-level labels, we mensurated our way on two different whole slide image classification problems. The results demonstrate that our proposed federated learning model based on hyper-network can effectively leverage multi-center data to develop a more accurate model which can be used to classify a whole slide image. Its improvements in terms of over the isolated local centers and the commonly used federated averaging baseline are significant. Code will be available. [ABSTRACT FROM AUTHOR]

Acute thoracic aortic dissection is a life-threatening disease, in which blood leaking from the damaged inner layer of the aorta causes dissection between the intimal and adventitial layers. The diagnosis of this disease is challenging. Chest x-rays are usually performed for initial screening or diagnosis, but the diagnostic accuracy of this method is not high. Recently, deep learning has been successfully applied in multiple medical image analysis tasks. In this paper, we attempt to increase the accuracy of diagnosis of acute thoracic aortic dissection based on chest x-rays by applying deep learning techniques. In aggregate, 3,331 images, comprising 716 positive images and 2615 negative images, were collected from 3,331 patients. Residual neural network 18 was used to detect acute thoracic aortic dissection. The diagnostic accuracy of the ResNet18 was observed to be 90.20% with a precision of 75.00%, recall of 94.44%, and F1-score of 83.61%. Further research is required to improve diagnostic accuracy based on aorta segmentation. [ABSTRACT FROM AUTHOR]

The detection of cancer stem-like cells (CSCs) is mainly based on molecular markers or functional tests giving a posteriori results. Therefore label-free and real-time detection of single CSCs remains a difficult challenge. The recent development of microfluidics has made it possible to perform high-throughput single cell imaging under controlled conditions and geometries. Such a throughput requires adapted image analysis pipelines while providing the necessary amount of data for the development of machine-learning algorithms. In this paper, we provide a data-driven study to assess the complexity of brightfield time-lapses to monitor the fate of isolated cancer stem-like cells in non-adherent conditions. We combined for the first time individual cell fate and cell state temporality analysis in a unique algorithm. We show that with our experimental system and on two different primary cell lines our optimized deep learning based algorithm outperforms classical computer vision and shallow learning-based algorithms in terms of accuracy while being faster than cutting-edge convolutional neural network (CNNs). With this study, we show that tailoring our deep learning-based algorithm to the image analysis problem yields better results than pre-trained models. As a result, such a rapid and accurate CNN is compatible with the rise of high-throughput data generation and opens the door to on-the-fly CSC fate analysis. [ABSTRACT FROM AUTHOR]

Large epidemiological studies such as the UK Biobank (UKBB) or German National Cohort (NAKO) provide unprecedented health-related data of the general population aiming to better understand determinants of health and disease. As part of these studies, Magnetic Resonance Imaging (MRI) is performed in a subset of participants allowing for phenotypical and functional characterization of different organ systems. Due to the large amount of imaging data, automated image analysis is required, which can be performed using deep learning methods, e. g. for automated organ segmentation. In this paper we describe a computational pipeline for automated segmentation of abdominal organs on MRI data from 20,000 participants of UKBB and NAKO and provide results of the quality control process. We found that approx. 90% of data sets showed no relevant segmentation errors while relevant errors occurred in a varying proportion of data sets depending on the organ of interest. Image-derived features based on automated organ segmentations showed relevant deviations of varying degree in the presence of segmentation errors. These results show that large-scale, deep learning-based abdominal organ segmentation on MRI data is feasible with overall high accuracy, but visual quality control remains an important step ensuring the validity of down-stream analyses in large epidemiological imaging studies. [ABSTRACT FROM AUTHOR]

For medical image analysis, there is always an immense need for rich details in an image. Typically, the diagnosis will be served best if the fine details in the image are retained and the image is available in high resolution. In medical imaging, acquiring high-resolution images is challenging and costly as it requires sophisticated and expensive instruments, trained human resources, and often causes operation delays. Deep learning based super resolution techniques can help us to extract rich details from a low-resolution image acquired using the existing devices. In this paper, we propose a new Generative Adversarial Network (GAN) based architecture for medical images, which maps low-resolution medical images to high-resolution images. The proposed architecture is divided into three steps. In the first step, we use a multi-path architecture to extract shallow features on multiple scales instead of single scale. In the second step, we use a ResNet34 architecture to extract deep features and upscale the features map by a factor of two. In the third step, we extract features of the upscaled version of the image using a residual connection-based mini-CNN and again upscale the feature map by a factor of two. The progressive upscaling overcomes the limitation for previous methods in generating true colors. Finally, we use a reconstruction convolutional layer to map back the upscaled features to a high-resolution image. Our addition of an extra loss term helps in overcoming large errors, thus, generating more realistic and smooth images. We evaluate the proposed architecture on four different medical image modalities: (1) the DRIVE and STARE datasets of retinal fundoscopy images, (2) the BraTS dataset of brain MRI, (3) the ISIC skin cancer dataset of dermoscopy images, and (4) the CAMUS dataset of cardiac ultrasound images. The proposed architecture achieves superior accuracy compared to other state-of-the-art super-resolution architectures. [ABSTRACT FROM AUTHOR]

