Crowdsourcing Airway Annotations in Chest Computed Tomography Images

Measuring airways in chest computed tomography (CT) scans is important for characterizing diseases such as cystic fibrosis, yet very time-consuming to perform manually. Machine learning algorithms offer an alternative, but need large sets of annotated scans for good performance. We investigate whether crowdsourcing can be used to gather airway annotations. We generate image slices at known locations of airways in 24 subjects and request the crowd workers to outline the airway lumen and airway wall. After combining multiple crowd workers, we compare the measurements to those made by the experts in the original scans. Similar to our preliminary study, a large portion of the annotations were excluded, possibly due to workers misunderstanding the instructions. After excluding such annotations, moderate to strong correlations with the expert can be observed, although these correlations are slightly lower than inter-expert correlations. Furthermore, the results across subjects in this study are quite variable. Although the crowd has potential in annotating airways, further development is needed for it to be robust enough for gathering annotations in practice. For reproducibility, data and code are available online: \url{http://github.com/adriapr/crowdairway.git}

The development of bronchiectasis on chest computed tomography in children with cystic fibrosis: can pre-stages be identified?

Objective: Bronchiectasis is an important component of cystic fibrosis (CF) lung disease but little is known about its development. We aimed to study the development of bronchiectasis and identify determinants for rapid progression of bronchiectasis on chest CT. Methods: Forty-three patients with CF with at least four consecutive biennial volumetric CTs were included. Areas with bronchiectasis on the most recent CT were marked as regions of interest (ROIs). These ROIs were generated on all preceding CTs using deformable image registration. Observers indicated whether: bronchiectasis, mucus plugging, airway wall thickening, atelectasis/consolidation or normal airways were present in the ROIs. Results: We identified 362 ROIs on the most recent CT. In 187 (51.7 %) ROIs bronchiectasis was present on all preceding CTs, while 175 ROIs showed development of bronchiectasis. In 139/175 (79.4 %) no pre-stages of bronchiectasis were identified. In 36/175 (20.6 %) bronchiectatic airways the following pre-stages were identified: mucus plugging (17.7 %), airway wall thickening (1.7 %) or atelectasis/consolidation (1.1 %). Pancreatic insufficiency was more prevalent in the rapid progressors compared to the slow progressors (p = 0.05). Conclusion: Most bronchiectatic airways developed within 2 years without visible pre-stages, underlining the treacherous nature of CF lung disease. Mucus plugging was the most frequent pre-stage. Key Points: • Development of bronchiectasis in cystic fibrosis lung disease on CT.• Most bronchiectatic airways developed within 2 years without pre-stages.• The most frequently identified pre-stage was mucus plugging.• This study underlines the treacherous nature of CF lung disease

Diet-Induced Swine Model with Obesity/Leptin Resistance for the Study of Metabolic Syndrome and Type 2 Diabetes

The objective of the present study was to determine the suitability of a swine breed with leptin resistance and predisposition to obesity (the Iberian pig) as model for studies on metabolic syndrome and type 2 diabetes. Thus, six Iberian sows had ad libitum access to food enriched with saturated fat (SFAD group; food consumption was estimated to be 4.5 kg/animal/day) whilst four females acted as controls and were fed with 2 kg/animal/day of a commercial maintenance diet. After three months of differential feeding, SFAD animals developed central obesity, dyslipidemia, insulin resistance and impaired glucose tolerance, and elevated blood pressure; the five parameters associated with the metabolic syndrome. Thus, the current study characterizes the Iberian pig as a robust, amenable, and reliable translational model for studies on nutrition-associated diseases

Diagnosis of bronchiectasis and airway wall thickening in children with cystic fibrosis: Objective airway-artery quantification

Objectives: To quantify airway and artery (AA)-dimensions in cystic fibrosis (CF) and control patients for objective CT diagnosis of bronchiectasis and airway wall thickness (AWT). Methods: Spirometer-guided inspiratory and expiratory CTs of 11 CF and 12 control patients were collected retrospectively. Airway pathways were annotated semi-automatically to reconstruct three-dimensional bronchial trees. All visible AA-pairs were measured perpendicular to the airway axis. Inner, outer and AWT (outer−inner) diameter were divided by the adjacent artery diameter to compute AinA-, AoutA- and AWTA-ratios. AA-ratios were predicted using mixed-effects models including disease status, lung volume, gender, height and age as covariates. Results: Demographics did not differ significantly between cohorts. Mean AA-pairs CF: 299 inspiratory; 82 expiratory. Controls: 131 inspiratory; 58 expiratory. All ratios were significantly larger in inspiratory compared to expiratory CTs for both groups (p<0.001). AoutA- and AWTA-ratios were larger in CF than in controls, independent of lung volume (p<0.01). Difference of AoutA- and AWTA-ratios between patients with CF and controls increased significantly for every following airway generation (p<0.001). Conclusion: Diagnosis of bronchiectasis is highly dependent on lung volume and more reliably diagnosed using outer airway diameter. Difference in bronchiectasis and AWT severity between the two cohorts increased with each airway generation. Key points: • More peripheral airways are visible in CF patients compared to controls.• Structural lung changes in CF patients are greater with each airway generation.• Number of airways visualized on CT could quantify CF lung disease.• For objective airway disease quantification on CT, lung volume standardization is required

