| 1. |
- Svensson, Lennart, et al.
(författare)
-
ProViz : a tool for explorative 3-D visualization and template matching in electron tomograms
- 2017
-
Ingår i: Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization. - : Taylor & Francis. - 2168-1163 .- 2168-1171. ; 5:6, s. 446-454
-
Tidskriftsartikel (refereegranskat)abstract
- Visual understanding is a key aspect when studying electron tomography data-sets, aside quantitative assessments such as registration of high-resolution structures. We here present the free software tool ProViz (Protein Visualization) for visualisation and template matching in electron tomograms of biological samples. The ProViz software contains methods and tools which we have developed, adapted and computationally optimised for easy and intuitive visualisation and analysis of electron tomograms with low signal-to-noise ratio. ProViz complements existing software in the application field and serves as an easy and convenient tool for a first assessment and screening of the tomograms. It provides enhancements in three areas: (1) improved visualisation that makes connections as well as intensity differences between and within objects or structures easier to see and interpret, (2) interactive transfer function editing with direct visual result feedback using both piecewise linear functions and Gaussian function elements, (3) computationally optimised template matching and tools to visually assess and interactively explore the correlation results. The visualisation capabilities and features of ProViz are demonstrated on various biological volume data-sets: bacterial filament structures in vitro, a desmosome and the transmembrane cadherin connections therein in situ, and liposomes filled with doxorubicin in solution. The explorative template matching is demonstrated on a synthetic IgG data-set.
|
|
| 2. |
- Lif, Hanna M., et al.
(författare)
-
Persistent discrepancies in orbital morphology after surgical treatment of unicoronal craniosynostosis : a critical image-based analysis
- 2023
-
Ingår i: Journal of Neurosurgery. - : Journal of Neurosurgery Publishing Group (JNSPG). - 1933-0707 .- 1933-0715. ; 31:6, s. 574-583
-
Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: Unicoronal craniosynostosis (UCS) is characterized by complex orbital deformity and is typically treated by asymmetrical fronto-orbital remodeling (FOR) during the 1st year of life. The aim of this study was to elucidate to what extent orbital morphology is corrected by surgical treatment.METHODS: The extent to which orbital morphology was corrected by surgical treatment was tested by analysis of differences in volume and shape between synostotic, nonsynostotic, and control orbits at two time points. In total, 147 orbits were analyzed from patient CT images obtained preoperatively (mean age 9.3 months), at follow-up (mean age 3.0 years), and in matched controls. Semiautomatic segmentation software was used to determine orbital volume. For analysis of orbital shape and asymmetry, geometrical models, signed distance maps, principal modes of variation, and three objective parameters (mean absolute distance, Hausdorff distance, and dice similarity coefficient) were generated by statistical shape modeling.RESULTS: Orbital volumes on both the synostotic and nonsynostotic sides were significantly smaller at follow-up than volumes in controls and significantly smaller both preoperatively and at follow-up than orbital volumes on the nonsynostotic side. Significant differences in shape were identified globally and locally, both preoperatively and at 3 years of age. Compared with controls, deviations were mostly found on the synostotic side at both time points. Asymmetry between synostotic and nonsynostotic sides was significantly decreased at follow-up, but not compared with the inherent asymmetry of controls. On a group level, the preoperative synostotic orbit was mainly expanded in the anterosuperior and anteroinferior regions and smallest on the temporal side. At follow-up, the mean synostotic orbit was still larger superiorly but also expanded in the anteroinferior temporal region. Overall, the morphology of nonsynostotic orbits was more simi-lar to that of controls than to synostotic orbits. However, the individual variation in orbital shape was greatest for nonsynostotic orbits at follow-up.CONCLUSIONS: In this study, the authors presented what is, to their knowledge, the first objective automatic 3D bony evaluation of orbital shape in UCS, defining in greater detail than has been done previously how synostotic orbits differ from nonsynostotic and control orbits, and how orbital shape changes from 9.3 months of age preoperatively to 3 years of age at the postoperative follow-up. Despite surgical treatment, both local and global deviations in shape persist. These findings may have implications for future directions in the development of surgical treatment. Future studies connecting orbital morphology to ophthalmic disorders, aesthetics, and genetics could provide further insight to enable better outcomes in UCS.
|
|
| 3. |
- Levasseur, Julie, et al.
