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Image processing is the main topic of discussion in the field of computer vision technology. With the increase in the number of images used over time, the types of images with different resolution qualities are becoming more diverse. Low image resolution leads to uncertainty in the task of image processing. Therefore, a method with high performance is needed for image processing. In image processing, there is a Convolutional Neural Networks (CNN) architecture for semantic segmentation of pixels called U-Net. U-Net is formed by an encoder network and decoder network that will later produce segmented images. In this paper, researchers applied the U-Net architecture to the lung CT image dataset, which has different resolutions in each image, to segment the image that produces a segmented lung image. In this study, we conducted experiments for many training and testing data ratios while also comparing the model performances between the single resolution dataset and the multiresolution dataset. The results showed that the segmentation accuracy using a single resolution dataset is as follows: 5 to 5 ratio is 66.00%, 8 to 2 ratio is 88.96%, and 9 to 1 ratio is 94.47%. For the multiresolution dataset, the application is: 5 to 5 ratio is 82.42%, 8 to 2 ratio is 90.12%, and 9 to 1 ratio is 93.66%. And for the result, the training time using single resolution dataset are: 5 to 5 ratio is 59.94 seconds, 8 to 2 ratio is 87.16 seconds, and 9 to 1 ratio is 195.34 seconds, as for multiresolution data application are: 5 to 5 ratio is 49.60 seconds, 8 to 2 ratio is 102.08 seconds, and 9 to 1 ratio is 199.79 seconds. Based on those results, we obtained the best accuracy for single resolution at a 9:1 ratio and the best training time for multiresolution at a 5:5 ratio. Doi: 10.28991/ESJ-2023-07-02-014 Full Text: PDF

[Abstract] One of the main challenges in times of sanitary emergency is to quickly develop computer aided diagnosis systems with a limited number of available samples due to the novelty, complexity of the case and the urgency of its implementation. This is the case during the current pandemic of COVID-19. This pathogen primarily infects the respiratory system of the afflicted, resulting in pneumonia and in a severe case of acute respiratory distress syndrome. This results in the formation of different pathological structures in the lungs that can be detected by the use of chest X-rays. Due to the overload of the health services, portable X-ray devices are recommended during the pandemic, preventing the spread of the disease. However, these devices entail different complications (such as capture quality) that, together with the subjectivity of the clinician, make the diagnostic process more difficult and suggest the necessity for computer-aided diagnosis methodologies despite the scarcity of samples available to do so. To solve this problem, we propose a methodology that allows to adapt the knowledge from a well-known domain with a high number of samples to a new domain with a significantly reduced number and greater complexity. We took advantage of a pre-trained segmentation model from brain magnetic resonance imaging of a unrelated pathology and performed two stages of knowledge transfer to obtain a robust system able to segment lung regions from portable X-ray devices despite the scarcity of samples and lesser quality. This way, our methodology obtained a satisfactory accuracy of 0.9761 ± 0.0100 for patients with COVID-19, 0.9801 ± 0.0104 for normal patients and 0.9769 ± 0.0111 for patients with pulmonary diseases with similar characteristics as COVID-19 (such as pneumonia) but not genuine COVID-19. ; Xunta de Galicia; ED431C 2020/24 ; Xunta de Galicia; IN845D 2020/38 ; Xunta de Galicia; ED431G 2019/01 ; This research was funded by Instituto de Salud Carlos III, Government of Spain, DTS18/00136 research project; Ministerio de Ciencia e Innovación y Universidades, Government of Spain, RTI2018-095894-B-I00 research project, Ayudas para la formación de profesorado universitario (FPU), grant Ref. FPU18/02271; Ministerio de Ciencia e Innovación, Government of Spain through the research project with reference PID2019-108435RB-I00; Consellería de Cultura, Educación e Universidade, Xunta de Galicia, Grupos de Referencia Competitiva, grant Ref. ED431C 2020/24; Axencia Galega de Innovación (GAIN), Xunta de Galicia, grant Ref. IN845D 2020/38; CITIC, as Research Center accredited by Galician University System, is funded by "Consellería de Cultura, Educación e Universidade from Xunta de Galicia", supported in an 80% through ERDF Funds, ERDF Operational Programme Galicia 2014-2020, and the remaining 20% by "Secretaría Xeral de Universidades" (Grant ED431G 2019/01).

