Classification of chronic venous disorders using an ensemble optimization of convolutional neural networks

Chronic Venous Disorders (CVD) of lower limbs are one of the most prevalent medical conditions, affecting 35% of adults in Europe and North America. The early diagnosis of CVD is critical, however, the diagnosis relies on a visual recognition of the various venous disorders which is time- consuming and dependent on the physician's expertise. Thus, automatic strategies for the classification of the CVD severity are claimed. This paper proposed an automatic ensemble-based strategy of Deep Convolutional Neural Networks (DCNN) for the classification of CVDs severity from medical images. First, a clinical dataset containing 1376 images of patients' legs with CVD of 5 different levels of severity was constructed. Then, the constructed dataset was randomly split into training, testing, and validation datasets. Subsequently, a set of DCNN were individually applied to the images for classification. Finally, instead of a traditional voting ensemble strategy, extracted feature vectors from each DCNN were concatenated and fed into a new ensemble optimization network. Experiments showed that the proposed strategy achieved a classification with 93.8%, 93.4%, 92.4% of accuracy, precision, and recall, respectively. Moreover, compared to the traditional ensemble strategy, improvement in the accuracy of ~2% was registered. The proposed strategy showed to be accurate and robust for the diagnosis of CVD severity from medical images. Nevertheless, further research using an extensive clinical database is required to validate the potential of this strategy.The authors acknowledge Fundação para a Ciência e a Tecnologia (FCT), Portugal and the European Social Found, European Union, for funding support through the “Programa Operacional Capital Humano” (POCH) in the scope of the PhD grants SFRH/BD/136721/2018 (B. Oliveira) and SFRH/BD/136670/2018 (H. Torres). Moreover, authors gratefully acknowledge the funding of the projects "NORTE-01-0145-FEDER000045” and "NORTE-01-0145-FEDER-000059", supported by Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). It was also funded by national funds, through the FCT and FCT/MCTES in the scope of the project LASI-LA/P/0104/2020, UIDB/00319/2020, UIDB/05549/2020 and UIDP/05549/2020

Characterization of the workspace and limits of operation of laser treatments for vascular lesions of the lower limbs

The increase of the aging population brings numerous challenges to health and aesthetic segments. Here, the use of laser therapy for dermatology is expected to increase since it allows for non-invasive and infection-free treatments. However, existing laser devices require doctors’ manually handling and visually inspecting the skin. As such, the treatment outcome is dependent on the user’s expertise, which frequently results in ineffective treatments and side effects. This study aims to determine the workspace and limits of operation of laser treatments for vascular lesions of the lower limbs. The results of this study can be used to develop a robotic-guided technology to help address the aforementioned problems. Specifically, workspace and limits of operation were studied in eight vascular laser treatments. For it, an electromagnetic tracking system was used to collect the real-time positioning of the laser during the treatments. The computed average workspace length, height, and width were 0.84 ± 0.15, 0.41 ± 0.06, and 0.78 ± 0.16 m, respectively. This corresponds to an average volume of treatment of 0.277 ± 0.093 m3. The average treatment time was 23.2 ± 10.2 min, with an average laser orientation of 40.6 ± 5.6 degrees. Additionally, the average velocities of 0.124 ± 0.103 m/s and 31.5 + 25.4 deg/s were measured. This knowledge characterizes the vascular laser treatment workspace and limits of operation, which may ease the understanding for future robotic system development.The authors acknowledge Fundação para a Ciência e a Tecnologia (FCT), Portugal and the European Social Fund, European Union, for funding support through [the “Programa Operacional Capital Humano” (POCH) in the scope of the PhD], grants number [SFRH/BD/136721/2018 (B. Oliveira) and SFRH/BD/136670/2018 (H. Torres)]. Moreover, authors gratefully acknowledge the funding of the projects “NORTE-01-0145-FEDER-000045” and “NORTE-01-0145-FEDER-000059”, supported by [Northern Portugal Regional Operational Programme (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER)]. It was also funded by [national funds, through the FCT and FCT/MCTES in the scope of the projects UIDB/05549/2020, UIDP/05549/2020, and LASI-LA/P/0104/2020]

