Advances in image segmentation techniques, brought by convolutional neural network (CNN) architectures like U-Net, show promise for tasks such as automated cancer screening. Recently, these methods have been extended to detect different instances of the same class, which could be used to, for example, characterize individual cells in whole-slide images. Still, the amount of data needed and the number of parameters in the network are substantial. To alleviate these problems, we modify a method of semantic instance segmentation to also enforce equivariance to the p4 symmetry group of 90-degree rotations and translations. We perform four experiments on a synthetic dataset of scattered sticks and a subset of the Kaggle 2018 Data Science Bowl, the BBBC038 dataset, consisting of segmented nuclei images. Results indicate that the rotation-equivariant architecture yields similar accuracy as a baseline architecture. Furthermore, we observe that the rotation-equivariant architecture converges faster than the baseline. This is a promising step towards reducing the training time during development of methods based on deep learning.
With the increasing use of three-dimensional (3D) models and Computer Aided Design (CAD) in the medical domain, virtual surgical planning is now frequently used. Most of the current solutions focus on bone surgical operations. However, for head and neck oncologic resection, soft tissue ablation and reconstruction are common operations. In this paper, we propose a method to provide a fast and efficient estimation of shape and dimensions of soft tissue resections. Our approach takes advantage of a simple sketch-based interface which allows the user to paint the contour of the resection on a patient specific 3D model reconstructed from a computed tomography (CT) scan. The volume is then virtually cut and carved following this pattern. From the outline of the resection defined on the skin surface as a closed curve, we can identify which areas of the skin are inside or outside this shape. We then use distance transforms to identify the soft tissue voxels which are closer from the inside of this shape. Thus, we can propagate the shape of the resection inside the soft tissue layers of the volume. We demonstrate the usefulness of the method on patient specific CT data.
We present a method to simplify the structure of the surface skeleton of a 3D
Efficient shape representations are important for many image processing applications. Distance transform based algorithms can be used to compute the set of centres of maximal discs/spheres, that represents a shape. This paper describes a method that reduc
Skeletonization will probably become as valuable a tool for shape analysis in 3D, as it is in 2D. We present a topology preserving 3D skeletonization method which computes both surface and curve skeletons whose voxels are labelled with the D-6 distance to
We extend the shape signature based on the distance of the boundary points from the shape centroid, to the case of fuzzy sets. The analysis of the transition from crisp to fuzzy shape descriptor is first given in the continuous case. This is followed by a study of the specific issues induced by the discrete representation of the objects in a computer.
We analyze two methods for calculating the signature of a fuzzy shape, derived from two ways of defining a fuzzy set: first, by its membership function, and second, as a stack of its α-cuts. The first approach is based on measuring the length of a fuzzy straight line by integration of the fuzzy membership function, while in the second one we use averaging of the shape signatures obtained for the individual α-cuts of the fuzzy set. The two methods, equivalent in the continuous case for the studied class of fuzzy shapes, produce different results when adjusted to the discrete case. A statistical study, aiming at characterizing the performances of each method in the discrete case, is done. Both methods are shown to provide more precise descriptions than their corresponding crisp versions. The second method (based on averaged Euclidean distance over the α-cuts) outperforms the others.
Objective The aim of the present study was to compare the reliability and agreement between a computer tomography-based method (CT) and digitalised 2D radiographs (XR) when measuring change in dorsal angulation over time in distal radius fractures. Materials and methods Radiographs from 33 distal radius fractures treated with external fixation were retrospectively analysed. All fractures had been examined using both XR and CT at six times over 6 months postoperatively. The changes in dorsal angulation between the first reference images and the following examinations in every patient were calculated from 133 follow-up measurements by two assessors and repeated at two different time points. The measurements were analysed using Bland-Altman plots, comparing intra- and inter-observer agreement within and between XR and CT. Results The mean differences in intra- and inter-observer measurements for XR, CT, and between XR and CT were close to zero, implying equal validity. The average intra- and inter-observer limits of agreement for XR, CT, and between XR and CT were +/- 4.4 degrees, +/- 1.9 degrees and +/- 6.8 degrees respectively. Conclusions For scientific purpose, the reliability of XR seems unacceptably low when measuring changes in dorsal angulation in distal radius fractures, whereas the reliability for the semi-automatic CT-based method was higher and is therefore preferable when a more precise method is requested.