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that produces pulmonary damage. Radiological imaging is the preferred technique for the assessment of TB longitudinal course. Computer-assisted identification of biomarkers eases the work of the radiologist by providing a quantitative assessment of disease. Lung segmentation is the step before biomarker extraction. In this study, we present an automatic procedure that enables robust segmentation of damaged lungs that have lesions attached to the parenchyma and are affected by respiratory movement artifacts in a Mycobacterium Tuberculosis infection model. Its main steps are the extraction of the healthy lung tissue and the airway tree followed by elimination of the fuzzy boundaries. Its performance was compared with respect to a segmentation obtained using: (1) a semi-automatic tool and (2) an approach based on fuzzy connectedness. A consensus segmentation resulting from the majority voting of three experts' annotations was considered our ground truth. The proposed approach improves the overlap indicators (Dice similarity coefficient, 94% ± 4%) and the surface similarity coefficients (Hausdorff distance, 8.64 mm ± 7.36 mm) in the majority of the most difficult-to-segment slices. Results indicate that the refined lung segmentations generated could facilitate the extraction of meaningful quantitative data on disease burden. ; The research leading to these results received funding from the Innovative Medicines Initiative (www.imi.europa.eu) Joint Undertaking under grant agreement no. 115337, whose resources comprise funding from the European Union's Seventh Framework Programme (FP7/2007–2013) and EFPIA companies' in kind contribution. This work was partially funded by projects TEC2013-48552-C2-1-R, RTC-2015-3772-1, TEC2015-73064-EXP and TEC2016-78052-R from the Spanish Ministerio de Economía, Industria y Competitividad, TOPUS S2013/MIT-3024 project from the regional government of Madrid and by the Department of Health, UK.

Presented at the 4th XoveTIC Conference, A Coruña, Spain, 7–8 October 2021. ; [Abstract] COVID-19 is characterized by its impact on the respiratory system and, during the global outbreak of 2020, specific protocols had to be designed to contain its spread within hospitals. This required the use of portable X-ray devices that allow for a greater flexibility in terms of their arrangement in rooms not specifically designed for such purpose. However, their poor image quality, together with the subjectivity of the expert, can hinder the diagnosis process. Therefore, the use of automatic methodologies is advised. Even so, their development is challenging due to the scarcity of available samples. For this reason, we present a COVID-19-specific methodology able to segment these portable chest radiographs with a reduced number of samples via multiple transfer learning phases. This allows us to extract knowledge from two related fields and obtain a robust methodology with limited data from the target domain. Our proposal aims to help both experts and other computer-aided diagnosis systems to focus their attention on the region of interest, ignoring unrelated information. ; Instituto de Salud Carlos III, Government of Spain, DTS18/00136 research project; Ministerio de Ciencia e Innovación y Universidades, Government of Spain, RTI2018-095894-B-I00 research project, Ayudas para la formación de profesorado universitario (FPU), grant ref. FPU18/02271; Ministerio de Ciencia e Innovación, Government of Spain through the research project with reference PID2019-108435RB-I00; Consellería de Cultura, Educación e Universidade, Xunta de Galicia, Grupos de Referencia Competitiva, grant ref. ED431C 2020/24 and through the postdoctoral grant contract ref. ED481B 2021/059; Axencia Galega de Innovación (GAIN), Xunta de Galicia, grant ref. IN845D 2020/38; CITIC, Centro de Investigación de Galicia ref. ED431G 2019/01, receives financial support from Consellería de Educación, Universidade e Formación Profesional, Xunta de Galicia, through the ERDF (80%) and Secretaría Xeral de Universidades (20%) ; Xunta de Galicia; ED431C 2020/24 ; Xunta de Galicia; ED481B 2021/059 ; Xunta de Galicia; IN845D 2020/38 ; Xunta de Galicia; ED431G 2019/01

