Polymorph segmentation representation for medical image computing

Molecular MR Imaging of Prostate Cancer by Specified Iron Oxide Nanoparticles With PSMA-11 Peptides: A Preclinical Study

BACKGROUND

Prostate-specific membrane antigen (PSMA) can provide a prostate cancer (PCa) detection approach in positron emission tomography (PET) using Food and Drug Administration (FDA)-approved PSMA-11 peptide. There are some studies evaluated magnetic-nanoprobes for PSMA detection by MRI, using non-FDA-approved ligands including antibodies or peptides, which are not as specific as PSMA-11.

PURPOSE

To assess targeted iron oxide nanoparticles (IONPs) by PSMA-11 peptides as a potential specific nano-molecular probes to investigate a PSMA+ PCa-xenograft model by MRI.

STUDY TYPE

Prospective.

ANIMAL MODEL

Twenty male C57BL6 nude mice induced subcutaneously PSMA+ LNCaP cell line tumor.

FIELD STRENGTH/SEQUENCE

1.5 T, T2-W Fast Spin echo and T2*-W Gradient echo.

ASSESSMENT

Coated IONPs with Carboxymethylated-dextran (DNPs) and with bovine serum albumin (BNPs), as well as, targeted DNPs with PSMA-11-HYNIC peptide (TDNPs) and targeted BNPs with PSMA-11-HBED peptide (TBNPs) were injected intravenously with dose 2.8 mg Fe/kg. Coronal T2-W and the T2*-W images were obtained before and 4 hours and 6 hours post-injection. Signal intensity (SI) and relative signal enhancement (RSE) were computed in two- and three-dimensional analyses. Histological analysis of tumors was evaluated, and the Fe distribution within the body based on atomic absorption spectroscopy was calculated.

STATISTICAL TESTS

One-way ANOVA followed by Tukey's multiple comparison test, Paired-samples T-test, P < 0.05 was considered significant.

RESULTS

A reduction in T2-W SI was achieved as 22 ± 7%, 59 ± 3%, 65 ± 5%, and 78 ± 3% respectively for BNPs, TBNPs, DNPs, and TDNPs 6 hours post-injection. The most difference between targeted and non-targeted groups was observed at 6 hours for PSMA-11-HBED, and at 4 hours for PSMA-11-HYNIC. RSE indicated 88.6 ± 3.1% and 80.7 ± 3.2% enhanced contrast between tumor and muscle region for TBNPs and TDNPs on T2*-W images.

CONCLUSIONS

Both TBNPs and TDNPs are promising novel nano-molecular probes for PSMA+ PCa tumor detection. The injection dose of non-targeted IONPs can be reduced by using targeted nanoprobes three times for BNPs and two times for DNPs.

EVIDENCE LEVEL

1 TECHNICAL EFFICACY: Stage 1.

Vein of Galen aneurysmal malformation: does size affect outcome?

PURPOSE

To validate a semiautomated method for segmenting vein of Galen aneurysmal malformations (VGAM) and to assess the relationship between VGAM volume and other angioarchitectural features, cardiological findings, and outcomes.

METHODS

In this retrospective study, we selected all subjects with VGAM admitted to the Gaslini Children's Hospital between 2009 and 2022. Clinical data were retrieved from electronic charts. We compared 3D-Slicer segmented VGAM volumes obtained by two independent observers using phase-contrast MR venography to those obtained with manual measurements performed on T2-weighted images. The relationship between VGAM volumes and clinical and neuroimaging features was then explored.

RESULTS

Forty-three subjects with VGAM (22 males, mean age 6.56 days) were included in the study. Manual and semiautomated VGAM volumes were well correlated for both readers (r = 0.86 and 0.82, respectively). Regarding reproducibility, the inter-rater interclass correlation coefficients were 0.885 for the manual method and 0.992 for the semiautomated method (p < 0.001). The standard error for repeated measures was lower for the semiautomated method (0.04 versus 0.40 of manual method). Higher VGAM volume was associated with superior sagittal sinus narrowing, jugular bulb stenosis, and aqueductal stenosis (p < 0.05). A weak correlation was found between VGAM volume and straight sinus dilatation (r = 0.331) and superior sagittal sinus index (r =  - 0.325). No significant associations were found with cardiac findings, post-embolization complications, and outcome (p > 0.05).

