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2020 Other Open Access

Analisi di immagini tomografiche ad alta risoluzione attraverso reti neurali convoluzionali per lo studio delle interstiziopatie polmonari
Buongiorno R
The term Interstitial Lung Disease (ILD) refers to a large group of lung disorders, most of which cause scars of the interstitium, usually referred to as pulmonary fibrosis. Fibrosis reduces the ability of the air sacs to capture and carry oxygen into the bloodstream, leading to a progressive loss of the ability to breathe. Although ILDs are rare if taken individually, together they represent the most frequent cause of non-obstructive chronic lung disease. Nowadays, there are more than 200 different types of ILDs with varying causes, prognosis and therapies. Thus, identifying the correct type of ILD is necessary to make an accurate diagnosis. The Idiopathic Pulmonary Fibrosis (IPF) is a chronic, progressive fibrosing interstitial pneumonia, which is classified among the ILDs with the poorest prognosis. The high variability and unpredictability of IPF course have traditionally made its clinical management hard. The recent introduction of antifibrotic drugs has opened novel therapeutic options for mild to moderate IPF. In this respect, treatment decisions highly rely on the assessment and quantification of IPF impact on the interstitium and its progression over time. High-Resolution Computed Tomography (HRCT) has demonstrated to have a key role in this frame, as it represents a non-invasive diagnostic modality to evaluate and quantify the extent of lung interstitium affected by IPF. In fact, IPF shows a typical radiological pattern, called Usual Interstitial Pneumonia (UIP) pattern, whose presence is usually assessed by radiologists to diagnose IPF. The HRCT features that characterize the UIP pattern are the presence and positioning of specific lung parenchymal anomalies, known as honeycombing , ground-glass opacification and fine reticulation. These anomalies appear in the HRCT scans with specific textural characteristics that are detected via a visual inspection of the imaging data. Assessing the diffusion of these anomalies is instrumental to understand the impact of IPF and to monitor its evolution over time. Quantitative and reliable approaches are in high demand in this respect, as the visual examination by radiologists suffers, by its nature, of poor reproducibility. To overcome this issue, much research is being conducted to develop new techniques for automatic detection of lung diseases that may support radiologists during the diagnostic pathway, particularly in HRCT image analysis. Indeed, HRCT images evaluation by a Machine Learning (ML)- based algorithm might provide low-cost, reliable, real time automatic identification of UIP pattern with human-level accuracy in order to objectively quantify the percentage of lung volume affected by the disease in a reproducible way. The purpose of this study was to develop a tool for UIP pattern recognition in HRCT images of patients with IPF using a deep-learning method based on a Convolutional Neural Network (CNN), called UIP-net. UIP-net takes as input a lung HRCT image with 492x492 pixels and outputs the corresponding binary map for the discrimination of disease and normal tissue. To train and evaluate the CNN, a dataset of 5000 images, derived by 20 CT scans from the same scanner, was used. The network performance yielded 83.7% BF-score and 84.6% sensitivity but in order to refine the binary masks produced by UIP-net, a post-processing operation was carried out. With post-processing, vessels, air-ways and tissue wrongly classified as belonging to the lungs were removed from the outputted masks. After post-processing, the results increased to 96.7% BF-score and 85.9% sensitivity. Thus, the network performance, in terms of BF-score and sensitivity, demonstrated that CNNs have the potential to reliably detect disease in order to evaluate its progression and become a supportive tool for radiologists. Future works include adding more data to the training set in order to add multiple layers to the network to distinguish and quantify the different HRCT features of UIP pattern, improving the reproducibility and reliability of the CNN and using it for the detection of HRCT manifestations of Covid-19.