(författare)
-
Orbital volume and shape in Treacher Collins syndrome
- 2018
-
Ingår i: Journal of Cranio-Maxillofacial Surgery. - : CHURCHILL LIVINGSTONE. - 1010-5182 .- 1878-4119. ; 46:2, s. 305-311
-
Tidskriftsartikel (refereegranskat)abstract
- Orbito-palpebral reconstruction is a challenge in Treacher Collins syndrome (TCS). This study investigates orbital phenotypes in TCS using cephalometry and orbital shape analysis. Eighteen TCS and 52 control patients were included in this study, using the Dr Warehouse database. Orbital cephalometry was based on 20 landmarks, 10 planes, 16 angles, and 22 distances. Orbits were segmented. Registration-based, age-specific mean models were generated using semi-automatic segmentation, and aligned and compared using color-coded distance maps - mean absolute distance (MAD), Hausdorff distance (HD), and Dice similarity coefficient (DSC). Symmetry was assessed by mirroring and DSC computing. Central orbital depth ( COD) and medial orbital depth ( MOD) allowed 100% of orbits to be classified. COD and lateral orbital depth (LOD) were different from the controls. Average MAD between TCS and controls was <= 1.5 mm, while for HD it was > 1.5 mm, and for DSC <1. TCS orbits were more asymmetrical than controls, and orbital volumes were smaller when age was considered as a confounding factor, and had a trend for normalization with age. This report emphasizes the importance of combining different morphometric approaches in the phenotype characterization of non-trivial structures such as the orbit, and supports composite skeletal and soft-tissue strategies for the management of the peri-orbital region.
|
|
| 4. |
- Moafi, Roya, et al.
(författare)
-
Haptic-Assisted Surgical Planning (HASP) in a Case of Bilateral Mandible Fracture
- 2022
-
Ingår i: International Medical Case Reports Journal. - : Dove Medical Press Limited. - 1179-142X. ; 15, s. 707-712
-
Tidskriftsartikel (refereegranskat)abstract
- Restoring normal skeletal anatomy in patients with complex trauma to the mandible can be difficult, the difficulty often increasing with an edentulous mandible. This study describes a case of a displaced edentulous bilateral mandibular fracture, which was preoperatively planned with the in-house haptic-assisted surgery planning system (HASP). A model of the virtually restored mandible was 3D-printed at the hospital and a reconstruction plate was outlined beforehand with the printed mandible as a template and served as a guide during surgery. This case suggests HASP as a valuable preoperative tool in the planning phase when dealing with maxillofacial trauma cases. With the application of virtual planning, the authors could analyze the desired outcome and were further supported in surgery by the guidance of the reconstruction plate outlined on the restored model of the mandible.
|
|
| 5. |
- Nilsson, Johanna, et al.
(författare)
-
Evaluation of in-house, haptic assisted surgical planning for virtual reduction of complex mandibular fractures
- 2021
-
Ingår i: International Journal of Computer Assisted Radiology and Surgery. - : Springer. - 1861-6410 .- 1861-6429. ; 16:6, s. 1059-1068
-
Tidskriftsartikel (refereegranskat)abstract
- 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.