CONCLUSIONS

Semiautomated VGAM volumetry is feasible and reliable with improved reproducibility compared to the manual method. VGAM volume is not a prognostic factor for clinical outcome, but it is related to other venous findings with potential hemodynamic effects.

Head model dataset for mixed reality navigation in neurosurgical interventions for intracranial lesions

Mixed reality navigation (MRN) technology is emerging as an increasingly significant and interesting topic in neurosurgery. MRN enables neurosurgeons to "see through" the head with an interactive, hybrid visualization environment that merges virtual- and physical-world elements. Offering immersive, intuitive, and reliable guidance for preoperative and intraoperative intervention of intracranial lesions, MRN showcases its potential as an economically efficient and user-friendly alternative to standard neuronavigation systems. However, the clinical research and development of MRN systems present challenges: recruiting a sufficient number of patients within a limited timeframe is difficult, and acquiring low-cost, commercially available, medically significant head phantoms is equally challenging. To accelerate the development of novel MRN systems and surmount these obstacles, the study presents a dataset designed for MRN system development and testing in neurosurgery. It includes CT and MRI data from 19 patients with intracranial lesions and derived 3D models of anatomical structures and validation references. The models are available in Wavefront object (OBJ) and Stereolithography (STL) formats, supporting the creation and assessment of neurosurgical MRN applications.

Antenatal Endotoxin Induces Dysanapsis in Experimental Bronchopulmonary Dysplasia

Bronchopulmonary dysplasia (BPD), the chronic lung disease of prematurity, is characterized by impaired lung development with sustained functional abnormalities due to alterations of airways and the distal lung. Although clinical studies have shown striking associations between antenatal stress and BPD, little is known about the underlying pathogenetic mechanisms. Whether dysanapsis, the concept of discordant growth of the airways and parenchyma, contributes to late respiratory disease as a result of antenatal stress is unknown. We hypothesized that antenatal endotoxin (ETX) impairs juvenile lung function as a result of altered central airway and distal lung structure, suggesting the presence of dysanapsis in this preclinical BPD model. Fetal rats were exposed to intraamniotic ETX (10 μg) or saline solution (control) 2 days before term. We performed extensive structural and functional evaluation of the proximal airways and distal lung in 2-week-old rats. Distal lung structure was quantified by stereology. Conducting airway diameters were measured using micro-computed tomography. Lung function was assessed during invasive ventilation to quantify baseline mechanics, response to methacholine challenge, and spirometry. ETX-exposed pups exhibited distal lung simplification, decreased alveolar surface area, and decreased parenchyma-airway attachments. ETX-exposed pups exhibited decreased tracheal and second- and third-generation airway diameters. ETX increased respiratory system resistance and decreased lung compliance at baseline. Only Newtonian resistance, specific to large airways, exhibited increased methacholine reactivity in ETX-exposed pups compared with controls. ETX-exposed pups had a decreased ratio of FEV in 0.1 second to FVC and a normal FEV in 0.1 second, paralleling the clinical definition of dysanapsis. Antenatal ETX causes abnormalities of the central airways and distal lung growth, suggesting that dysanapsis contributes to abnormal lung function in juvenile rats.

The role of 3D technology in the practical education of congenital coarctation and its treatment-a feasibility pilot study

BACKGROUND

Coarctation of the aorta (CoA) is a congenital disease with an incidence of 4 out of 10,000 live births, therefore proper education of its treatment is essential. Understanding the disease and the wide array of treatment options is often difficult. Additive manufacturing technology can be used to produce 3D printed hands-on surgical training tools (HOSTT), which can be used for the education and practical training of CoA. This study aimed to investigate the effectiveness of a 3D printable HOSTT for the simulation of coarctation surgery, and it' possible role in practical education.

METHODS

Participants were medical students of Semmelweis University between the second and sixth academic year. A virtual 3D model of an aorta with CoA was generated from a computed tomography angiography scan. Each participant received a 3D-printed aorta phantom and performed either one of four surgical treatment modalities. The simulated surgeries included end-to-end anastomosis, end-to-side anastomosis, prosthetic patch, and subclavian flap aortoplasty. Participants provided feedback, evaluating their understanding of the disease and its treatment by the four surgical reconstruction modalities on a seven-point Likert scale before and after the sessions.