This paper describes the master thesis project 3DIS4U: Design and implementation of a distributed visualization system with a stereoscopic display carried out at Uppsala University. The main contributions of the thesis are the installation and evaluation of a wallsized stereoscopic display in a class room-like environment and improvement of the quality, interactivity and usability of visualizations at Uppsala University by connecting the system to one of UPPMAX high-performance computing (HPC) clusters. The project involved modifications to open source softwares, mainly the Visualization ToolKit (VTK) and ParaView. Furthermore, software was developed to aid users in creating interactive stereoscopic simulations. Software was installed and modified for better usability. The option of using HPC resources for larger interactive visualizations also exists. As a final step, evaluations of the display and of the software were carried out together with background research on distributed rendering techniques to be able to produce a proposal for further development of the project. The result of this work is a class room environment which in a few minutes can be turned into a visualization studio with a stereoscopic Linköpings universitetdisplay with the ability to create interactive visualizations. The lecture room retains its function as a class room and can support up to 30 simultaneous viewers.
Intentional cranial deformations (ICD) have been observed worldwide but are especially prevalent in preColombian cultures. The purpose of this study was to assess the consequences of ICD on three cranial cavities (intracranial cavity, orbits, and maxillary sinuses) and on cranial vault thickness, in order to screen for morphological changes due to the external constraints exerted by the deformation device. We acquired CT-scans for 39 deformed and 19 control skulls. We studied the thickness of the skull vault using qualitative and quantitative methods. We computed the volumes of the orbits, of the maxillary sinuses, and of the intracranial cavity using haptic-aided semi-automatic segmentation. We finally defined 3D distances and angles within orbits and maxillary sinuses based on 27 anatomical landmarks and measured these features on the 58 skulls. Our results show specific bone thickness patterns in some types of ICD, with localized thinning in regions subjected to increased pressure and thickening in other regions. Our findings confirm that volumes of the cranial cavities are not affected by ICDs but that the shapes of the orbits and of the maxillary sinuses are modified in circumferential deformations. We conclude that ICDs can modify the shape of the cranial cavities and the thickness of their walls but conserve their volumes. These results provide new insights into the morphological effects associated with ICDs and call for similar investigations in subjects with deformational plagiocephalies and craniosynostoses.
A major concern in FGFR2 craniofaciosynostosis is oculo-orbital disproportion, such that orbital malformation provides poor accommodation and support for the orbital contents and peri-orbita, leading to insufficient eyelid closure, corneal exposure and eventually to functional visual impairment. Fronto-facial monobloc osteotomy followed by distraction osteogenesis aims to correct midfacial growth deficiencies in Crouzon–Pfeiffer syndrome patients. Fronto-facial bipartition osteotomy followed by distraction is a procedure of choice in Apert syndrome patients. These procedures modify the shape and volume of the orbit and tend to correct oculo-orbital disproportion. Little is known about the detailed 3D shape of the orbital phenotype in CPS and AS, and about how this is modified by fronto-facial surgery.
Twenty-eight patients with CMS, 13 patients with AS and 40 control patients were included. CT scans were performed before and after fronto-facial surgery. Late post-operative scans were available for the Crouzon–Pfeiffer syndrome group. Orbital morphology was investigated using conventional three-dimensional cephalometry and shape analysis after mesh-based segmentation of the orbital contents.
We characterized the 3D morphology of CPS and AS orbits and showed how orbital shape is modified by surgery. We showed that monobloc-distraction in CPS and bipartition-distraction in AS specifically address the morphological characteristics of the two syndromes.
We describe surface area measurements based on local estimates of isosurfaces originating from a marching cubes representation. We show how improved precision and accuracy
The Image Foresting Transform (IFT) is a framework forimage partitioning, commonly used for interactive segmentation. Givenan image where a subset of the image elements (seed-points) have beenassigned user-defined labels, the IFT completes the labeling by computingminimal cost paths from all image elements to the seed-points. Eachimage element is then given the same label as the closest seed-point. Inits original form, the IFT produces crisp segmentations, i.e., each imageelement is assigned the label of exactly one seed-point. Here, we proposea modified version of the IFT that computes region boundaries withsub-pixel precision by allowing mixed labels at region boundaries. Wedemonstrate that the proposed sub-pixel IFT allows properties of thesegmented object to be measured with higher precision.
