Daniel Simões Lopes | INESC-ID, IST, Universidade de Lisboa (original) (raw)

Papers by Daniel Simões Lopes

Many aspects of healthcare are becoming increasingly entwined with 3D imaging as a means of diagn... more Many aspects of healthcare are becoming increasingly entwined with 3D imaging as a means of diagnosis, surgical navigation and procedure planning as an alternative to expensive and invasive techniques. Here, Dr. Daniel Simões Lopes tells us about the IT-MEDEX project, which is working to make 3D medical images ever more powerful and usable on an array of devices.

Visual quality of volume rendering for medical imagery strongly depends on the underlying transfe... more Visual quality of volume rendering for medical
imagery strongly depends on the underlying transfer function.
Conventional Windows–Icons–Menus–Pointer interfaces
typically refer the user to browse a lengthy catalog
of predefined transfer functions or to pain-staking refine
the transfer function by clicking and dragging several independent
handles. To turn the standard design process less
difficult and tedious, this paper proposes novel interactions
on a sketch-based interface that supports the design of 1D
transfer functions via touch gestures to directly control voxel opacity and easily assign colors. User can select different
types of transfer function shapes including ramp function,
free hand curve drawing, and slider bars similar to those of
a mixing table. An assorted array of thumbnails provides an
overview of the data when editing the transfer function. User
performance is evaluated by comparing the time and effort
necessary to complete a number of tests with sketch-based
and conventional interfaces. Users were able to more rapidly
explore and understand volume data using the sketch-based
interface, as the number of design iterations necessary to
obtain a desirable transfer function was reduced. In addition,
informal evaluation sessions carried out with professionals
(two senior radiologists, a general surgeon and two scientific
illustrators) provided valuable feedback on how suitable the
sketch-based interface is for illustration, patient communication
and medical education.

Current state-of-the-art point cloud visualization techniques have shortcomings when dealing with... more Current state-of-the-art point cloud visualization techniques have shortcomings when dealing with sparse and less accurate data or close-up interactions. In this paper, we present a visualization technique called stroke-based splat-ting, which applies concepts of stroke-based rendering to surface-aligned splatting, allowing for better shape perception at lower resolutions and close-ups. We create a painterly depiction of the data with an impressionistic aesthetic, which is a metaphor the user is culturally trained to recognize, thus attributing higher quality to the visualization. This is achieved by shaping each object-aligned splat as a brush stroke, and orienting it according to globally coherent tangent vectors from the Householder formula, creating a painterly depiction of the scanned cloud. Each splat is sized according to a color-based clustering analysis of the data, ensuring the consistency of brush strokes within neighborhood areas. By controlling brush shape generation parameters and blending factors between neighboring splats, the user is able to simulate different painting styles in real time. We have tested our method with data sets captured by commodity laser scanners as well as publicly available high-resolution point clouds, both having highly interactive frame rates in all cases. In addition, a user study was conducted comparing our approach to state-of-the-art point cloud visualization techniques. Users considered stroke-based splatting a valuable technique as it provides a higher or similar visual quality to current approaches.

Analyzing medical volume datasets requires interactive visualization so that users can extract an... more Analyzing medical volume datasets requires interactive visualization so that users can extract anatomo-physiological information in real-time. Conventional volume rendering systems rely on 2D input devices, such as mice and keyboards, which are known to hamper 3D analysis as users often struggle to obtain the desired orientation that is only achieved after several attempts. In this paper, we address which 3D analysis tools are better performed with 3D hand cursors operating on a touchless interface comparatively to a 2D input devices running on a conventional WIMP interface. The main goals of this paper are to explore the capabilities of (simple) hand gestures to facilitate sterile manipulation of 3D medical data on a touchless interface, without resorting on wearables, and to evaluate the surgical feasibility of the proposed interface next to senior surgeons (N = 5) and interns (N = 2). To this end, we developed a touchless interface controlled via hand gestures and body postures to rapidly rotate and position medical volume images in three-dimensions, where each hand acts as an interactive 3D cursor. User studies were conducted with laypeople, while informal evaluation sessions were carried with senior surgeons, radiologists and professional biomedical engineers. Results demonstrate its usability as the proposed touchless interface improves spatial awareness and a more fluent interaction with the 3D volume than with traditional 2D input devices, as it requires lesser number of attempts to achieve the desired orientation by avoiding the composition of several cumulative rotations, which is typically necessary in WIMP interfaces. However, tasks requiring precision such as clipping plane visualization and tagging are best performed with mouse-based systems due to noise, incorrect gestures detection and problems in skeleton tracking that need to be addressed before tests in real medical environments might be performed.