RESULTS

21 medical students participated in this study. Participants' average rating of their understanding of CoA disease and it treatment options before practical training was 4.62 ± 1.07. After training, their average rating increased to 6.19 ± 1.08, showing statistically significant difference.

CONCLUSIONS

Within this study's limitations, the applied HOSTT, manufactured using 3D printing, was effective for the practical training of CoA's surgical treatment methods for medical students.

3D Fractal Dimension Analysis: Prognostic Value of Right Ventricular Trabecular Complexity in Participants with Arrhythmogenic Cardiomyopathy

BACKGROUND

Arrhythmogenic cardiomyopathy (ACM) is characterized by progressive myocardial fibro-fatty infiltration accompanied by trabecular disarray. Traditionally, two-dimensional (2D) instead of 3D fractal dimension (FD) analysis has been used to evaluate trabecular disarray. However, the prognostic value of trabecular disorder assessed by 3D FD measurement remains unclear.

PURPOSE

To investigate the prognostic value of right ventricular trabecular complexity in ACM patients using 3D FD analysis based on cardiac MR cine images.

STUDY TYPE

Retrospective.

POPULATION

85 ACM patients (mean age: 45 ± 17 years, 52 male).

FIELD STRENGTH/SEQUENCE

3.0T/cine imaging, T2-short tau inversion recovery (T2-STIR), and late gadolinium enhancement (LGE).

ASSESSMENT

Using cine images, RV (right ventricular) volumetric and functional parameters were obtained. RV trabecular complexity was measured with 3D fractal analysis by box-counting method to calculate 3D-FD. Cox and logistic regression models were established to evaluate the prognostic value of 3D-FD for major adverse cardiac events (MACE).

STATISTICAL TESTS

Cox regression and logistic regression to explore the prognostic value of 3D-FD. C-index, time-dependent receiver operating characteristic (ROC) curves and area under the ROC curve (AUC) to evaluate the incremental value of 3D-FD. Intraclass correlation coefficient for interobserver variability. P < 0.05 indicated statistical significance.

RESULTS

26 MACE were recorded during the 60 month follow-up (interquartile range: 48-67 months). RV 3D-FD significantly differed between ACM patients with MACE (2.67, interquartile range: 2.51 ~ 2.81) and without (2.52, interquartile range: 2.40 ~ 2.67) and was a significant independent risk factor for MACE (hazard ratio, 1.02; 95% confidence interval: 1.01, 1.04). In addition, prognostic model fitness was significantly improved after adding 3D-FD to RV global longitudinal strain, LV involvement, and 5-year risk score separately.

DATA CONCLUSION

The myocardial trabecular complexity assessed through 3D FD analysis was found associated with MACE and provided incremental prognostic value beyond conventional ACM risk factors.

EVIDENCE LEVEL

4 TECHNICAL EFFICACY: Stage 1.

Quantitative image signature and machine learning-based prediction of outcomes in cerebral cavernous malformations

PURPOSE

There is increasing interest in novel prognostic tools and predictive biomarkers to help identify, with more certainty, cerebral cavernous malformations (CCM) susceptible of bleeding if left untreated. We developed explainable quantitative-based machine learning models from magnetic resonance imaging (MRI) in a large CCM cohort to demonstrate the value of artificial intelligence and radiomics in complementing natural history studies for hemorrhage and functional outcome prediction.

MATERIALS AND METHODS

One-hundred-eighty-one patients from a prospectively registered cohort of 366 adults with CCM were included. Fluid attenuated inversion recovery (FLAIR) T2-weighted brain images were preprocessed, and CCM and surrounding edema were segmented before radiomic feature computation. Minority class oversampling, dimensionality reduction and feature selection methods were applied. With prospective hemorrhage as primary outcome, machine learning models were built, cross-validated, and compared using clinico-radiologic, radiomic, and combined features. SHapley Additive exPlanations (SHAP) was used for interpretation to determine the radiomic features with most contribution to hemorrhage prediction.