|
|
| 6. |
- Nysjö, Johan, 1985-
(författare)
-
Interactive 3D Image Analysis for Cranio-Maxillofacial Surgery Planning and Orthopedic Applications
- 2016
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Modern medical imaging devices are able to generate highly detailed three-dimensional (3D) images of the skeleton. Computerized image processing and analysis methods, combined with real-time volume visualization techniques, can greatly facilitate the interpretation of such images and are increasingly used in surgical planning to aid reconstruction of the skeleton after trauma or disease. Two key challenges are to accurately separate (segment) bone structures or cavities of interest from the rest of the image and to interact with the 3D data in an efficient way. This thesis presents efficient and precise interactive methods for segmenting, visualizing, and analysing 3D computed tomography (CT) images of the skeleton. The methods are validated on real CT datasets and are primarily intended to support planning and evaluation of cranio-maxillofacial (CMF) and orthopedic surgery.Two interactive methods for segmenting the orbit (eye-socket) are introduced. The first method implements a deformable model that is guided and fitted to the orbit via haptic 3D interaction, whereas the second method implements a user-steered volumetric brush that uses distance and gradient information to find exact object boundaries.The thesis also presents a semi-automatic method for measuring 3D angulation changes in wrist fractures. The fractured bone is extracted with interactive mesh segmentation, and the angulation is determined with a technique based on surface registration and RANSAC.Lastly, the thesis presents an interactive and intuitive tool for segmenting individual bones and bone fragments. This type of segmentation is essential for virtual surgery planning, but takes several hours to perform with conventional manual methods. The presented tool combines GPU-accelerated random walks segmentation with direct volume rendering and interactive 3D texture painting to enable quick marking and separation of bone structures. It enables the user to produce an accurate segmentation within a few minutes, thereby removing a major bottleneck in the planning procedure.
|
|
| 7. |
- Nysjö, Johan, 1985-, et al.
(författare)
-
Rapid and Precise Orbit Segmentation through Interactive 3D Painting
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- In this paper, we present an efficient interactive tool for segmenting and measuring the volume of the bony orbit (eye-socket) in computed tomography (CT) images. The tool implements a 3D painting interface that allows the user to quickly segment or "paint" the fat and soft-tissue content of the orbit by sweeping a volumetric brush over the image. The brush modifies and updates the segmentation result in real-time and takes distance and gradient information into account to fill out and find the exact boundaries of the orbit. A smooth and consistent delineation of the anterior boundary is obtained by fitting a thin-plate spline to user-selected landmarks. We evaluate the tool on 10 CT images of intact and fractured orbits and show that it achieves high intra- and inter-operator precision (mean spatial overlap 95%, less than 1 ml volume variability) and produces segmentation results that are similar to manually corrected reference segmentations, but only requires a few minutes of interaction time.
|
|
| 8. |
- Sandy, Ronak, et al.
(författare)
-
Orbital shape in intentional skull deformations and adult sagittal craniosynostoses
- 2018
-
Ingår i: Journal of Anatomy. - : Wiley. - 0021-8782 .- 1469-7580. ; 233:3, s. 302-310
-
Tidskriftsartikel (refereegranskat)abstract
- Intentional cranial deformations are the result of external mechanical forces exerted on the skull vault that modify the morphology of various craniofacial structures such as the skull base, the orbits and the zygoma. In this controlled study, we investigated the 3D shape of the orbital inner mould and the orbital volume in various types of intentional deformations and in adult non-operated scaphocephaly - the most common type of craniosynostosis - using dedicated morphometric methods. CT scans were performed on 32 adult skulls with intentional deformations, 21 adult skull with scaphocephaly and 17 non-deformed adult skulls from the collections of the Museum national d'Histoire naturelle in Paris, France. The intentional deformations group included six skulls with Toulouse deformations, eight skulls with circumferential deformations and 18 skulls with antero-posterior deformations. Mean shape models were generated based on a semi-automatic segmentation technique. Orbits were then aligned and compared qualitatively and quantitatively using colour-coded distance maps and by computing the mean absolute distance, the Hausdorff distance, and the Dice similarity coefficient. Orbital symmetry was assessed after mirroring, superimposition and Dice similarity coefficient computation. We showed that orbital shapes were significantly and symmetrically modified in intentional deformations and scaphocephaly compared with non-deformed control skulls. Antero-posterior and circumferential deformations demonstrated a similar and severe orbital deformation pattern resulting in significant smaller orbital volumes. Scaphocephaly and Toulouse deformations had similar deformation patterns but had no effect on orbital volumes. This study showed that intentional deformations and scaphocephaly significantly interact with orbital growth. Our approach was nevertheless not sufficient to identify specific modifications caused by the different types of skull deformations or by scaphocephaly.
|
|
| 9. |
|
|
| 10. |
- Unander-Scharin, Jesper, et al.