Breast tissue superposition or parenchymal density have been known as Digital Mammography's (DM) ... more Breast tissue superposition or parenchymal density have been known as Digital Mammography's (DM) main limitations. More expensive and case-specific tools such as MRI and ultrasound imaging may be used to address this problem, but 2D DM remains the most practical and cost-effective approach. Digital Breast Tomo-synthesis (DBT) has the ability to overcome both problems. However, the images produced by this technique are affected by the limited resolution between slices, which combined with a lack of a viewing mode make it difficult to visualize the true 3D structure of the breast. This is unfortunate since stereo static 3D representations can improve real lesion detection. In this paper, we propose a new interactive visualization approach to DBT that explores all three dimensions of the volume data. Our approach allows combining DBT slices to generate a 3D representation of the breast in order to improve the radiologist's depth perception. Preliminary results suggest that this alternative has the potential to achieve similar visual enhancement of lesions, as well as to reduce the time required to locate and classify these.

The continuous progression of cubitus varus and valgus can lead to more severe problems, therefor... more The continuous progression of cubitus varus and valgus can lead to more severe problems, therefore requiring an efficient corrective method . The most used technique is closing wedge osteotomy at the distal portion of the humerus [1,2]. However, its preoperative planning based on two 2D radiographs is not well suited to deal with a three dimensional bone malformation. This work presents a software interface that relies on the combination of the usual radiographs with a 3D model of the distal portion of the humerus, enabling the simulation of the surgical approach and the 3D representation of the postoperative humerus.

Physicians take advantage of desktop and mobile software to perform their work, although current ... more Physicians take advantage of desktop and mobile software to perform their work, although current visualization systems still rely on interaction approaches that do not go beyond 2D interfaces. The advent of portable devices, such as tablets, coupled with the growing need to explore and apply 3D image manipulation techniques, motivated our team to develop a tool for 3D medical image exploration and visualization using tangible and spatially aware mobile touch interfaces running on mobile devices. Our approach was validated with user tests using a medical image visualization prototype. Our results show that for 3D manipulation, mobile devices can improve the experience in comparison with traditional techniques. Testing the proposed system with healthcare professionals will be performed as future work.

A sedentary lifestyle and bad eating habits are leading causes of cerebral vascular accidents or ... more A sedentary lifestyle and bad eating habits are leading causes of cerebral vascular accidents or stroke . Physical rehabilitation is often required to recover from upper extremity complications that commonly follow stroke. While computer-based interactive methods have been proposed to help defray person-hour costs, most require expensive dedicated hardware, lack good interfaces featuring user-centered biofeedback to better detect compensatory movements or assist the collaboration between patients and physiotherapists . To approach these problems, we propose an inexpensive solution built with commercial off-theshelf hardware to promote upper limb rehabilitation and collaboration between stroke patients and physiotherapists. Materials and Methods: The proposed system relies on a Kinect v2 to track the patient's body movement, a PC running Windows 10 and a pair of displays. Two distinct but related graphical user interfaces were developed: (i) a physiotherapist interface that contains a rich set of biofeedback portraying important patient kinematic data (e.g., shoulder flexion-extension and abduction-adduction angles) and compensatory movements (e.g., shoulder unevenness) in realtime; and (ii) a patient interface which displays a series of targets to be sequentially reached through arm elevation. Informal evaluations were performed by two physiotherapists and three physical medicine and rehabilitation physicians to validate both interfaces. Each participant was asked to verify if the proposed interfaces could help analyse or aid the treatment of acute stroke patients with physical limitations of the upper limbs. Results: In the conducted interviews, all the interviewed participants indicated that distinct interfaces for the physiotherapist and patient is a meaningful feature, as the patient interface must be very minimalistic to avoid unnecessary distractions, whereas the physiotherapist must contain the full range of kinematic data. For the patient interface, it is important to track the completed repetitions, the session time of the proposed task and to display a few targets to be reached. As for the physiotherapist interface, it is important to visualize the vertical (sagittal plane) and horizontal (transverse plane) angles of the arm movement and, most noticeably, in which angle ranges the compensatory movements occur. Discussion and Conclusions: The proposed interfaces have received positive response from several rehabilitation professionals. Although still in a pilot phase, the minimalistic design of the patient interface is devoid of graphical distractions, only delivering the necessary biofeedback for tracking shoulder movements by following predefined targets. On the other hand, the physiotherapist interface presents the necessary kinematic data and activity metrics to assist the evaluation and treatment of acute stroke patients.