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis that produces pulmonary damage. Radiological imaging is the preferred technique for the assessment of TB longitudinal course. Computer-assisted identification of biomarkers eases the work of the radiologist by providing a quantitative assessment of disease. Lung segmentation is the step before biomarker extraction. In this study, we present an automatic procedure that enables robust segmentation of damaged lungs that have lesions attached to the parenchyma and are affected by respiratory movement artifacts in a Mycobacterium Tuberculosis infection model. Its main steps are the extraction of the healthy lung tissue and the airway tree followed by elimination of the fuzzy boundaries. Its performance was compared with respect to a segmentation obtained using: (1) a semi-automatic tool and (2) an approach based on fuzzy connectedness. A consensus segmentation resulting from the majority voting of three experts' annotations was considered our ground truth. The proposed approach improves the overlap indicators (Dice similarity coefficient, 94\% +/- 4\%) and the surface similarity coefficients (Hausdorff distance, 8.64 mm +/- 7.36 mm) in the majority of the most difficult-to-segment slices. Results indicate that the refined lung segmentations generated could facilitate the extraction of meaningful quantitative data on disease burden. ; We thank Estibaliz Gomez de Mariscal, Paula Martin Gonzalez and Mario Gonzalez Arjona for helping with the manual lung annotation. The research leading to these results received funding from the Innovative Medicines Initiative (www.imi.europa.eu) Joint Undertaking under grant agreement no. 115337, whose resources comprise funding from the European Union's Seventh Framework Programme (FP7/2007-2013) and EFPIA companies' in kind contribution. This work was partially funded by projects TEC2013-48552-C2-1-R, RTC-2015-3772-1, TEC2015-73064-EXP and TEC2016-78052-R from the Spanish Ministerio de Economia, Industria y Competitividad, TOPUS S2013/MIT-3024 project from the regional government of Madrid and by the Department of Health, UK. ; Sí

Four-dimensional (4D) flow magnetic resonance imaging (4D Flow MRI) enables acquisition of time-resolved three-directional velocity data in the entire heart and all major thoracic vessels. The segmentation of these tissues is typically performed using semi-automatic methods. Some of which primarily rely on the velocity data and result in a segmentation of the vessels only during the systolic phases. Other methods, mostly applied on the heart, rely on separately acquired balanced Steady State Free Precession (b-SSFP) MR images, after which the segmentations are superimposed on the 4D Flow MRI. While b-SSFP images typically cover the whole cardiac cycle and have good contrast, they suffer from a number of problems, such as large slice thickness, limited coverage of the cardiac anatomy, and being prone to displacement errors caused by respiratory motion. To address these limitations we propose a multi-atlas segmentation method, which relies only on 4D Flow MRI data, to automatically generate four-dimensional segmentations that include the entire thoracic cardiovascular system present in these datasets. The approach was evaluated on 4D Flow MR datasets from a cohort of 27 healthy volunteers and 83 patients with mildly impaired systolic left-ventricular function. Comparison of manual and automatic segmentations of the cardiac chambers at end-systolic and end-diastolic timeframes showed agreements comparable to those previously reported for automatic segmentation methods of b-SSFP MR images. Furthermore, automatic segmentation of the entire thoracic cardiovascular system improves visualization of 4D Flow MRI and facilitates computation of hemodynamic parameters. ; Funding details: 310612; Funding details: FP7, Seventh Framework Programme; Funding details: 621-2014-6191, VR, Vetenskapsrådet; Funding details: 223615; Funding details: 20140398; Funding text: This work was partially funded by the FP7-funded project DOPPLER-CIP [grant number 223615]; the European Union's Seventh Framework Programme ( FP7/2007-2013 ) [grant number 310612 ]; the Swedish Research Council [grant number 621-2014-6191 ]; and the Swedish Heart and Lung Foundation [grant number 20140398 ].