RESULTS

The highest performances in hemorrhage predictions on the test set were combining radiomic and clinico-radiological features with an area under the curve (AUC) of 83% using linear regression and selected features, and an F1 score of 61% and 85% sensitivity using K-nearest neighbors with principal component analysis (PCA). Multilayer perceptron had the best performance predicting modified Rankin Scale ≥ 2 with an AUC of 74% using PCA derived features. For interpretation of the selected radiomic signature XGBoost model, Shapley additive explanations highlighted 6 radiomic features contributing the most to hemorrhage prediction.

CONCLUSION

Quantitative image-based modeling using machine learning has the potential to highlight novel imaging biomarkers that predict hemorrhagic and functional outcomes, ensuring more precise and personalized care for CCM patients.

Alveolar cleft reconstruction utilizing a particulate autogenous tooth graft and a novel split-thickness papilla curtain flap - A retrospective study

During secondary alveolar cleft grafting, the use of autogenous cancellous bone harvested from the iliac crest is still considered the gold standard. Due to the risk of donor-site morbidity and excessive graft resorption, alternative grafting materials (e.g. intraoral bone, xenografts) have been tested. Autogenous tooth bone graft (ATB) is a novel material derived from extracted teeth. ATB has successfully been used in pre-prosthetic and periodontal surgery for hard-tissue reconstruction. Seven patients with unilateral cleft lip and palate were treated with ATB, using their own deciduous teeth for grafting. Defects were accessed utilizing a novel split-thickness papilla curtain flap. Cone-beam computed tomography scans were taken prior to and 3 months following cleft surgery to assess graft integration, graft stability, and the volume of the newly formed hard tissues. Hard-tissue gain, as measured at the 3-month follow-up, averaged 0.65 cm3 ± 0.26 cm3. Results showed acceptable graft integration and stability at the 3-month follow-up, with no adverse effects or excessive resorption of the graft. The use of ATB might be a feasible alternative for alveolar cleft grafting. However, long-term studies using a large sample size are required to derive further conclusions.

Validation of a scanning technique with minimal compression for measuring muscle volume with freehand 3D ultrasound

Freehand 3D ultrasound (3D-US) is a promising technique for measuring muscle volume but it requires gel pads or water tanks to limit probe compression on the skin which makes it hard to use in clinical applications. Our objectives were to measure the effect of different compressions on muscle volume in order to assess the clinical applicability of a minimal compression method for lower limb muscles. 4 muscles of the lower limb on 15 healthy volunteers were scanned with a new commercial freehand 3D-US setup accessible to clinical experimentators. Each muscle was scanned with 3 levels of compression: standard compression, minimal compression and gel pad (method validated against MRI). Volume was calculated using software segmentation tools. Acquisitions and segmentations were done by the same examiner. There was a significant impact of standard compression on volume measurements, but no difference between minimal compression and gel pad. Standard compression underestimated volume with a mean bias of 16 mL. For minimal compression, 75 % of measured differences were below the predefined clinically acceptable limits of 10 mL. Mean bias for this method was 1.1 mL. In conclusion, standard compression in freehand 3D-US induces a systematic bias in volume calculations. But, with a trained examiner and the necessary precautions to minimize compression, this bias could be abolished and become acceptable in clinical applications. When a high accuracy is required, gel pads could still be important to consider.

Development and validation of a radiofrequency ablation treatment planning system for vertebral metastases

PURPOSE

Bone-targeted radiofrequency ablation (RFA) is widely used in the treatment of vertebral metastases. While radiation therapy utilizes established treatment planning systems (TPS) based on multimodal imaging to optimize treatment volumes, current RFA of vertebral metastases has been limited to qualitative image-based assessment of tumour location to direct probe selection and access. This study aimed to design, develop and evaluate a computational patient-specific RFA TPS for vertebral metastases.

METHODS

A TPS was developed on the open-source 3D slicer platform, including procedural setup, dose calculation (based on finite element modelling), and analysis/visualization modules. Usability testing was carried out by 7 clinicians involved in the treatment of vertebral metastases on retrospective clinical imaging data using a simplified dose calculation engine. In vivo evaluation was performed in a preclinical porcine model (n = 6 vertebrae).