Monitoring a patient's breathing cycle is very important to identify early signs of serious compl... more Monitoring a patient's breathing cycle is very important to identify early signs of serious complications manifested by decreased oxygen saturation, respiratory acidosis, and cardiac disturbances (e.g. cardiac arrest). This work presents a signal processing technique to measure respiratory frequency by relying only the skeletal tracking data of an inexpensive depth camera. Our approach aims to be useful for reading the breath frequency automatically in a non-invasive and markerless manner. This study applies a pass-band filter that magnifies the micro-movements (1) of skeleton's joints to compute the respiratory frequency. Materials and Methods: The Microsoft Kinect v2 was used as a depth camera which computes a skeletal representation of the human body, which consists of 25 notable points (joints and body extremities). Here, we only consider the 5 torso points to analyze the breathing movement. To evaluate the system, we collected data from 6 subjects along 4 acquisitions of during 60 seconds each: seated with a normal breath; standing with a normal breath; seated with a heavy breath; and standing with a heavy breath. To assess our approach, we considered as ground truth data acquired from the BioSignalsPlux Researcher device. Informed consent was received from 6 volunteers (2 female, 4 male) with no history of lung disease or pain.

Meshes are considered the gold standard regarding contact geometries of many mechanical models, e... more Meshes are considered the gold standard regarding contact geometries of many mechanical models, even those represented with discrete surface contact elements. However, meshes may not be the best formulations when controlled precision and execution time become paramount. In this paper, we address parametric and implicit formulations for precise contact distance estimations between superovoidal shapes, which generalize superellipsoids. Parametric and implicit models provide more compact descriptions than meshes, while making it possible to approximate mechanical parts with great precision. Contrary to meshes, these geometric representations can then support fast calculation of distances with arbitrary precision without paying a storage or computation time penalty. We performed a benchmark study to compare different superellipsoidal and superovoidal contact geometry representations, including implicit surfaces, parametric surfaces and triangular meshes. We tested 10,000 contact pairs and also considered two application cases: robot fingers of an iCub and dental occlusion during bite. Our results show that the implicit model is the most efficient contact geometry representation, followed by parametric and mesh surfaces. In addition, results show that either implicit or parametric superovoids can provide more accurate distance estimations than meshes in practical settings where precise contact points, surface normals and clearance estimations are required.

Reading room conditions such as illumination, ambient light, human factors and display luminance,... more Reading room conditions such as illumination, ambient light, human factors and display luminance, play an important role on how radiologists analyze and interpret images. Indeed, serious diagnostic errors can appear when observing images through everyday monitors. Typically, these occur whenever professionals are ill-positioned with respect to the display or visualize images under improper light and luminance conditions. In this work, we show that virtual reality can assist radiodiagnostics by considerably diminishing or cancel out the effects of unsuitable ambient conditions. Our approach combines immersive head-mounted displays with interactive surfaces to support professional radiologists in analyzing medical images and formulating diagnostics. We evaluated our prototype with two senior medical doctors and four seasoned radiology fellows. Results indicate that our approach constitutes a viable, flexible, portable and cost-efficient option to traditional radiology reading rooms.

Too often illustrating and visualizing 3D geological concepts are performed by sketching in 2D me... more Too often illustrating and visualizing 3D geological concepts are performed by sketching in 2D mediums, which may limit drawing performance of initial concepts. Here, the potential of expeditious geological modeling brought by hand gestures is explored. A spatial interaction system was developed to enable rapid modeling, editing, and exploration of 3D layer-cake objects. User interactions are acquired with motion capture and touch screen technologies. Virtual immersion is guaranteed by using stereoscopic technology. The novelty consists of performing expeditious modeling of coarse geological features with only a limited set of hand gestures. Results from usability-studies show that the proposed system is more efficient when compared to a windows-icon-menu-pointer modeling application.