Many image segmentation methods utilize graph structures for representing images, where the flexibility and generality of the abstract structure is beneficial. By using a fuzzy object representation, i.e., allowing partial belongingness of elements to image objects, the unavoidable loss of information when representing continuous structures by finite sets is significantly reduced,enabling feature estimates with sub-pixel precision.This work presents a framework for object representation based on fuzzysegmented graphs. Interpreting the edges as one-dimensional paths betweenthe vertices of a graph, we extend the notion of a graph cut to that of a located cut, i.e., a cut with sub-edge precision. We describe a method for computing a located cut from a fuzzy segmentation of graph vertices. Further,the notion of vertex coverage segmentation is proposed as a graph theoretic equivalent to pixel coverage segmentations and a method for computing such a segmentation from a located cut is given. Utilizing the proposed framework,we demonstrate improved precision of area measurements of synthetic two-dimensional objects. We emphasize that although the experiments presented here are performed on two-dimensional images, the proposed framework is defined for general graphs and thus applicable to images of any dimension.
The image Foresting (IFT) is a framework for image partitioning, commonly used for interactive segmentation. Given an image where a subset of the image elements (seed-points) have been assigned correct segmentation labels, the IFT completes the labeling by computing minimal cost paths from all image elements to the seed-points. Each image element is then given the same label as the closest seed-point. Here, we propose the relaxed IFT (RIFT). This modified version of the IFT features an additional parameter to control the smoothness of the segmentation boundary. The RIFT yields more intuitive segmentation results in the presence of noise and weak edges, while maintaining a low computational complexity. We show an application of the method to the refinement of manual segmentations of a thoracolumbar muscle in magnetic resonance images. The performed study shows that the refined segmentations are qualitatively similar to the manual segmentations, while intra-user variations are reduced by more than 50%.
Graph-based methods have become well-established tools for image segmentation. Viewing the image as a weighted graph, these methods seek to extract a graph cut that best matches the image content.Many of these methods are interactive, in that they allow a human operator to guide the segmentation process by specifying a set of hard constraints that the cut must satisfy. Typically, these constraints are given in one of two forms: regional constraints (a set of vertices that must be separated by the cut) or boundary constraints (a set of edges that must be included in the cut). Here, we propose a new type of hard constraints,that includes both regional constraints and boundary constraints as special cases. We also present an efficient method for computing cuts that satisfy a set of generalized constraints, while globally minimizing a graph-cut measure.
Designing interactive segmentation methods for digital volume images is difficult, mainly because efficient 3D interaction is much
harder to achieve than interaction with 2D images. To overcome this issue, we use a system that combines stereo graphics and haptics to facilitate efficient 3D interaction. We propose a new method, based on the 2D live-wire method, for segmenting volume images. Our method consists of two parts: an interface for drawing 3D live-wire curves onto the boundary of an object in a volume image, and an algorithm for connecting two such curves to create a discrete surface.
Objective: To evaluate a novel methodology using industrial scanners as a reference, and assess in vivo accuracy of 3 intraoral scanners (IOS) and conventional impressions. Further, to evaluate IOS precision in vivo.
Methods: Four reference-bodies were bonded to the buccal surfaces of upper premolars and incisors in five subjects. After three reference-scans, ATOS Core 80 (ATOS), subjects were scanned three times with three IOS systems: 3M True Definition (3M), CEREC Omnicam (OMNI) and Trios 3 (TRIOS). One conventional impression (IMPR) was taken, 3M Impregum Penta Soft, and poured models were digitized with laboratory scanner 3shape D1000 (D1000). Best-fit alignment of reference-bodies and 3D Compare Analysis was performed. Precision of ATOS and D1000 was assessed for quantitative evaluation and comparison. Accuracy of IOS and IMPR were analyzed using ATOS as reference. Precision of IOS was evaluated through intra-system comparison.
Results: Precision of ATOS reference scanner (mean 0.6 mu m) and D1000 (mean 0.5 mu m) was high. Pairwise multiple comparisons of reference-bodies located in different tooth positions displayed a statistically significant difference of accuracy between two scanner-groups: 3M and TRIOS, over OMNI (p value range 0.0001 to 0.0006). IMPR did not show any statistically significant difference to IOS. However, deviations of IOS and IMPR were within a similar magnitude. No statistical difference was found for IOS precision.
Conclusion: The methodology can be used for assessing accuracy of IOS and IMPR in vivo in up to five units bilaterally from midline. 3M and TRIOS had a higher accuracy than OMNI. IMPR overlapped both groups. Clinical significance: Intraoral scanners can be used as a replacement for conventional impressions when restoring up to ten units without extended edentulous spans.