The Psychedelic State Induced by Ayahuasca Modulates the Activity and Connectivity of the Default Mode Network

The experiences induced by psychedelics share a wide variety of subjective features, related to the complex changes in perception and cognition induced by this class of drugs. A remarkable increase in introspection is at the core of these altered states of consciousness. Self-oriented mental activity has been consistently linked to the Default Mode Network (DMN), a set of brain regions more active during rest than during the execution of a goal-directed task. Here we used fMRI technique to inspect the DMN during the psychedelic state induced by Ayahuasca in ten experienced subjects. Ayahuasca is a potion traditionally used by Amazonian Amerindians composed by a mixture of compounds that increase monoaminergic transmission. In particular, we examined whether Ayahuasca changes the activity and connectivity of the DMN and the connection between the DMN and the task-positive network (TPN). Ayahuasca caused a significant decrease in activity through most parts of the DMN, including its most consistent hubs: the Posterior Cingulate Cortex (PCC)/Precuneus and the medial Prefrontal Cortex (mPFC). Functional connectivity within the PCC/Precuneus decreased after Ayahuasca intake. No significant change was observed in the DMN-TPN orthogonality. Altogether, our results support the notion that the altered state of consciousness induced by Ayahuasca, like those induced by psilocybin (another serotonergic psychedelic), meditation and sleep, is linked to the modulation of the activity and the connectivity of the DMN.The Brazilian Federal Agencies: CNPq, CAPES; FINEP; The Sao Paulo State financial agency (FAPESP)

Segmentation of kidney and renal collecting system on 3D computed tomography images

Surgical training for minimal invasive kidney interventions (MIKI) has huge importance within the urology field. Within this topic, simulate MIKI in a patient-specific virtual environment can be used for pre-operative planning using the real patient's anatomy, possibly resulting in a reduction of intra-operative medical complications. However, the validated VR simulators perform the training in a group of standard models and do not allow patient-specific training. For a patient-specific training, the standard simulator would need to be adapted using personalized models, which can be extracted from pre-operative images using segmentation strategies. To date, several methods have already been proposed to accurately segment the kidney in computed tomography (CT) images. However, most of these works focused on kidney segmentation only, neglecting the extraction of its internal compartments. In this work, we propose to adapt a coupled formulation of the B-Spline Explicit Active Surfaces (BEAS) framework to simultaneously segment the kidney and the renal collecting system (CS) from CT images. Moreover, from the difference of both kidney and CS segmentations, one is able to extract the renal parenchyma also. The segmentation process is guided by a new energy functional that combines both gradient and region-based energies. The method was evaluated in 10 kidneys from 5 CT datasets, with different image properties. Overall, the results demonstrate the accuracy of the proposed strategy, with a Dice overlap of 92.5%, 86.9% and 63.5%, and a point-to-surface error around 1.6 mm, 1.9 mm and 4 mm for the kidney, renal parenchyma and CS, respectively.NORTE-01-0145-FEDER0000I3, and NORTE-01-0145-FEDER-024300, supported by Northern Portugal Regional Operational Programme (Norte2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER), and also been funded by FEDER funds, through Competitiveness Factors Operational Programme (COMPETE), and by national funds, through the FCT-Fundacao para a Ciência e Tecnologia, under the scope of the project POCI-01-0145-FEDER-007038. The authors acknowledge FCT-Fundação para a Ciância e a Tecnologia, Portugal, and the European Social Found, European Union, for funding support through the Programa Operacional Capital Humano (POCH).info:eu-repo/semantics/publishedVersio

Automatic strategy for extraction of anthropometric measurements for the diagnostic and evaluation of deformational plagiocephaly from infant’s head models