Please see the related video: https://vimeo.com/128858924

Remodeling is a biological phenomenon that is present in all the stages of development of bone ti... more Remodeling is a biological phenomenon that is present in all the stages of development of bone tissue. Understanding how bone tissue adapts to a certain biomechanical environment is crucial for reliable computational simulations. The purpose of this work is to study the remodeling of a calf bone having in mind the development of an intramedullary interlocking nail for orthopedic veterinary applications. In fact, the treatment of fractures of bone diaphyses of large animals, such as horses and bovines, is still a challenge in orthopedic veterinary. The main products available are adapted from human devices and they are too expensive.

Medical imaging modalities, such as computed tomography (CT) and magnetic res-onance (MR), provid... more Medical imaging modalities, such as computed tomography (CT) and magnetic res-onance (MR), provide 3D anatomophysiological data that allow clinicians and surgeons to carry out important medical decisions. For the biomechanical engineering community, medical images are perceived as the input signal for a geometric modeling pipeline that outputs accurate 3D CAD and mesh models. These models are extensively used for finite element (FE) analysis in order to study several biomedical phenomena. Our framework for 3D anatomical modeling starts by filtering image data to reduce noise and artifacts: an anisotropic diffusion filter plays here an essential role. The structures of interest are then partitioned into voxelized images, using, for instance, a 3D snake segmentation al-gorithm with a contour evolution equation solved by a level set method. To convert this type of image data into surface data, mesh-based or CAD-based geometric modeling re-construction approaches may be adopted. The mos...

Journal of Biomechanics, 2012

One of the major difficulties of the finite element method applied to computational biomechanics ... more One of the major difficulties of the finite element method applied to computational
biomechanics is the complexity associated with the development of patient-specific
anatomical models. In this paper, a geometric modeling pipeline developed to create 3-D
models from medical image data is presented. Several image and geometric processing blocks
make part of the pipeline: image acquisition, image segmentation, surface mesh adjustment,
solid model generation and finite element modeling. The input of the pipeline is an ordered
stack of medical images with high spatial resolution and tissue contrast. The pipeline outputs
geometric models, such as triangular surface meshes and solid models, and finite element
meshes suitable for stress analysis, among other applications like visualization and rapid
prototyping. The examples here presented are modeled based on computed tomography data,
them being, the solid models and the finite element meshes of vertebrae C5 and C6, scapula,
humerus, clavicle, mandible and teeth.

The response of bovine bone to the presence of an implant is analysed with the aim of simulating ... more The response of bovine bone to the presence of an implant is analysed with the aim of simulating bone remodelling in a developing model of a polymeric intramedullary interlocking nail for veterinary use. A 3-D finite element model of the femur diaphysis is built based on computed tomography images and using a CAD-based modelling pipeline. The bone remodelling process after the surgery is analysed and compared with the healthy bone. The remodelling law assumes that bone adapts to the mechanical environment. For the analyses a consistent set of loads is determined for the bovine walk cycle. The remodelling results reproduce the morphologic features of bone and provide evidence of the difference on the bone behaviour when comparing metallic and polymeric nails. Our findings indicate that an intramedullary polymeric nail has the advantage over the metallic one of improving long-term bone healing and possibly avoiding the need of the implant removal.

Many aspects of healthcare are becoming increasingly entwined with 3D imaging as a means of diagn... more Many aspects of healthcare are becoming increasingly entwined with 3D imaging as a means of diagnosis, surgical navigation and procedure planning as an alternative to expensive and invasive techniques. Here, Dr. Daniel Simões Lopes tells us about the IT-MEDEX project, which is working to make 3D medical images ever more powerful and usable on an array of devices.

Visual quality of volume rendering for medical imagery strongly depends on the underlying transfe... more Visual quality of volume rendering for medical
imagery strongly depends on the underlying transfer function.
Conventional Windows–Icons–Menus–Pointer interfaces
typically refer the user to browse a lengthy catalog
of predefined transfer functions or to pain-staking refine
the transfer function by clicking and dragging several independent
handles. To turn the standard design process less
difficult and tedious, this paper proposes novel interactions
on a sketch-based interface that supports the design of 1D
transfer functions via touch gestures to directly control voxel opacity and easily assign colors. User can select different
types of transfer function shapes including ramp function,
free hand curve drawing, and slider bars similar to those of
a mixing table. An assorted array of thumbnails provides an
overview of the data when editing the transfer function. User
performance is evaluated by comparing the time and effort
necessary to complete a number of tests with sketch-based
and conventional interfaces. Users were able to more rapidly
explore and understand volume data using the sketch-based
interface, as the number of design iterations necessary to
obtain a desirable transfer function was reduced. In addition,
informal evaluation sessions carried out with professionals
(two senior radiologists, a general surgeon and two scientific
illustrators) provided valuable feedback on how suitable the
sketch-based interface is for illustration, patient communication
and medical education.