Objectives: To evaluate an in situ reference acquisition method for implant positions in complete edentulous maxillae using an industrial scanner and allowing for in vivo trueness analysis of the restorative workflow. To assess in vivo trueness and precision of intraoral scanners (IOS) using different acquisition protocols. Furthermore, to compare IOS trueness with impression-based models and implant-supported fixed dentures (IFD) in a parallel study on the same cohort using the same in situ reference scan.
Methods: Six scan-bodies mounted to maxillary implants in five subjects were reference scanned (REF) using an industrial scanner. Subjects were scanned with IOS three times using three different protocols: control (CT), dental floss assisted (DF), and acrylic splint (SP). CAD-files of scan-bodies with inter-aligned analogues were geometry-aligned to REF, and SP. Scan-bodies were aligned to CT and DF in proprietary dental laboratory software and exported with analogue positions. Resulting six CAD-analogues per scan were Globally Aligned using a consistent geometry-based alignment. Deviations were computed after a Reference Point System Alignment at the implant/prosthetic platform for Cartesian axes with a linear Resultant.
Results: Resultant trueness was CT: 41±11 μm, DF: 49±22 μm, SP: 55±8 μm. Resultant precision was CT: 48±7μm, DF: 50±7 μm, SP: 45±6 μm
Conclusions: This method is applicable for assessing trueness of maxillary full-arch implant scans in vivo. The CTprotocol was most accurate. CT trueness showed no difference to digitised impression-based models in parallelstudy. CT was more accurate than IFD in a parallel study. CT displayed similar numerical trueness as existing invitro studies.
Critical significance: Using IOS to acquire full-arch implant scans is controversial. The modified protocol in thispilot shows promising results in the maxilla where great care was taken to manage non-attached tissues when amodified scanning pattern was used. However, other IOS may show varying results in vivo. A completed scan doesnot necessarily equate to an accurate scan.
Objectives: To evaluate a method for in situ reference acquisition of implant positions in complete edentulous maxillae using an industrial scanner. To assess in vivo trueness of full-arch implant-supported fixed dentures (IFD) and dental models based on conventional impressions.
Methods: In five subjects, scan-bodies were mounted to six maxillary implants and scanned three times using an industrial scanner (REF). Original impression-based models used to manufacture existing IFDs, (MOD1), and models fabricated from new polyether impressions, (MOD2), were scanned three times with a laboratory scanner. Scan-bodies were aligned and exported with analogue positions corresponding to implant positions. Implant analogues were mounted onto existing IFDs and scanned three times (BRIDGE). CAD files of scan-bodies with inter-aligned CAD-analogues were geometry-aligned to REF. CAD-analogues were aligned to exported files of MOD1 and MOD2, and to BRIDGE. Resulting six CAD-analogues were Globally Aligned using a consistent geometry-based alignment. Deviations were computed after a Reference Point System Alignment at the implant/prosthetic platform for Cartesian axes and a linear Resultant.
Results:REF precision was 9.3 ± 1 µm. In vivo trueness for Resultant was MOD1: 36±16 µm, MOD2: 28±7 µm and BRIDGE: 70±23 µm, where MOD1 and MOD2 were statistically significantly different from BRIDGE. In vitro manufacturing trueness of Resultant when MOD1 acted reference for BRIDGE was: 69 ± 22.
Conclusions: This method can be applied for assessing in vivo trueness. CAD/CAM processed IFD showed deviations twice that of impression-based models, however, errors from impressions and subsequent model scans were not additive to the entire workflow.
To develop an accurate and suitable method for measuring the embryonic heart rate in vitro, a system combining Laplacian eigenmaps and empirical mode decomposition has been proposed. The proposed method assess the heart activity in two steps; signal generation and heart signal analysis. Signal generation is achieved by Laplacian eigenmaps (LEM) in conjunction with correlation co-efficient, while the signal analysis of the heart motion has been performed by the modified empirical mode decomposition (EMD). LEM helps to find the template for the atrium and the ventricle respectively, whereas EMD helps to find the non-linear trend term without defining any regression model. The proposed method also removes the motion artifacts produced due to the the non-rigid deformation in the shape of the embryo, the noise induced during the data acquisition, and the higher order harmonics. To check the authenticity of the proposed method, 151 videos have been investigated. Experimental results demonstrate the superiority of the proposed method in comparison to three recent methods.