Deformational Plagiocephaly (DP) refers to an asymmetrical distortion of an infant's skull resulting from external forces applied over time. The diagnosis of this condition is performed using asymmetry indexes that are estimated from specific anatomical landmarks, whose are manually defined on head models acquired using laser scans. However, this manual identification is susceptible to intra-/inter-observer variability, being also time-consuming. Therefore, automatic strategies for the identification of the landmarks and, consequently, extraction of asymmetry indexes, are claimed. A novel pipeline to automatically identify these landmarks on 3D head models and to estimate the relevant cranial asymmetry indexes is proposed. Thus, a template database is created and then aligned with the unlabelled patient through an iterative closest point (ICP) strategy. Here, an initial rigid alignment followed by an affine one are applied to remove global misalignments between each template and the patient. Next, a non-rigid alignment is used to deform the template information to the patient-specific shape. The final position of each landmark is computed as a local weight average of all candidate results. From the identified landmarks, a head's coordinate system is automatically estimated and later used to estimate cranial asymmetry indexes. The proposed framework was evaluated in 15 synthetic infant head's model. Overall, the results demonstrated the accuracy of the identification strategy, with a mean average distance of 2.8 +/- 0.6 mm between the identified landmarks and the ground-truth. Moreover, for the estimation of cranial asymmetry indexes, a performance comparable to the inter-observer variability was achieved.The present submission corresponds to original research work of the authors and has never been submitted elsewhere. Moreover, this work was funded by the project NORTE-01-0145-FEDER-024300, supported by Northern Portugal Regional Operational Programme (Norte2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). Moreover, this work has been also supported by FCT - Fundação para a Ciência e Tecnologia within the Project Scope: UID/CEC/00319/2019. Furthermore, the authors acknowledge FCT, Portugal, and the European Social Found, European Union, for funding support through the "Programa Operacional Capital Humano" (POCH) in the scope of the PhD grants SFRH/BD/136721/2018 (Bruno Oliveira), SFRH/BD/136670/2018 (Helena R. Torres), and SFRH/BD/131545/2017 (Fernando Veloso)

Top-down human pose estimation with depth images and domain adaptation

In this paper, a method for estimation of human pose is proposed, making use of ToF (Time of Flight) cameras. For this, a YOLO based object detection method was used, to develop a top-down method. In the first stage, a network was developed to detect people in the image. In the second stage, a network was developed to estimate the joints of each person, using the image result from the first stage. We show that a deep learning network trained from scratch with ToF images yields better results than taking a deep neural network pretrained on RGB data and retraining it with ToF data. We also show that a top-down detector, with a person detector and a joint detector works better than detecting the body joints over the entire image.This work is supported by: European Structural and Investment Funds in the FEDER component, through the Operational Competitiveness and Internationalization Programme (COMPETE 2020) [Project no 002797; Funding Reference: POCI-01-0247-FEDER-002797]

Automated generation of synthetic in-car dataset for human body pose detection

In this paper, a toolchain for the generation of realistic synthetic images for human body pose detection in an in-car environment is proposed. The toolchain creates a customized synthetic environment, comprising human models, car, and camera. Poses are automatically generated for each human, taking into account a per-joint axis Gaussian distribution, constrained by anthropometric and range of motion measurements. Scene validation is done through collision detection. Rendering is focused on vision data, supporting time-of-flight (ToF) and RGB cameras, generating synthetic images from these sensors. Ground-truth data is then generated, comprising the car occupants' body pose (2D/3D), as well as full body RGB segmentation frames with different body parts' labels. We demonstrate the feasibility of using synthetic data, combined with real data, to train distinct machine learning agorithms, demonstrating the improvement in their algorithmic accuracy for the in-car scenario.This work is supported by: European Structural and Investment Funds in the FEDER component, through the Operational Competitiveness and Internationalization Programme (COMPETE 2020) [Project no 039334; Funding Reference: POCI-01-0247-FEDER-039334]

Deep learning-based detection of anthropometric landmarks in 3D infants head models