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2020 Other Open Access

Analisi di immagini tomografiche ad alta risoluzione attraverso reti neurali convoluzionali per lo studio delle interstiziopatie polmonari
Buongiorno R, Colantonio S, Germanese D
Le interstiziopatie polmonari (Interstitial Lung Disease, ILD) sono patologie croniche che causano la cicatrizzazione del parenchima polmonare e dell'interstizio alveolare e la compromissione della funzionalità respiratoria. Dal momento che sono più di 200 le patologie raggruppate nella categoria delle ILD, una precisa identificazione è fondamentale per individuare la terapia migliore e formulare una prognosi. L'esame radiologico di riferimento è la tomografia computerizzata del torace ad alta risoluzione (High Resolution Computed Tomography, HRCT) e rappresenta un passaggio cruciale nel processo di diagnosi; nell'analizzare le immagini, infatti, il radiologo deve stabilire se vi è Usual Interstitial Pneumoniae (UIP), ovvero presenza di pattern istopatologici tipici della malattia, e valutarne l'estensione, correlata con la gravità delle alterazioni fisiologiche. Tuttavia, l'incidenza rara delle interstiziopatie fa sì che non tutti i radiologi abbiano un grado di esperienza adatto a individuare visivamente l'anomalia. Inoltre, la malattia si diffonde lungo tutti i polmoni e la segmentazione manuale risulta faticosa. Nel tentativo di rimediare alla variabilità intra- ed inter-osservatore, sono state sviluppate tecniche per il riconoscimento automatico dei pattern UIP; vi sono approcci basati sull'analisi dell'istogramma e della texture dell'immagine ma, dal momento che i classificatori sono stati addestrati su label definite da operatori clinici diversi, presentano comunque un bias che è causa di identificazioni errate, o mancate, dei pattern. Il deep learning, invece, si distingue dalle tecniche tradizionali perché fornisce strumenti che imparano autonomamente a classificare i dati. L'obiettivo del lavoro è stato, quindi, progettare e sviluppare la UIP-net, una rete neurale convoluzionale ad-hoc per la segmentazione automatica dei pattern UIP in immagini HRCT di pazienti con Fibrosi Idiopatica Polmonare (IPF), che è una sotto-categoria delle ILD.DOI: 10.32079/isti-tr-2020/007
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2021 Conference article Open Access

UIP-net: a decoder-encoder CNN for the detection and quantification of usual interstitial pneumoniae pattern in lung CT scan images
Buongiorno R, Germanese D, Romei C, Tavanti L, De Liperi A, Colantonio S
A key step of the diagnosis of Idiopathic Pulmonary Fibrosis (IPF) is the examination of high-resolution computed tomography images (HRCT). IPF exhibits a typical radiological pattern, named Usual Interstitial Pneumoniae (UIP) pattern, which can be detected in non-invasive HRCT investigations, thus avoiding surgical lung biopsy. Unfortunately, the visual recognition and quantification of UIP pattern can be challenging even for experienced radiologists due to the poor inter and intra-reader agreement. This study aimed to develop a tool for the semantic segmentation and the quantification of UIP pattern in patients with IPF using a deep-learning method based on a Convolutional Neural Network (CNN), called UIP-net. The proposed CNN, based on an encoder-decoder architecture, takes as input a thoracic HRCT image and outputs a binary mask for the automatic discrimination between UIP pattern and healthy lung parenchyma. To train and evaluate the CNN, a dataset of 5000 images, derived by 20 CT scans of different patients, was used. The network performance yielded 96.7% BF-score and 85.9% sensitivity. Once trained and tested, the UIP-net was used to obtain the segmentations of other 60 CT scans of different patients to estimate the volume of lungs affected by the UIP pattern. The measurements were compared with those obtained using the reference software for the automatic detection of UIP pattern, named Computer Aided Lungs Informatics for Pathology Evaluation and Rating (CALIPER), through the Bland-Altman plot. The network performance assessed in terms of both BF-score and sensitivity on the test-set and resulting from the comparison with CALIPER demonstrated that CNNs have the potential to reliably detect and quantify pulmonary disease in order to evaluate its progression and become a supportive tool for radiologists.DOI: 10.1007/978-3-030-68763-2_30
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2022 Contribution to book Open Access