The management of complex mandible fractures, i.e severely comminuted or fractures of edentulous/atrophic mandibles, can be challenging. This is due to the three-dimensional loss of bone, which limits the possibility for accurate anatomic reduction. Virtual surgery planning (VSP) can provide improved accuracy and shorter operating times, but is often not employed for trauma cases because of time constraints and complex user interfaces limited to two-dimensional interaction with three-dimensional data. In this study, we evaluate the accuracy, precision, and time efficiency of the Haptic Assisted Surgery Planning system (HASP), an in-house VSP system that supports stereo graphics, six degrees-of-freedom input and haptics, to improve the surgical planning. Three operators performed planning in HASP on Computed Tomography (CT) and Come Beam Computed Tomography (CBCT) images of a plastic skull model and on twelve retrospective cases with complex mandible fractures. The result shows an accuracy and reproducibility of less than 2mm when using HASP, with an average planning time of 15 minutes, including time for segmentation in the software BoneSplit. This study presents an in-house haptic assisted planning tool for cranio-maxillofacial surgery with high usability that can be used for preoperative planning and evaluation of complex mandible fractures.
Real‐time virtual reality requires efficient rendering methods to deal with high‐ resolution stereoscopic displays and low latency head‐tracking. Our proposed RayCaching method renders isosurfaces of large volume datasets by amortizing raycasting over several frames and caching primary rays as small bricks that can be efficiently rasterized. An occupancy map in form of a clipmap provides level of detail and ensures that only bricks corresponding to visible points on the isosurface are being cached and rendered. Hard shadows and ambient occlusion from secondary rays are also accumulated and stored in the cache. Our method supports real‐time isosurface rendering with dynamic isovalue and allows stereoscopic visualization and exploration of large volume datasets at framerates suitable for virtual reality applications.
Exploiting parallelism in haptic rendering algorithms for rigid body collision simulation can be difficult due to the haptic feedback loop imposing strict real-time constraints on the computations. In this paper, we show that the classical Voxmap PointShell algorithm can be efficiently vectorised via the single-program multiple-data (SPMD) programming model of the Intel SPMD Program Compiler (ISPC) compiler and programming language. Our vectorised version provides an average 3.0x speedup compared to a corresponding scalar implementation, for a static hierarchical pointshell on a single CPU core. In addition, we propose a dynamic pointshell that does not require any pre-processing and allows a fixed point budget to be set per frame. The speedup obtained by the vectorisation means that a larger number of contact queries can be processed per haptic frame, while maintaining a desired haptic framerate. In an empirical study, we demonstrate that this increased fidelity in collision simulation translates directly to a higher user accuracy in assembly of fractured virtual objects.
User-friendly virtual surgery planning(VSP) systems for reconstructive surgery, such as cranio-maxillofacial (CMF) surgery, that can be used by the surgeons themselves without help of a technician have the potential to shorten the pre-operative planning from days to hours. An important part of such systems is the design of surgical guides and plates for osteosynthesis. We describe a method for generating surgical guide and plate models from computed tomography (CT) images, using signed distance fields and constructive solidgeometry (CSG). We implement the method as an extension to our Haptics-Assisted Surgery Plan-ning (HASP) system that enables a user to quickly design guide and plate models with stereo graphics and haptic feedback. We find that surgical guide and plate models can be efficiently generated from segmented CT images with our method. We also find that an anti-aliased distance transform can improve the accuracy and precision of the modelingin this application.
The wrist is the most common location for long-bone fractures in humans. To evaluate the healing process of such fractures, it is of interest to measure the fracture displacement, particularly the angle between the joint line and the long axis of the fractured long bone. We propose to measure this angle in 3D computed tomography (CT) images of fractured wrists. As a first step towards this goal, we here present a fast and precise semi-automatic method for determining the long axis of the radius bone in CT images. To facilitate user interaction in 3D, we utilize stereo graphics, head tracking, 3D input, and haptic feedback.
The clinically established method to assess the displacement of a distal radius fracture is to manually measure two reference angles,the dorsal angle and the radial angle, in consecutive 2D X-ray images of the wrist. This approach has the disadvantage of being sensitive to operator errors since the measurements are performed on 2D projections of a 3D structure. In this paper, we present a semi-automatic system for measuring relative changes in the dorsal angle in 3D computed tomography (CT) images of fractured wrists. We evaluate the proposed 3D measurement method on 28 post-operative CT images of fractured wrists and compare it with the radiographic 2D measurement method used in clinical practice. The results show that our proposed 3D measurement method has a high intra- and inter-operator precision and is more precise and robust than the conventional 2D measurement method.