Current state-of-the-art point cloud visualization techniques have shortcomings when dealing with... more Current state-of-the-art point cloud visualization techniques have shortcomings when dealing with sparse and less accurate data or close-up interactions. In this paper, we present a visualization technique called stroke-based splat-ting, which applies concepts of stroke-based rendering to surface-aligned splatting, allowing for better shape perception at lower resolutions and close-ups. We create a painterly depiction of the data with an impressionistic aesthetic, which is a metaphor the user is culturally trained to recognize, thus attributing higher quality to the visualization. This is achieved by shaping each object-aligned splat as a brush stroke, and orienting it according to globally coherent tangent vectors from the Householder formula, creating a painterly depiction of the scanned cloud. Each splat is sized according to a color-based clustering analysis of the data, ensuring the consistency of brush strokes within neighborhood areas. By controlling brush shape generation parameters and blending factors between neighboring splats, the user is able to simulate different painting styles in real time. We have tested our method with data sets captured by commodity laser scanners as well as publicly available high-resolution point clouds, both having highly interactive frame rates in all cases. In addition, a user study was conducted comparing our approach to state-of-the-art point cloud visualization techniques. Users considered stroke-based splatting a valuable technique as it provides a higher or similar visual quality to current approaches.

Analyzing medical volume datasets requires interactive visualization so that users can extract an... more Analyzing medical volume datasets requires interactive visualization so that users can extract anatomo-physiological information in real-time. Conventional volume rendering systems rely on 2D input devices, such as mice and keyboards, which are known to hamper 3D analysis as users often struggle to obtain the desired orientation that is only achieved after several attempts. In this paper, we address which 3D analysis tools are better performed with 3D hand cursors operating on a touchless interface comparatively to a 2D input devices running on a conventional WIMP interface. The main goals of this paper are to explore the capabilities of (simple) hand gestures to facilitate sterile manipulation of 3D medical data on a touchless interface, without resorting on wearables, and to evaluate the surgical feasibility of the proposed interface next to senior surgeons (N = 5) and interns (N = 2). To this end, we developed a touchless interface controlled via hand gestures and body postures to rapidly rotate and position medical volume images in three-dimensions, where each hand acts as an interactive 3D cursor. User studies were conducted with laypeople, while informal evaluation sessions were carried with senior surgeons, radiologists and professional biomedical engineers. Results demonstrate its usability as the proposed touchless interface improves spatial awareness and a more fluent interaction with the 3D volume than with traditional 2D input devices, as it requires lesser number of attempts to achieve the desired orientation by avoiding the composition of several cumulative rotations, which is typically necessary in WIMP interfaces. However, tasks requiring precision such as clipping plane visualization and tagging are best performed with mouse-based systems due to noise, incorrect gestures detection and problems in skeleton tracking that need to be addressed before tests in real medical environments might be performed.

Breast tissue superposition or parenchymal density have been known as Digital Mammography's (DM) ... more Breast tissue superposition or parenchymal density have been known as Digital Mammography's (DM) main limitations. More expensive and case-specific tools such as MRI and ultrasound imaging may be used to address this problem, but 2D DM remains the most practical and cost-effective approach. Digital Breast Tomo-synthesis (DBT) has the ability to overcome both problems. However, the images produced by this technique are affected by the limited resolution between slices, which combined with a lack of a viewing mode make it difficult to visualize the true 3D structure of the breast. This is unfortunate since stereo static 3D representations can improve real lesion detection. In this paper, we propose a new interactive visualization approach to DBT that explores all three dimensions of the volume data. Our approach allows combining DBT slices to generate a 3D representation of the breast in order to improve the radiologist's depth perception. Preliminary results suggest that this alternative has the potential to achieve similar visual enhancement of lesions, as well as to reduce the time required to locate and classify these.

The continuous progression of cubitus varus and valgus can lead to more severe problems, therefor... more The continuous progression of cubitus varus and valgus can lead to more severe problems, therefore requiring an efficient corrective method . The most used technique is closing wedge osteotomy at the distal portion of the humerus [1,2]. However, its preoperative planning based on two 2D radiographs is not well suited to deal with a three dimensional bone malformation. This work presents a software interface that relies on the combination of the usual radiographs with a 3D model of the distal portion of the humerus, enabling the simulation of the surgical approach and the 3D representation of the postoperative humerus.