Artificial Intelligence for chest imaging against COVID-19: an insight into image segmentation methods
Buongiorno R, Germanese D, Colligiani L, Fanni Sc, Romei C, Colantonio S
The coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus 2, emerged in late 2019 and soon developed as a pandemic leading to a world health crisis.Chest imaging examination plays a vital role in the clinical management and prognostic evaluation of COVID-19 since the imaging pathological findings reflect the inflammatory process of the lungs.Particularly, thanks to its highest sensitivity and resolution, Computer Tomography chest imaging serves well in the distinction of the different parenchymal patterns and manifestations of COVID-19. It is worth noting that detecting and quantifying such manifestations is a key step in evaluating disease impact and tracking its progression or regression over time. Nevertheless, the visual inspection or, even worse, the manual delimitation of such manifestations may be greatly time-consuming and overwhelming for radiologists, especially when pressed by the urgent needs of patient care.Image segmentation tools, powered by Artificial Intelligence, may sensibly reduce radiologists' workload as they may automate or, at least, facilitate the delineation of the pathological lesions and the other regions of interest for disease assessment. This delineation lays the basis for further diagnostic and prognostic analyses based on quantitative information extracted from the segmented lesions.This chapter overviews the Artificial Intelligence methods for the segmentation of chest Computed Tomography images. The focus is in particular on Deep Learning approaches, as these have lately become the mainstream approach to image segmentation. A novel method, leveraging attention-based learning, is presented and evaluated. Finally, a discussion of the potential, limitations, and still open challenges of the field concludes the chapter.DOI: 10.1016/b978-0-323-90531-2.00008-4
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2023 Contribution to book Open Access

Introduction to machine learning in medicine
Buongiorno R, Caudai C, Colantonio S, Germanese D
This chapter aimed to describe, as simply as possible, what Machine Learning is and how it can be used fruitfully in the medical field.DOI: 10.1007/978-3-031-25928-9_3
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2023 Journal article Open Access

Enhancing COVID-19 CT image segmentation: a comparative study of attention and recurrence in UNet models
Buongiorno R, Del Corso G, Germanese D, Colligiani L, Python L, Romei C, Colantonio S
Imaging plays a key role in the clinical management of Coronavirus disease 2019 (COVID-19) as the imaging findings reflect the pathological process in the lungs. The visual analysis of High-Resolution Computed Tomography of the chest allows for the differentiation of parenchymal abnormalities of COVID-19, which are crucial to be detected and quantified in order to obtain an accurate disease stratification and prognosis. However, visual assessment and quantification represent a time-consuming task for radiologists. In this regard, tools for semi-automatic segmentation, such as those based on Convolutional Neural Networks, can facilitate the detection of pathological lesions by delineating their contour. In this work, we compared four state-of-the-art Convolutional Neural Networks based on the encoder-decoder paradigm for the binary segmentation of COVID-19 infections after training and testing them on 90 HRCT volumetric scans of patients diagnosed with COVID-19 collected from the database of the Pisa University Hospital. More precisely, we started from a basic model, the well-known UNet, then we added an attention mechanism to obtain an Attention-UNet, and finally we employed a recurrence paradigm to create a Recurrent-Residual UNet (R2-UNet). In the latter case, we also added attention gates to the decoding path of an R2-UNet, thus designing an R2-Attention UNet so as to make the feature representation and accumulation more effective. We compared them to gain understanding of both the cognitive mechanism that can lead a neural model to the best performance for this task and the good compromise between the amount of data, time, and computational resources required. We set up a five-fold cross-validation and assessed the strengths and limitations of these models by evaluating the performances in terms of Dice score, Precision, and Recall defined both on 2D images and on the entire 3D volume.From the results of the analysis, it can be concluded that Attention-UNet outperforms the other models by achieving the best performance of 81,93%, in terms of 2D Dice score, on the test set. Additionally, we conducted statistical analysis to assess the performance differences among the models. Our findings suggest that integrating the recurrence mechanism within the UNet architecture leads to a decline in the model's effectiveness for our particular application.Source: JOURNAL OF IMAGING, vol. 9 (issue 12)
DOI: 10.3390/jimaging9120283
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2024 Other Embargo