Lung MRI and impairment of diaphragmatic function in Pompe disease

Background: Pompe disease is a progressive metabolic myopathy. Involvement of respiratory muscles leads to progressive pulmonary dysfunction, particularly in supine position. Diaphragmatic weakness is considered to be the most important component. Standard spirometry is to some extent indicative but provides too little insight into diaphragmatic dynamics. We used lung MRI to study diaphragmatic and chest-wall movements in Pompe disease. Methods: In ten adult Pompe patients and six volunteers, we acquired two static spirometer-controlled MRI scans during maximum inspiration and expiration. Images were manually segmented. After normalization for lung size, changes in lung dimensions between inspiration and expiration were used for analysis; normalization was based on the cranial-caudal length ratio (representing vertical diaphragmatic displacement), and the anterior-posterior and left-right length ratios (representing chest-wall movements due to thoracic muscles). Results: We observed striking dysfunction of the diaphragm in Pompe patients; in some patients the diaphragm did not show any displacement. Patients had smaller cranial-caudal length ratios than volunteers (p &lt; 0.001), indicating diaphragmatic weakness. This variable strongly correlated with forced vital capacity in supine position (r = 0.88) and postural drop (r = 0.89). While anterior-posterior length ratios also differed between patients and volunteers (p = 0.04), left-right length ratios did not (p = 0.1). Conclusions: MRI is an innovative tool to visualize diaphragmatic dynamics in Pompe patients and to study chest-walland diaphragmatic movements in more detail. Our data indicate that diaphragmatic displacement may be severely disturbed in patients with Pompe disease

Дискретно-континуальные системы: подходы, модели, программно-модельные комплексы

<div><p>Background</p><p>Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness.</p><p>Methods</p><p>The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle.</p><p>Results</p><p>Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls) of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls.</p><p>Conclusion</p><p>Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response.</p></div

Monte Carlo flattening filter design to high energy intraoperative electron beam homogenization

[EN] Intraoperative radiotherapy using mobile linear accelerators is used for a wide variety of malignancies. However, when large fields are used in combination with high energies, a deterioration of the flatness dose profile is measured with respect to smaller fields and lower energies. Indeed, for the LIAC HWL of Sordina, this deterioration is observed for the 12 MeV beam combined with 10 cm (or larger) diameter applicator. Aimed to solve this problem, a flattening filter has been designed and validated evaluating the feasibility of its usage at the upper part of the applicator. The design of the filter was based on Monte Carlo simulations because of its accuracy in modeling components of clinical devices, among other purposes. The LIAC 10 cm diameter applicator was modeled and simulated independently by two different research groups using two different MC codes, reproducing the heterogeneity of the 12 MeV energy beam. Then, an iterative process of filter design was carried out. Finally, the MC designed conical filter with the optimal size and height to obtain the desired flattened beam was built in-house using a 3D printer. During the experimental validation of the applicator-filter, percentage depth dose, beam profiles, absolute and peripheral dose measurements were performed to demonstrate the effectiveness of the filter addition in the applicator. These measurements conclude that the beam has been flattened, from 5.9% with the standard configuration to 1.6% for the configuration with the filter, without significant increase of the peripheral dose. Consequently, the new filter-applicator LIAC configuration can be used also in a conventional surgery room. A reduction of 16% of the output dose and a reduction of 1.1 mm in the D50 of the percentage depth dose was measured with respect to the original configuration. This work is a proof-of-concept that demonstrates that it is possible to add a filter able to flatten the beam delivered by the Sordina LIAC HWL. Future studies will focus on more refined technical solutions fully compatible with the integrity of the applicator, including its sterilization, to be safely introduced in the clinical practice.The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Giuseppe Felici reports a relationship with S.I.T. Sordina IORT Technologies S.p.A. that includes: employment. We thank the professionals and facilities at the 3D printing and metrology department in the Mechanics Unit at IFIC. JV thanks I. Diaz for measuring the PLA density. We thank S.I.T. SORDINA IORT Tech-nologies SpA for providing the applicator used for testing the filter during the measurements. JV, FB, and JP would like to acknowledge the Spanish "Ministerio de Ciencia e Innovacion" (MCIN) grant PID2021-125096NB-I00 funded by MCIN/AEI/10.13039 and the "Generalitat Valenciana" (GVA) grant PROMETEO/2021/064.Oliver-Gil, S.; Vijande, J.; Tejedor-Aguilar, N.; Miró Herrero, R.; Rovira-Escutia, JJ.; Ballester, F.; Juste-Vidal, B.... (2023). Monte Carlo flattening filter design to high energy intraoperative electron beam homogenization. Radiation Physics and Chemistry. 212. https://doi.org/10.1016/j.radphyschem.2023.11110221

Automatic detection of crop rows in maize fields with high weeds pressure

This paper proposes a new method, oriented to crop row detection in images from maize fields with high weed pressure. The vision system is designed to be installed onboard a mobile agricultural vehicle, i.e. submitted to gyros, vibrations and undesired movements. The images are captured under image perspective, being affected by the above undesired effects. The image processing consists of three main processes: image segmentation, double thresholding, based on the Otsu’s method, and crop row detection. Image segmentation is based on the application of a vegetation index, the double thresholding achieves the separation between weeds and crops and the crop row detection applies least squares linear regression for line adjustment. Crop and weed separation becomes effective and the crop row detection can be favorably compared against the classical approach based on the Hough transform. Both gain effectiveness and accuracy thanks to the double thresholding that makes the main finding of the paper