Physicians take advantage of desktop and mobile software to perform their work, although current ... more Physicians take advantage of desktop and mobile software to perform their work, although current visualization systems still rely on interaction approaches that do not go beyond 2D interfaces. The advent of portable devices, such as tablets, coupled with the growing need to explore and apply 3D image manipulation techniques, motivated our team to develop a tool for 3D medical image exploration and visualization using tangible and spatially aware mobile touch interfaces running on mobile devices. Our approach was validated with user tests using a medical image visualization prototype. Our results show that for 3D manipulation, mobile devices can improve the experience in comparison with traditional techniques. Testing the proposed system with healthcare professionals will be performed as future work.

A sedentary lifestyle and bad eating habits are leading causes of cerebral vascular accidents or ... more A sedentary lifestyle and bad eating habits are leading causes of cerebral vascular accidents or stroke . Physical rehabilitation is often required to recover from upper extremity complications that commonly follow stroke. While computer-based interactive methods have been proposed to help defray person-hour costs, most require expensive dedicated hardware, lack good interfaces featuring user-centered biofeedback to better detect compensatory movements or assist the collaboration between patients and physiotherapists . To approach these problems, we propose an inexpensive solution built with commercial off-theshelf hardware to promote upper limb rehabilitation and collaboration between stroke patients and physiotherapists. Materials and Methods: The proposed system relies on a Kinect v2 to track the patient's body movement, a PC running Windows 10 and a pair of displays. Two distinct but related graphical user interfaces were developed: (i) a physiotherapist interface that contains a rich set of biofeedback portraying important patient kinematic data (e.g., shoulder flexion-extension and abduction-adduction angles) and compensatory movements (e.g., shoulder unevenness) in realtime; and (ii) a patient interface which displays a series of targets to be sequentially reached through arm elevation. Informal evaluations were performed by two physiotherapists and three physical medicine and rehabilitation physicians to validate both interfaces. Each participant was asked to verify if the proposed interfaces could help analyse or aid the treatment of acute stroke patients with physical limitations of the upper limbs. Results: In the conducted interviews, all the interviewed participants indicated that distinct interfaces for the physiotherapist and patient is a meaningful feature, as the patient interface must be very minimalistic to avoid unnecessary distractions, whereas the physiotherapist must contain the full range of kinematic data. For the patient interface, it is important to track the completed repetitions, the session time of the proposed task and to display a few targets to be reached. As for the physiotherapist interface, it is important to visualize the vertical (sagittal plane) and horizontal (transverse plane) angles of the arm movement and, most noticeably, in which angle ranges the compensatory movements occur. Discussion and Conclusions: The proposed interfaces have received positive response from several rehabilitation professionals. Although still in a pilot phase, the minimalistic design of the patient interface is devoid of graphical distractions, only delivering the necessary biofeedback for tracking shoulder movements by following predefined targets. On the other hand, the physiotherapist interface presents the necessary kinematic data and activity metrics to assist the evaluation and treatment of acute stroke patients.

Monitoring a patient's breathing cycle is very important to identify early signs of serious compl... more Monitoring a patient's breathing cycle is very important to identify early signs of serious complications manifested by decreased oxygen saturation, respiratory acidosis, and cardiac disturbances (e.g. cardiac arrest). This work presents a signal processing technique to measure respiratory frequency by relying only the skeletal tracking data of an inexpensive depth camera. Our approach aims to be useful for reading the breath frequency automatically in a non-invasive and markerless manner. This study applies a pass-band filter that magnifies the micro-movements (1) of skeleton's joints to compute the respiratory frequency. Materials and Methods: The Microsoft Kinect v2 was used as a depth camera which computes a skeletal representation of the human body, which consists of 25 notable points (joints and body extremities). Here, we only consider the 5 torso points to analyze the breathing movement. To evaluate the system, we collected data from 6 subjects along 4 acquisitions of during 60 seconds each: seated with a normal breath; standing with a normal breath; seated with a heavy breath; and standing with a heavy breath. To assess our approach, we considered as ground truth data acquired from the BioSignalsPlux Researcher device. Informed consent was received from 6 volunteers (2 female, 4 male) with no history of lung disease or pain.