Optimizing medical image segmentation using a priori knowledge in attention mechanism-enriched convolutional neural networks
Buongiorno Rossana, Colantonio Sara, Germanese Danila, Ducange Pietro
In recent years, there has been a remarkable shift in medical image segmentation, driven by the intersection of Deep Learning (DL) and medical imaging technologies. This convergence has led to significant progress, fundamentally altering how medical image analysis is approached. DL methods, notably Convolutional Neural Networks (CNNs), have played a pivotal role in this transformation by revolutionizing the field of medical image segmentation. They facilitate the automatic extraction of features from raw image data, achieving unparalleled levels of accuracy and sensitivity. However, despite these advances, persistent challenges such as computational demands, data quality and availability, interpretability, and model generalization hinder the broad adoption of DL models in clinical environments. Moreover, while CNNs manage to autonomously extract and analyze image features with a good level of detail, they often struggle to identify regions in images that exhibit complexities that are challenging even to the human eye. To address these issues, attention and recurrence mechanisms have been introduced. The former enhances the network's ability to focus on relevant regions in the image while ignoring irrelevant background, whereas the latter studies long-range dependencies between different areas of the image to obtain broader contextual information. The first part of this doctoral thesis thoroughly examines and analyzes attention and recurrence mechanisms to determine their efficacy in binary medical image segmentation. Specifically, the objective was to identify the mechanism that strikes the optimal balance between resource utilization, data availability, and accurate segmentation outcomes for the given problem statement. The results of this analysis have shown that attention mechanisms improve segmentation accuracy by dynamically adjusting weights assigned to different image regions, and optimizing data requirements. However, effectively directing CNN's attention remained challenging in scenarios requiring a clear and precise differentiation between subtle variations crucial for accurate diagnoses. These challenges formed the basis for the second part of the thesis, which explores the integration of spatial priors into CNN architectures, specifically within a UNet-based framework enriched with the attention mechanism, namely the Attention UNet. More precisely, by incorporating prior knowledge about the spatial location of objects to be segmented, the proposed approach aims to enhance CNN effectiveness in the segmentation task. A new framework, called SPI-net, was designed for this purpose. SPI-net features an Attention-UNet as a backbone, an upstream block aimed at obtaining spatial prior, and an additional novel branch featuring long skip connections to inject nuanced context-aware information into the decoding pathway of the network. This improves its understanding of underlying structures and enhances segmentation accuracy. The experimental application and evaluation of SPI-net focused on the segmentation of COVID-19 infections, leveraging prior knowledge of disease spatial location to guide CNN attention. The results demonstrate the efficacy of SPI-net in accurately delineating disease patterns, outperforming traditional segmentation approaches. The comparative analysis highlights the limitations of conventional pre-processing operations, emphasizing the importance of integrating spatial priors into CNN architectures. Overall, this research contributes to the advancement of medical image segmentation by implicitly incorporating prior knowledge into CNNs, offering insights and empirical evidence to enhance segmentation accuracy and interpretability. The findings extend beyond COVID-19 segmentation, offering a promising framework for various medical imaging applications and contributing to the evolution of CNNs as reliable tools in healthcare diagnostics.

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2023 Conference article Open Access

AI trustworthiness in prostate cancer imaging: a look at algorithmic and system transparency
Colantonio S, Berti A, Buongiorno R, Del Corso G, Pachetti E, Pascali Ma, Kalantzopoulos C, Kalokyri V, Kondylakis H, Tachos N, Fotiadis D, Giannini V, Mazzetti S, Regge D, Papanikolaou N, Marias K, Tsiknakis M
A responsible approach to artificial intelligence and machine learning technologies, grounded in sound scientific foundations, technical robustness, rigorous testing and validation, risk-based continuous monitoring and alignment with human values is imperative to guarantee their favourable impact and prevent any adverse effects they may have on individuals and communities. An essential aspect of responsible development is transparency, which constitutes a fundamental principle of the European approach towards artificial intelligence. Transparency can be achieved at different levels, such as data origin and use, system development, operation and usage. In this paper, we present the techniques implemented and delivered in the EU H2020 ProCAncer-I project to meet the transparency requirements at the different levels required.DOI: 10.1109/ieeeconf58974.2023.10404432
Project(s): ProCAncer-I via OpenAIRE