Deformational plagiocephaly (DP) is a cranial deformity characterized by an asymmetrical distortion of an infant's skull. The diagnosis and evaluation of DP are performed using cranial asymmetry indexes obtained from cranial measurements, which can be estimated using anthropometric landmarks of the infant's head. However, manual labeling of these landmarks is a time-consuming and tedious task, being also prone to observer variability. In this paper, a novel framework to automatically detect anthropometric landmarks of 3D infant's head models is described. The proposed method is divided into two stages: (i) unfolding of the 3D head model surface; and (ii) landmarks' detection through a deep learning strategy. In the first stage, an unfolding strategy is used to transform the 3D mesh of the head model to a flattened 2D version of it. From the flattened mesh, three 2D informational maps are generated using specific head characteristics. In the second stage, a deep learning strategy is used to detect the anthropometric landmarks in a 3-channel image constructed using the combination of informational maps. The proposed framework was validated in fifteen 3D synthetic models of infant's head, being achieved, in average for all landmarks, a mean distance error of 3.5 mm between the automatic detection and a manually constructed ground-truth. Moreover, the estimated cranial measurements were comparable to the ones obtained manually, without statistically significant differences between them for most of the indexes. The obtained results demonstrated the good performance of the proposed method, showing the potential of this framework in clinical practice.The present submission corresponds to original research work of the authors and has never been submitted elsewhere. Moreover, this work was funded by the project NORTE-01-0145-FEDER-024300, supported by Northern Portugal Regional Operational Programme (Norte2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). Moreover, this work has been also supported by FCT - Fundação para a Ciência e Tecnologia within the Project Scope: UID/CEC/00319/2019. Furthermore, the authors acknowledge FCT, Portugal, and the European Social Found, European Union, for funding support through the "Programa Operacional Capital Humano" (POCH) in the scope of the PhD grants SFRH/BD/136670/2018 (Helena R. Torres), SFRH/BD/136721/2018 (Bruno Oliveira), and SFRH/BD/131545/2017 (Fernando Veloso)

A system for the generation of in-car human body pose datasets

Published online: 8 October 2020With the advent of autonomous vehicles, detection of the occupants’ posture is crucial to tackle the needs of infotainment interaction or passive safety systems. Generative approaches have been recently proposed for human body pose in-car detection, but this type of approaches requires a large training dataset for a feasible accuracy. This requirement poses a difficulty, given the substantial time required to annotate such large amount of data. In the in-car scenario, this requirement risk increases even further, since a robust human body pose ground-truth system capable of working in it is needed but inexistent. Currently, the gold standard for human body pose capture is based on optical systems, requiring up to 39 visible markers for a plug-in gait model, which in this case are not feasible given the occlusions inside the car. Other solutions, such as inertial suits, also have limitations linked to magnetic sensitivity and global positioning drift. In this paper, a system for the generation of images for human body pose detection in an in-car environment is proposed. To this end, we propose to smartly combine inertial and optical systems to suppress their individual limitations: By combining the global positioning of 3 visible head markers provided by the optical system with the inertial suit’s relative human body pose, we obtain an occlusion-ready, drift-free full-body global positioning system. This system is then spatially and temporally calibrated with a time-of-flight sensor, automatically obtaining in-car image data with (multi-person) pose annotations. Besides quantifying the inertial suit inherent sensitivity and accuracy, the feasibility of the overall system for human body pose capture in the in-car scenario was demonstrated. Our results quantify the errors associated with the inertial suit, pinpoint some sources of the system’s uncertainty and propose how to minimize some of them. Finally, we demonstrate the feasibility of using system generated data (which was made publicly available), independently or mixed with two publicly available generic datasets (not in-car), to train 2 machine learning algorithms, demonstrating the improvement in their algorithmic accuracy for the in-car scenario.This work is supported by: European Structural and Investment Funds in the FEDER component, through the Operational Competitiveness and Internationalization Programme (COMPETE 2020) [Project n.º 002797; Funding Reference: POCI-01-0247-FEDER-002797]