Coronavirus sickness (COVID-19) recently adversely disrupted the medical care system and the entire economy. Doctors, researchers, and specialists are working on new-fangled methods to detect COVID-19 relatively efficiently, such as constructing computerized COVID-19 detection systems. Medical imaging, such as Computed Tomography (CT), has a lot of opportunity as a solution to RT-PCR approaches for quantitative assessment and disease monitoring. COVID-19 diagnosis based on CT images can provide speedy and accurate results. A quantitative criterion for diagnosis is provided by an automated segmentation method of infection areas in the lungs. As an outcome, automatic image segmentation is in high demand as a clinical decision aid tool. To detect COVID-19, Computed Tomography images might be employed instead of the time-consuming RT-PCR assay. In this research, a unique technique is provided for segmenting infection areas in the lungs using CT scan images from COVID-19 patients. "Ground Glass Opacity (GGO)" regions were detected using Novel Adaptive Histogram Binning Based Lesion Segmentation (NAHBLS) method. Many metrics were also employed to evaluate the proposed method, including "Sorensen–Dice similarity", "Sensitivity", "Specificity", "Precision", and "Accuracy" measures. Experiments have shown that the proposed method can effectively separate the lung infections with good accuracy. The results show that the proposed Novel Adaptive Histogram Binning Based Lesion Segmentation based on automatic approach is effective at segmenting the lesion region of the image and calculated the Infection Rate (IR) over the lung region in Computed Tomography scan.

We propose HookNet, a semantic segmentation model for histopathology whole-slide images, which combines context and details via multiple branches of encoder-decoder convolutional neural networks. Concentric patches at multiple resolutions with different fields of view, feed different branches of HookNet, and intermediate representations are combined via a hooking mechanism. We describe a framework to design and train HookNet for achieving high-resolution semantic segmentation and introduce constraints to guarantee pixel-wise alignment in feature maps during hooking. We show the advantages of using HookNet in two histopathology image segmentation tasks where tissue type prediction accuracy strongly depends on contextual information, namely (1) multi-class tissue segmentation in breast cancer and, (2) segmentation of tertiary lymphoid structures and germinal centers in lung cancer. We show the superiority of HookNet when compared with single-resolution U-Net models working at different resolutions as well as with a recently published multi-resolution model for histopathology image segmentation. We have made HookNet publicly available by releasing the source coder as well as in the form of web-based applications) :3 based on the grand-challenge.org platform. (C) 2020 The Authors. Published by Elsevier B.V. ; Funding Agencies|European UnionEuropean Commission [825292]; Radboud Institute of Health Sciences (RIHS), Nijmegen, The NetherlandsNetherlands Government; Alpe dHuZes/Dutch Cancer Society Fund [KUN 2014-7032]

Purpose: Computed tomography (CT) images enable capturing specific manifestations of tuberculosis (TB) that are undetectable using common diagnostic tests, which suffer from limited specificity. In this study, we aimed to automatically quantify the burden of Mycobacterium tuberculosis (Mtb) using biomarkers extracted from x-ray CT images. Procedures: Nine macaques were aerosol-infected with Mtb and treated with various antibiotic cocktails. Chest CT scans were acquired in all animals at specific times independently of disease progression. First, a fully automatic segmentation of the healthy lungs from the acquired chest CT volumes was performed and air-like structures were extracted. Next, unsegmented pulmonary regions corresponding to damaged parenchymal tissue and TB lesions were included. CT biomarkers were extracted by classification of the probability distribution of the intensity of the segmented images into three tissue types: (1) Healthy tissue, parenchyma free from infection; (2) soft diseased tissue, and (3) hard diseased tissue. The probability distribution of tissue intensities was assumed to follow a Gaussian mixture model. The thresholds identifying each region were automatically computed using an expectation-maximization algorithm. Results: The estimated longitudinal course of TB infection shows that subjects that have followed the same antibiotic treatment present a similar response (relative change in the diseased volume) with respect to baseline. More interestingly, the correlation between the diseased volume (soft tissue + hard tissue), which was manually delineated by an expert, and the automatically extracted volume with the proposed method was very strong (R2 ≈ 0.8). ; The research leading to these results received funding from the Innovative Medicines Initiative (www.imi.europa.eu) Joint Undertaking under grant agreement no. 115337, whose resources comprise funding from EU FP7/2007-2013 and EFPIA companies in-kind contribution. This study was partially funded by projects TEC2013-48552-C2-1-R, RTC-2015-3772-1, TEC2015-73064-EXP and TEC2016-78052-R from the Spanish Ministry of Economy, Industry and Competitiveness (MEIC), TOPUS S2013/MIT-3024 project from the regional government of Madrid and by the Department of Health, UK. LEV is funded by the Intramural Research Program of NIAID, NIH. The CNIC is supported by the MEIC and the Pro CNIC Foundation and is a Severo Ochoa Center of Excellence (SEV-2015-0505)