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2024 Conference article Restricted

Radiomics-based reliable predictions of side effects after radiotherapy for prostate cancer
Del Corso G., Pachetti E., Buongiorno R., Rodrigues A. C., Germanese D., Pascali M. A., Almeida J., Rodrigues N., Tsiknakis M., Papanikolaou N., Regge D., Marias K., Consortium Procancer-I, Colantonio S.
This work offers insight into the effectiveness of probabilistic models, specifically those based on ensemble approximations, in predicting adverse side effects following radiotherapy for prostate cancer. We trained a random forest model on radiomic features from 134 T2-weighted Magnetic Resonance (MRI) images of the prostate gland to identify patients experiencing acute or chronic rectal and urinary toxicity (AU-ROC ranging from 61.4% for endorectal coil acquisitions to 70.8% for the full dataset). We evaluated the reliability of the predictions using an ensemble approximation of simplified random forests obtained by an adaptive procedure of random subsampling of the training data. We used this reliability score to define a not-confident class and then recompute performance metrics more in accordance with a probabilistic approach. The outcomes we obtained (up to 7.9% increase in accuracy) indicate the approximated probabilistic models pledge more reliable predictions, thus being suitable for further investigation.DOI: 10.1109/isbi56570.2024.10635233
Project(s): ProCAncer-I via OpenAIRE

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2022 Conference article Open Access

Data models for an imaging bio-bank for colorectal, prostate and gastric cancer: the NAVIGATOR project
Berti A, Carloni G, Colantonio S, Pascali Ma, Manghi P, Pagano P, Buongiorno R, Pachetti E, Caudai C, Di Gangi D, Carlini E, Falaschi Z, Ciarrocchi E, Neri E, Bertelli E, Miele V, Carpi R, Bagnacci G, Di Meglio N, Mazzei Ma, Barucci A
Researchers nowadays may take advantage of broad collections of medical data to develop personalized medicine solutions. Imaging bio-banks play a fundamental role, in this regard, by serving as organized repositories of medical images associated with imaging biomarkers. In this context, the NAVIGATOR Project aims to advance colorectal, prostate, and gastric oncology translational research by leveraging quantitative imaging and multi-omics analyses. As Project's core, an imaging bio-bank is being designed and implemented in a web-accessible Virtual Research Environment (VRE). The VRE serves to extract the imaging biomarkers and further process them within prediction algorithms. In our work, we present the realization of the data models for the three cancer use-cases of the Project. First, we carried out an extensive requirements analysis to fulfill the necessities of the clinical partners involved in the Project. Then, we designed three separate data models utilizing entity-relationship diagrams. We found diagrams' modeling for colorectal and prostate cancers to be more straightforward, while gastric cancer required a higher level of complexity. Future developments of this work would include designing a common data model following the Observational Medical Outcomes Partnership Standards. Indeed, a common data model would standardize the logical infrastructure of data models and make the bio-bank easily interoperable with other bio-banks.DOI: 10.1109/bhi56158.2022.9926910
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2023 Conference article Open Access

Exploring the potentials and challenges of AI in supporting clinical diagnostics and remote assistance for the health and well-being of individuals
Berti A, Buongiorno R, Carloni G, Caudai C, Del Corso G, Germanese D, Pachetti E, Pascali Ma, Colantonio S
Innovative technologies powered by Artificial Intelligence have the big potential to support new models of care delivery, disease prevention and quality of life promotion. The ultimate goal is a paradigm shift towards more personalized, accessible, effective, and sustainable care and health systems. Nevertheless, despite the advances in the field over the last years, the adoption and deployment of AI technologies remains limited in clinical practice and real-world settings. This paper summarizes the activities that a multidisciplinary research group within the Signals and Images Lab of the Institute of Information Science and Technologies of the National Research Council of Italy is carrying out for exploring both the potential of AI in health and well-being as well as the challenges to their uptake in real-world settingsSource: CEUR WORKSHOP PROCEEDINGS. Pisa, Italy, 29-30/05/2023
Project(s): ProCAncer-I via OpenAIRE

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2023 Conference article Open Access