(författare)
-
Deep learning-based segmentation of intracranial volume and calvarial bones in pre- and postoperative CT-images of children with sagittal craniosynostosis
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background Image-based analysis of intracranial volume and craniofacial bones is highly valuable in studying outcome of surgery for craniosynostosis. Conventional segmentation of intracranial volume and calvarial bones is time consuming and subjective. Here, a deep learning approach is applied to perform fully automated image segmentation of the intracranial volume and calvarial bones in patients with non-syndromic sagittal craniosynostosis. We apply the established UNet architecture with its subsequent improvements as it has been used in numerous works for biomedical image segmentation since its inception.MethodsPre- and postoperative CT scans were collected from 50 + 52 patients with non-syndromic sagittal craniosynostosis. All participants underwent surgery between the ages of three and six months using the H-craniectomy technique. Manual reference annotations of the intracranial volume and calvarial bones (frontal-, parietal- and occipital bones) were produced using in-house developed software and further refined in 3DSlicer. Modified UNets with a ResNet encoder were trained to automate the segmentation tasks. Networks were trained locally on a single NVIDIA RTX 2080 graphics card and evaluated using 10-fold cross validation. ResultsThe average dice score for the intracranial volume networks was 0.983, and the extracted volume measurements deviated with a mean absolute error of 8.0 ± 5.4 ml from references. An average dice score of 0.798 was achieved for the calvarial bones network, subsequent descriptive statistics were extracted from the reference and generated segmentations to assess Hounsfield units as a proxy for bone density. ConclusionWe present a fully automated deep learning approach to assess intracranial volume and attributes of calvarial bones from pre- and postoperative CT images in patients with non-syndromic sagittal craniosynostosis. This framework can be applied to multi-center research with large study populations in a time efficient manner, and can be further developed for additional applications in craniofacial surgery.
|
|
| 11. |
- Unander-Scharin, Jesper, et al.
(författare)
-
Secondary Coronal Synostosis After Early Surgery for Sagittal Craniosynostosis : Implications for Cranial Growth
- 2020
-
Ingår i: The Journal of Craniofacial Surgery. - : Lippincott Williams & Wilkins. - 1049-2275 .- 1536-3732. ; 32:1, s. 113-117
-
Tidskriftsartikel (refereegranskat)abstract
- Secondary Coronal Synostosis (SCS) in patients operated for non-syndromic Sagittal Craniosynostosis is a postoperative phenomenon with unclear implications. The aim of this study was to investigate whether SCS is a negative or a benign occurrence in the postoperative course. The authors hypothesized that SCS is related to reduced cranial growth and intracranial hypertension. Thirty-one patients operated for SC at an early age with the H-craniectomy technique were included in the study. Associations between SCS and cranial shape, growth, and signs of intracranial hypertension were analyzed. Intracranial volume distribution was assessed by measuring partial intracranial volumes defined by skull base landmarks. A total of 12/31 patients developed SCS during the postoperative course. The presence of SCS was associated with a higher prevalence of gyral impressions and a larger normalization of Cranial Index due to less growth in the anteroposterior plane. The SCS group had a smaller postoperative intracranial volume due to less posterior intracranial volume as well as less growth in head circumference. Whether this is a growth restriction caused by the SCS or a secondary effect of less primary brain growth remains to be determined. However, the correlation between SCS, less cranial growth and gyral impressions does imply that SCS should be taken into consideration during clinical follow-up as a potentially adverse event.
|
|