RESULTS

Dose analysis was successfully performed, with generation and display of thermal dose volumes, thermal damage, dose volume histograms and isodose contours. Usability testing showed an overall positive response to the TPS as beneficial to safe and effective RFA. The in vivo porcine study showed good agreement between the manually segmented thermally damaged volumes vs. the damage volumes identified from the TPS (Dice Similarity Coefficient = 0.71 ± 0.03, Hausdorff distance = 1.2 ± 0.1 mm).

CONCLUSION

A TPS specifically dedicated to RFA in the bony spine could help account for tissue heterogeneities in both thermal and electrical properties. A TPS would enable visualization of damage volumes in 2D and 3D, assisting clinicians in decisions about potential safety and effectiveness prior to performing RFA in the metastatic spine.

Assessment of effectiveness and safety of thrombolytic therapy to pulmonary emboli by endobronchial ultrasound-guided transbronchial needle injection

Objective

Endobronchial ultrasound-guided transbronchial needle injection (EBUS-TBNI) may effectively treat acute pulmonary embolisms (PEs). Here, we assessed the effectiveness of clot dissolution and safety of tissue plasminogen activator (t-PA) injection using EBUS-TBNI in a 1-week survival study of a porcine PE model.

Methods

Six pigs with bilateral PEs were used: 3 for t-PA injection using EBUS-TBNI (TBNI group) and 3 for systemic administration of t-PA (systemic group). Once bilateral PEs were created, each 25 mg of t-PA injection using EBUS-TBNI for bilateral PEs (a total of 50 mg t-PA) and 100 mg of t-PA systemic administration was performed on day 1. Hemodynamic parameters, blood tests, and contrast-enhanced computed tomography scans were carried out at several time points. On day 7, pigs were humanely killed to evaluate the residual clot volume in the pulmonary arteries.

Results

The average of percent change of residual clot volumes was significantly lower in the TBNI group than in the systemic group (%: systemic group 36.6 ± 22.6 vs TBNI group 9.6 ± 6.1, P < .01) on day 3. Considering the elapsed time, the average decrease of clot volume per hour at pre-t-PA to post t-PA was significantly greater in the TBNI group than in the systemic group (mm3/hour: systemic 68.1 ± 68.1 vs TBNI 256.8 ± 148.1, P < .05). No hemorrhage was observed intracranially, intrathoracically, or intraperitoneally on any contrast-enhanced computed tomography images.

Conclusions

This study revealed that t-PA injection using EBUS-TBNI is an effective and safe way to dissolve clots.

Three-dimensional comparison of tooth-borne and tooth-bone-borne RME appliances: a randomized controlled trial with 5-year follow-up

OBJECTIVES

To compare the long-term skeletal effects of tooth-borne (TB) and tooth-bone-borne (TBB) rapid maxillary expansion in growing children, using 3D imaging.

MATERIALS AND METHODS

In total, 52 consecutive patients who met the eligibility criteria were recruited and allocated to either the TB group, mean age 9.3 years (SD 1.3), or the TBB group, mean age 9.5 years (SD 1.2). Cone-beam computed tomography records and plaster models were taken before (T0), directly after (T1), 1 year after (T2), and 5 years after expansion (T3).

RANDOMIZATION

Participants were randomly allocated in blocks of different sizes, using the concealed allocation principle in a 1:1 ratio. The randomization list was also stratified by sex to ensure homogeneity between groups.

BLINDING

Due to clinical limitations, only the outcome assessors were blinded to the groups to which the patients were allocated.

RESULTS

At T1, the midpalatal suture at its anterior part showed a statistically significant difference between the groups with a mean of 0.6 mm (CI 0.2-1.1) more expansion in the TBB group (P < 0.01). This difference was also more evident in boys at T1 with a mean of 0.8 mm (CI 0.2-1.4) (P < 0.01). These differences, however, blotted out at T2 and T3. The nasal width also showed similar differences between the groups, with a significantly larger expansion in the TBB group by a mean of 0.7 mm (CI 0.1-1.4) (P = 0.03). This group difference in favour of the TBB group was maintained at T2 (1.6 mm) and T3 (2.1 mm) (P < 0.01 T2 and T3, respectively).

CONCLUSIONS

Skeletal expansion in the midpalatal suture was significantly higher in the TBB group; however, the magnitude of this expansion was around 0.6 mm more and may not be clinically significant. Skeletal expansion at the level of the nasal cavity was significantly higher in the TBB group. There were no differences between boys and girls with regard to skeletal expansion.