Exploring the potentials and challenges of Artificial Intelligence in supporting clinical diagnostics and remote assistance for the health and well-being of individuals
Berti A., Buongiorno R., Carloni G., Caudai C., Del Corso G., Germanese D., Pachetti E., Pascali M. A., Colantonio S.
Innovative technologies powered by Artificial Intelligence have the big potential to support new models of care delivery, disease prevention and quality of life promotion. The ultimate goal is a paradigm shift towards more personalized, accessible, effective, and sustainable care and health systems. Nevertheless, despite the advances in the field over the last years, the adoption and deployment of AI technologies remains limited in clinical practice and real-world settings. This paper summarizes the activities that a multidisciplinary research group within the Signals and Images Lab of the Institute of Information Science and Technologies of the National Research Council of Italy is carrying out for exploring both the potential of AI in health and well-being as well as the challenges to their uptake in real-world settings.Source: CEUR WORKSHOP PROCEEDINGS, vol. 3486. Pisa, Italy, 29-30/05/2023

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2024 Conference article Open Access

From Covid-19 detection to cancer grading: how medical-AI is boosting clinical diagnostics and may improve treatment
Berti A., Buongiorno R., Carloni G., Caudai C., Conti F., Del Corso G., Germanese D., Moroni D., Pachetti E., Pascali M. A., Colantonio S.
The integration of artificial intelligence (AI) into medical imaging has guided an era of transformation in healthcare. This paper presents the research activities that a multidisciplinary research group within the Signals and Images Lab of the Institute of Information Science and Technologies of the National Research Council of Italy is carrying out to explore the great potential of AI in medical imaging. From the convolutional neural network-based segmentation of Covid-19 lung patterns to the radiomic signature for benign/malignant breast nodule discrimination, to the automatic grading of prostate cancer, this work highlights the paradigm shift that AI has brought to medical imaging, revolutionizing diagnosis and patient care.Source: CEUR WORKSHOP PROCEEDINGS, vol. 3762, pp. 336-341. Naples, Italy, 29-30/05/2024

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2021 Other Open Access

SI-Lab Annual Research Report 2020
Leone Gr, Righi M, Carboni A, Caudai C, Colantonio S, Kuruoglu Ee, Leporini B, Magrini M, Paradisi P, Pascali Ma, Pieri G, Reggiannini M, Salerno E, Scozzari A, Tonazzini A, Fusco G, Galesi G, Martinelli M, Pardini F, Tampucci M, Buongiorno R, Bruno A, Germanese D, Matarese F, Coscetti S, Coltelli P, Jalil B, Benassi A, Bertini G, Salvetti O, Moroni D
The Signal & Images Laboratory (http://si.isti.cnr.it/) is an interdisciplinary research group in computer vision, signal analysis, smart vision systems and multimedia data understanding. It is part of the Institute for Information Science and Technologies of the National Research Council of Italy. This report accounts for the research activities of the Signal and Images Laboratory of the Institute of Information Science and Technologies during the year 2020.DOI: 10.32079/isti-ar-2021/001
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2022 Other Open Access

SI-Lab annual research report 2021
Righi M, Leone G R, Carboni A, Caudai C, Colantonio S, Kuruoglu E E, Leporini B, Magrini M, Paradisi P, Pascali M A, Pieri G, Reggiannini M, Salerno E, Scozzari A, Tonazzini A, Fusco G, Galesi G, Martinelli M, Pardini F, Tampucci M, Berti A, Bruno A, Buongiorno R, Carloni G, Conti F, Germanese D, Ignesti G, Matarese F, Omrani A, Pachetti E, Papini O, Benassi A, Bertini G, Coltelli P, Tarabella L, Straface S, Salvetti O, Moroni D
The Signal & Images Laboratory is an interdisciplinary research group in computer vision, signal analysis, intelligent vision systems and multimedia data understanding. It is part of the Institute of Information Science and Technologies (ISTI) of the National Research Council of Italy (CNR). This report accounts for the research activities of the Signal and Images Laboratory of the Institute of Information Science and Technologies during the year 2021.DOI: 10.32079/isti-ar-2022/003
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