Cell tracking is one of the most critical tools for time-lapse image analysis to observe cell behavior and cell lineages over a long period of time. However, the accompanying graphical user interfaces are often difficult to use and do not incorporate seamless manual correction, data analysis tools, or simple training set design tools if it is machine learning based. In this paper, we introduce our cell tracking software "LIM Tracker". This software has a conventional tracking function consisting of recognition processing and link processing, a sequential search-type tracking function based on pattern matching, and a manual tracking function. LIM Tracker enables the seamless use of these functions. In addition, the system incorporates a highly interactive and interlocking data visualization method, which displays analysis result in real time, making it possible to flexibly correct the data and reduce the burden of tracking work. Moreover, recognition functions with deep learning (DL) are also available, which can be used for a wide range of targets including stain-free images. LIM Tracker allows researchers to track living objects with good usability and high versatility for various targets. We present a tracking case study based on fluorescence microscopy images (NRK-52E/EKAREV-NLS cells or MCF-10A/H2B-iRFP-P2A-mScarlet-I-hGem-P2A-PIP-NLS-mNeonGreen cells) and phase contrast microscopy images (Glioblastoma-astrocytoma U373 cells). LIM Tracker is implemented as a plugin for ImageJ/Fiji. The software can be downloaded from https://github.com/LIMT34/LIM-Tracker. [ABSTRACT FROM AUTHOR]

The rapid adoption of artificial intelligence methods in healthcare is coupled with the critical need for techniques to rigorously introspect models and thereby ensure that they behave reliably. This has led to the design of explainable AI techniques that uncover the relationships between discernible data signatures and model predictions. In this context, counterfactual explanations that synthesize small, interpretable changes to a given query while producing desired changes in model predictions have become popular. This under-constrained, inverse problem is vulnerable to introducing irrelevant feature manipulations, particularly when the model's predictions are not well-calibrated. Hence, in this paper, we propose the TraCE (training calibration-based explainers) technique, which utilizes a novel uncertainty-based interval calibration strategy for reliably synthesizing counterfactuals. Given the wide-spread adoption of machine-learned solutions in radiology, our study focuses on deep models used for identifying anomalies in chest X-ray images. Using rigorous empirical studies, we demonstrate the superiority of TraCE explanations over several state-of-the-art baseline approaches, in terms of several widely adopted evaluation metrics. Our findings show that TraCE can be used to obtain a holistic understanding of deep models by enabling progressive exploration of decision boundaries, to detect shortcuts, and to infer relationships between patient attributes and disease severity. [ABSTRACT FROM AUTHOR]

Texture features are designed to quantitatively evaluate patterns of spatial distribution of image pixels for purposes of image analysis and interpretation. Unexplained variations in the texture patterns often lead to misinterpretation and undesirable consequences in medical image analysis. In this paper we explore the ability of machine learning (ML) methods to design a radiology test of Osteoarthritis (OA) at early stage when the number of patients' cases is small. In our experiments we use high-resolution X-ray images of knees in patients which were identified with Kellgren–Lawrence scores progressing from 1. The existing ML methods have provided a limited diagnostic accuracy, whilst the proposed Group Method of Data Handling strategy of Deep Learning has significantly extended the diagnostic test. The comparative experiments demonstrate that the proposed framework using the Zernike-based texture features has significantly improved the diagnostic accuracy on average by 11%. This allows us to conclude that the designed model for early diagnostic of OA will provide more accurate radiology tests, although new study is required when a large number of patients' cases will be available. [ABSTRACT FROM AUTHOR]

Comet assay is a widely used method, especially in the field of genotoxicity, to quantify and measure DNA damage visually at the level of individual cells with high sensitivity and efficiency. Generally, computer programs are used to analyze comet assay output images following two main steps. First, each comet region must be located and segmented, and next, it is scored using common metrics (e.g., tail length and tail moment). Currently, most studies on comet assay image analysis have adopted hand-crafted features rather than the recent and effective deep learning (DL) methods. In this paper, however, we propose a DL-based baseline method, called DeepComet, for comet segmentation. Furthermore, we created a trainable and testable comet assay image dataset that contains 1037 comet assay images with 8271 manually annotated comet objects. From the comet segmentation test results with the proposed dataset, the DeepComet achieves high average precision (AP), which is an essential metric in image segmentation and detection tasks. A comparative analysis was performed between the DeepComet and the state-of-the-arts automatic comet segmentation programs on the dataset. Besides, we found that the DeepComet records high correlations with a commercial comet analysis tool, which suggests that the DeepComet is suitable for practical application. [ABSTRACT FROM AUTHOR]