At the beginning of 2020, the world was shocked by the emergence of the COVID-19 virus. This virus has spread to all corners of the world, not only in Indonesia. Therefore, the government needs to make efforts to break the chain of transmission of this virus. One of these efforts is to detect COVID-19 as early as possible. Using CT images can be one of the early detection efforts of early-phase lung infections in COVID-19 patients. The stage in detecting COVID-19 is by segmenting the image. In this study, segmentation was carried out using the Otsu Thresholding method on 8 axial CT images of the lungs of COVID-19 patients, consisting of 4 images of male patients and 4 images of female patients. Then the image segmentation results of male and female patients were compared and evaluated using ROC measurements, Threshold (T) values and analyzed for GGO (grand-glass opacity). The result can be seen that judging from the value of the ROC measurement results, the measurement of image segmentation evaluation of male patients is more accurate than female patients. The number of false negatives for male patients and female patients is the same, while the number of false positives for male patients is less than female patients. Threshold value of the image segmentation results of male and female patients is the same so that the density of image segmentation is the same. GGO (grand-glass opacity) for male COVID-19 patients aged between 45-55 years is fuller than female COVID-19 patients aged 45-55 years. This shows that men are more at risk of dying from COVID-19 than female.©2020 JNSMR UIN Walisongo. All rights reserved.

Abstract
Pulmonary delivery is not only of increasing importance to exploit local therapy for lung diseases like COVID-19, but also plays an essential role in interpreting health impact of inhaled hazardous (nano-)materials. Deciphering of biodistribution, biokinetics, and cell-mediated immunity of pulmonary delivered nanoparticles (NPs) remains insufficient. We applied state-of-the-art multimodal imaging and deep learning pipelines to elucidate the intricate deposition profiles and the fate of biopersistent NPs in the lung within cellular resolution. Spatially resolved delivery characteristics like inter- and intra-acinar distribution pattern and regional NP dosage were revealed by tissue-clearing light-sheet fluorescence microscopy for six common routes of pulmonary delivery, i.e., intranasal & oropharyngeal aspiration, intubated instillation, microsprayer application, ventilator-assisted & nose-only aerosol inhalation. Artificial intelligence-driven entire airway 3D segmentation (convolutional neural network) enabled accurate dosimetry of bronchial versus acinar/alveolar NP dose (B/A: 0.04 to 0.18 depending on delivery route) rather than the conventionally simplified 2D central-to-peripheral ratio (C/P: 1.32 to 3.79). Moreover, longitudinal 3D imaging revealed similar intra-acinar NP kinetics independent of delivery route. Inhaled NP relocation from the alveolar-epithelium to interstitium was traditionally claimed as the consequence of passive diffusion/transportation of NPs. This study, however, revealed that acinar NP transport can be attributed to the phagocytosis and migration of tissue-resident macrophages (TRMs) as evidenced by complementary analytical approaches (intravital microscopy, ex vivo 4D live-tissue microscopy, in situ immunofluorescence, ex vivo NP-lung interaction model, flow cytometry). Overall, this study elucidates holistic NP-lung delivery and biokinetics features and TRM immunity on the fate of biopersistent NPs.