TRIAL REGISTRATION

This trial was not registered on any external sites.

Possible Applications for a Biodegradable Magnesium Membrane in Alveolar Ridge Augmentation-Retrospective Case Report with Two Years of Follow-Up

Background and Objectives: A rigid, resorbable magnesium membrane was recently developed, combining the advantages of resorbable and non-resorbable membranes. Our aim was to describe the application of this membrane for guided bone regeneration (GBR). Materials and Methods: This case report described the treatment and 3D evaluation of two cases utilizing a resorbable magnesium barrier membrane. In Case #1, GBR was performed with a bilayer tunnel flap. The magnesium barrier was placed fixed subperiosteally through remote vertical incisions. In Case #2, GBR was performed using a split-thickness flap design. Volumetric and linear hard tissue alterations were assessed by 3D cone-beam computed tomography subtraction analysis, as well as with conventional intraoral radiography. Results: Case #1 showed a volumetric hard tissue gain of 0.12 cm3, whereas Case #2 presented a 0.36 cm3 hard tissue gain. No marginal peri-implant hard tissue loss could be detected at the two-year follow-up. Conclusions: The application of conventional resorbable collagen membranes would be difficult in either of the cases presented. However, the rigid structure of the magnesium membrane allowed for the limitations of conventional resorbable membranes to be overcome.

It Pays to Be Bumpy: Drag Reducing Armor in the Pacific Spiny Lumpsucker, Eumicrotremus orbis

Armor is a multipurpose set of structures that has evolved independently at least 30 times in fishes. In addition to providing protection, armor can manipulate flow, increase camouflage, and be sexually dimorphic. There are potential tradeoffs in armor function: increased impact resistance may come at the cost of maneuvering ability; and ornate armor may offer visual or protective advantages, but could incur excess drag. Pacific spiny lumpsuckers (Eumicrotremus orbis) are covered in rows of odontic, cone-shaped armor whorls, protecting the fish from wave driven impacts and the threat of predation. We are interested in measuring the effects of lumpsucker armor on the hydrodynamic forces on the fish. Bigger lumpsuckers have larger and more complex armor, which may incur a greater hydrodynamic cost. In addition to their protective armor, lumpsuckers have evolved a ventral adhesive disc, allowing them to remain stationary in their environment. We hypothesize a tradeoff between the armor and adhesion: little fish prioritize suction, while big fish prioritize protection. Using micro-CT, we compared armor volume to disc area over lumpsucker development and built 3D models to measure changes in drag over ontogeny. We found that drag and drag coefficients decrease with greater armor coverage and vary consistently with orientation. Adhesive disc area is isometric but safety factor increases with size, allowing larger fish to remain attached in higher flows than smaller fish.

VT3D: a visualization toolbox for 3D transcriptomic data

Data visualization empowers researchers to communicate their results that support scientific reasoning in an intuitive way. Three-dimension (3D) spatially resolved transcriptomic atlases constructed from multi-view and high-dimensional data have rapidly emerged as a powerful tool to unravel spatial gene expression patterns and cell type distribution in biological samples, revolutionizing the understanding of gene regulatory interactions and cell niches. However, limited accessible tools for data visualization impede the potential impact and application of this technology. Here we introduce VT3D, a visualization toolbox that allows users to explore 3D transcriptomic data, enabling gene expression projection to any 2D plane of interest, 2D virtual slice creation and visualization, and interactive 3D data browsing with surface model plots. In addition, it can either work on personal devices in standalone mode or be hosted as a web-based server. We apply VT3D to multiple datasets produced by the most popular techniques, including both sequencing-based approaches (Stereo-seq, spatial transcriptomics, and Slide-seq) and imaging-based approaches (MERFISH and STARMap), and successfully build a 3D atlas database that allows interactive data browsing. We demonstrate that VT3D bridges the gap between researchers and spatially resolved transcriptomics, thus accelerating related studies such as embryogenesis and organogenesis processes. The source code of VT3D is available at https://github.com/BGI-Qingdao/VT3D, and the modeled atlas database is available at http://www.bgiocean.com/vt3d_example.