Meshes are considered the gold standard regarding contact geometries of many mechanical models, e... more Meshes are considered the gold standard regarding contact geometries of many mechanical models, even those represented with discrete surface contact elements. However, meshes may not be the best formulations when controlled precision and execution time become paramount. In this paper, we address parametric and implicit formulations for precise contact distance estimations between superovoidal shapes, which generalize superellipsoids. Parametric and implicit models provide more compact descriptions than meshes, while making it possible to approximate mechanical parts with great precision. Contrary to meshes, these geometric representations can then support fast calculation of distances with arbitrary precision without paying a storage or computation time penalty. We performed a benchmark study to compare different superellipsoidal and superovoidal contact geometry representations, including implicit surfaces, parametric surfaces and triangular meshes. We tested 10,000 contact pairs and also considered two application cases: robot fingers of an iCub and dental occlusion during bite. Our results show that the implicit model is the most efficient contact geometry representation, followed by parametric and mesh surfaces. In addition, results show that either implicit or parametric superovoids can provide more accurate distance estimations than meshes in practical settings where precise contact points, surface normals and clearance estimations are required.

Reading room conditions such as illumination, ambient light, human factors and display luminance,... more Reading room conditions such as illumination, ambient light, human factors and display luminance, play an important role on how radiologists analyze and interpret images. Indeed, serious diagnostic errors can appear when observing images through everyday monitors. Typically, these occur whenever professionals are ill-positioned with respect to the display or visualize images under improper light and luminance conditions. In this work, we show that virtual reality can assist radiodiagnostics by considerably diminishing or cancel out the effects of unsuitable ambient conditions. Our approach combines immersive head-mounted displays with interactive surfaces to support professional radiologists in analyzing medical images and formulating diagnostics. We evaluated our prototype with two senior medical doctors and four seasoned radiology fellows. Results indicate that our approach constitutes a viable, flexible, portable and cost-efficient option to traditional radiology reading rooms.

Too often illustrating and visualizing 3D geological concepts are performed by sketching in 2D me... more Too often illustrating and visualizing 3D geological concepts are performed by sketching in 2D mediums, which may limit drawing performance of initial concepts. Here, the potential of expeditious geological modeling brought by hand gestures is explored. A spatial interaction system was developed to enable rapid modeling, editing, and exploration of 3D layer-cake objects. User interactions are acquired with motion capture and touch screen technologies. Virtual immersion is guaranteed by using stereoscopic technology. The novelty consists of performing expeditious modeling of coarse geological features with only a limited set of hand gestures. Results from usability-studies show that the proposed system is more efficient when compared to a windows-icon-menu-pointer modeling application.

Please see the related video: https://vimeo.com/128858924

Remodeling is a biological phenomenon that is present in all the stages of development of bone ti... more Remodeling is a biological phenomenon that is present in all the stages of development of bone tissue. Understanding how bone tissue adapts to a certain biomechanical environment is crucial for reliable computational simulations. The purpose of this work is to study the remodeling of a calf bone having in mind the development of an intramedullary interlocking nail for orthopedic veterinary applications. In fact, the treatment of fractures of bone diaphyses of large animals, such as horses and bovines, is still a challenge in orthopedic veterinary. The main products available are adapted from human devices and they are too expensive.

Medical imaging modalities, such as computed tomography (CT) and magnetic res-onance (MR), provid... more Medical imaging modalities, such as computed tomography (CT) and magnetic res-onance (MR), provide 3D anatomophysiological data that allow clinicians and surgeons to carry out important medical decisions. For the biomechanical engineering community, medical images are perceived as the input signal for a geometric modeling pipeline that outputs accurate 3D CAD and mesh models. These models are extensively used for finite element (FE) analysis in order to study several biomedical phenomena. Our framework for 3D anatomical modeling starts by filtering image data to reduce noise and artifacts: an anisotropic diffusion filter plays here an essential role. The structures of interest are then partitioned into voxelized images, using, for instance, a 3D snake segmentation al-gorithm with a contour evolution equation solved by a level set method. To convert this type of image data into surface data, mesh-based or CAD-based geometric modeling re-construction approaches may be adopted. The mos...