Assessment of the Extent of Intracerebral Hemorrhage Using 3D Modeling Technology

The second most common cause of stroke, accounting for 10% of hospital admissions, is intracerebral hemorrhage (ICH), and risk factors include diabetes, smoking, and hypertension. People with intracerebral bleeding experience symptoms that are related to the functions that are managed by the affected part of the brain. Having obtained 15 computed tomography (CT) scans from five patients with ICH, we decided to use three-dimensional (3D) modeling technology to estimate the bleeding volume. CT was performed on admission to hospital, and after one week and two weeks of treatment. We segmented the brain, ventricles, and hemorrhage using semi-automatic algorithms in Slicer 3D, then improved the obtained models in Blender. Moreover, the accuracy of the models was checked by comparing corresponding CT scans with 3D brain model cross-sections. The goal of the research was to examine the possibility of using 3D modeling technology to visualize intracerebral hemorrhage and assess its treatment.

Reliable Visualization of the Treatment Effect of Transperineal Focal Laser Ablation in Prostate Cancer Patients by Magnetic Resonance Imaging and Contrast-enhanced Ultrasound Imaging

Background

Transperineal focal laser ablation (TPLA) treatment for prostate cancer (PCa) is an experimental focal ablative therapy modality with low morbidity. However, a dosimetry model for TPLA is lacking.

Objective

To determine (1) the three-dimensional (3D) histologically defined ablation zone of single- and multifiber TPLA treatment for PCa correlated with magnetic resonance imaging (MRI) and contrast-enhanced ultrasound (CEUS) and (2) a reliable imaging modality of ablation zone volumetry.

Design setting and participants

This was a prospective, multicenter, and interventional phase I/II pilot study with an ablate-and-resect design. TPLA was performed in 12 patients with localized prostate cancer divided over four treatment regimens to evaluate potential variation in outcomes.

Intervention

TPLA was performed approximately 4 wk prior to robot-assisted radical prostatectomy (RARP) in a daycare setting using local anesthesia.

Outcome measurements and statistical analysis

Four weeks after TPLA, ablation zone volumetry was determined on prostate MRI and CEUS by delineation and segmentation into 3D models and correlated with whole-mount RARP histology using the Pearson correlation index.

Results and limitations

Twelve office-based TPLA procedures were performed successfully under continuous transrectal ultrasound guidance using local perineal anesthesia. No serious adverse events occurred. A qualitative analysis showed a clear demarcation of the ablation zone on T2-weighted MRI, dynamic contrast-enhanced MRI, and CEUS. On pathological evaluation, no remnant cancer was observed within the ablation zone. Ablation zone volumetry on CEUS and T2-weighted MRI compared with histology had a Pearson correlation index of r = 0.94 (95% confidence interval [CI] 0.74-0.99, p < 0.001) and r = 0.93 (95% CI 0.73-0.98, p < 0.001), respectively.

Conclusions

CEUS and prostate MRI could reliably visualize TPLA ablative effects after minimally invasive PCa treatment with a high concordance with histopathological findings and showed no remnant cancer.

Patient summary

The treatment effects of a novel minimally invasive ablation therapy device can reliably be visualized with radiological examinations. These results will improve planning and performance of future procedures.

White Matter Cerebrovascular Reactivity: Effects of Microangiopathy and Proximal Occlusions on the Dynamic BOLD Response

Introduction

Cerebral microangiopathy often manifests as white matter hyperintensities (WMH) on T2-weighted MR images and is associated with elevated stroke risk. Large vessel steno-occlusive disease (SOD) is also independently associated with stroke risk, however, the interaction of microangiopathy and SOD is not well understood. Cerebrovascular reactivity (CVR) describes the capacity of cerebral circulation to adapt to changes in perfusion pressure and neurovascular demand, and its impairment portends future infarctions. CVR can be measured with blood oxygen level dependent (BOLD) imaging following acetazolamide stimulus (ACZ-BOLD). We studied CVR differences between WMH and normal-appearing white matter (NAWM) in patients with chronic SOD, hypothesizing additive influences upon CVR measured by novel, fully dynamic CVR maxima ( CVR _max ).