Journal of Biomechanics, 2012

One of the major difficulties of the finite element method applied to computational biomechanics ... more One of the major difficulties of the finite element method applied to computational
biomechanics is the complexity associated with the development of patient-specific
anatomical models. In this paper, a geometric modeling pipeline developed to create 3-D
models from medical image data is presented. Several image and geometric processing blocks
make part of the pipeline: image acquisition, image segmentation, surface mesh adjustment,
solid model generation and finite element modeling. The input of the pipeline is an ordered
stack of medical images with high spatial resolution and tissue contrast. The pipeline outputs
geometric models, such as triangular surface meshes and solid models, and finite element
meshes suitable for stress analysis, among other applications like visualization and rapid
prototyping. The examples here presented are modeled based on computed tomography data,
them being, the solid models and the finite element meshes of vertebrae C5 and C6, scapula,
humerus, clavicle, mandible and teeth.

The response of bovine bone to the presence of an implant is analysed with the aim of simulating ... more The response of bovine bone to the presence of an implant is analysed with the aim of simulating bone remodelling in a developing model of a polymeric intramedullary interlocking nail for veterinary use. A 3-D finite element model of the femur diaphysis is built based on computed tomography images and using a CAD-based modelling pipeline. The bone remodelling process after the surgery is analysed and compared with the healthy bone. The remodelling law assumes that bone adapts to the mechanical environment. For the analyses a consistent set of loads is determined for the bovine walk cycle. The remodelling results reproduce the morphologic features of bone and provide evidence of the difference on the bone behaviour when comparing metallic and polymeric nails. Our findings indicate that an intramedullary polymeric nail has the advantage over the metallic one of improving long-term bone healing and possibly avoiding the need of the implant removal.

Introduction: Most medical specialties rely on 3D image data either for diagnosis, surgical plann... more Introduction: Most medical specialties rely on 3D image data either for diagnosis, surgical planning, surgical navigation, education or patient-clinician communication. Surprisingly, conventional medical image workstations do not promote proper visual insight nor visual collaboration between professionals. Redesigning conventional applications into visually rich and interactive platforms that seamlessly bring together professionals, devices and 3D medical images, may foster better healthcare by promoting visual insights and boost visual memory through collaboration [1-3]. To this end, we envision portable, accessible, and easy to deploy interactive visualization settings to be commonly adopted in clinical environments. This entails adopting novel technologies (e.g., interactive surfaces, augmented reality and virtual reality) into different healthcare workspaces. Consequently, designing novel medical user interfaces and medical user experiences can offer more natural ways to interact with and engage in collaborative tasks around 3D images.

Challenges and Approaches: Moving from conventional workstations to interactive visualization platforms brings about new and interesting challenges. By interacting with healthcare professionals, visiting their workspaces, analyzing their requirements and suggesting new ways to interact with 3D medical images, we have identified some major hurdles. For one (i) it is difficult to create and nurture a network of healthcare professionals interested on taking time off their office hours or after-hours to engage in research on a regular basis; (ii) a linguistic barrier stands between healthcare professionals and computer scientists, as clinicians and health technicians usually provide “big picture scenarios” lacking details crucial to interface design, requiring extra effort to develop a working set of specifications; (iii) many clinicians overlook the technical complexity hidden from the view of users, believing in easy-to-deploy “automagical” solutions; and (iv) it is not easy to identify current healthcare practices that could be improved by adopting interactive technologies. In order for healthcare professionals to realize that interactive visualization systems may bring added value over traditional practices, it is necessary to develop both well-designed and easy-to-learn medical user interfaces that promote more natural user experiences. In addition, these interactive visualization systems must also be cost-effective, accessible, portable, novel, yet familiar to enable professionals to collaboratively work either in loco or remotely. While developing such approaches is never an easy task [4], the potential rewards make it a very worthwhile endeavor.

Reading room conditions such as illumination, ambient light, human factors and display luminance,... more Reading room conditions such as illumination, ambient light, human factors and display luminance, play an important role on how radiologists analyze and interpret images. Serious diagnostic errors can appear when observing images through everyday monitors, as these occur whenever professionals are ill-positioned with respect to the display or visualize images under improper light and luminance conditions. In this work, we show that virtual reality can assist
radiodiagnostics by considerably diminishing or canceling out the effects of unsuitable ambient conditions. Our approach combines immersive head-mounted displays with interactive surfaces to
support professional radiologists in analyzing medical images and formulating diagnostics. We evaluated our prototype with two senior medical doctors and four seasoned radiology fellows.
Results indicate that our approach constitutes a viable, flexible, portable and cost-efficient option to traditional radiology reading rooms.