Methods

A cross sectional study was conducted to measure per-voxel, per-TR maximal CVR ( CVR _max ) using a custom computational pipeline in 23 subjects with angiographically-proven unilateral SOD. WMH and NAWM masks were applied to CVR _max maps. White matter was subclassified with respect to the SOD-affected hemisphere, including: i. contralateral NAWM; ii. contralateral WMH iii. ipsilateral NAWM; iv. ipsilateral WMH. CVR _max was compared between these groups with a Kruskal-Wallis test followed by a Dunn-Sidak post-hoc test for multiple comparisons.

Results

19 subjects (age 50±12 years, 53% female) undergoing 25 examinations met criteria. WMH volume was asymmetric in 16/19 subjects with 13/16 exhibiting higher volumes ipsilateral to SOD. Pairwise comparisons of CVR _max between groups was significant with ipsilateral WMH CVR _max lower than contralateral NAWM (p=0.015) and contralateral WMH (p=0.003) when comparing in-subject medians and lower than all groups when comparing pooled voxelwise values across all subjects (p<0.0001). No significant relationship between WMH lesion size and CVR _max was detected.

Conclusion

Our results suggest additive effects of microvascular and macrovascular disease upon white matter CVR, but with greater overall effects relating to macrovascular SOD than to apparent microangiopathy. Dynamic ACZ-BOLD presents a promising path towards a quantitative stroke risk imaging biomarker.

BACKGROUND

Cerebral white matter (WM) microangiopathy manifests as sporadic or sometimes confluent high intensity lesions in MR imaging with T2-weighting, and bears known associations with stroke, cognitive disability, depression and other neurological disorders ^1-5 . Deep white matter is particularly susceptible to ischemic injury owing to the deprivation of collateral flow between penetrating arterial territories, and hence deep white matter hyperintensities (WMH) may portend future infarctions ^6-8 . The pathophysiology of WMH is variable but commonly includes a cascade of microvascular lipohyalinosis and atherosclerosis together with impaired vascular endothelial and neurogliovascular integrity, leading to blood brain barrier dysfunction, interstitial fluid accumulation, and eventually tissue damage ^9-14 . Independent of the microcirculation, cervical and intracranial large vessel steno-occlusive disease (SOD) often results from atheromatous disease and is associated with increased risk of stroke owing to thromboembolic phenomena, hypoperfusion, or combinations thereof ^15-17 . White matter disease is more common in the affected hemisphere of patients with asymmetric or unilateral SOD, producing both macroscopic WMH detectable by routine structural MRI, as well as microstructural changes and altered structural connectivity detected by advanced diffusion microstructural imaging ^{18, 19} . An improved understanding of the interaction of microvascular disease (i.e., WMH) and macrovascular steno-occlusion could better inform stroke risk stratification and guide treatment strategies when coexistent. Cerebrovascular reactivity (CVR) is an autoregulatory adaptation characterized by the capacity of the cerebral circulation to respond to physiological or pharmacological vasodilatory stimuli ^20-22 . CVR may be heterogeneous and varies across tissue type and pathological states ^{1, 16} . Alterations in CVR are associated with elevated stroke risk in SOD patients, although white matter CVR, and in particular the CVR profiles of WMH, are only sparsely studied and not fully understood ^{1, 23-26} . We have previously employed blood oxygen level dependent (BOLD) imaging following a hemodynamic stimulus with acetazolamide (ACZ) in order to measure CVR (i.e. ACZ-BOLD) ^{21, 27, 28} . Despite the emergence of ACZ-BOLD as a technique for clinical and experimental use, poor signal-to-noise characteristics of the BOLD effect have generally limited its interpretation to coarse, time-averaged assessment of the terminal ACZ response at arbitrarily prescribed delays following ACZ administration (e.g. 10-20 minutes) ²⁹ . More recently, we have introduced a dedicated computational pipeline to overcome historically intractable signal-to-noise ratio (SNR) limitations of BOLD, enabling fully dynamic characterization of the cerebrovascular response, including identification of previously unreported, unsustained or transient CVR maxima ( CVR _max ) following hemodynamic provocation ^{27, 30} . In this study, we compared such dynamic interrogation of true CVR maxima between WMH and normal appearing white matter (NAWM) among patients with chronic, unilateral SOD in order to quantify their interaction and to assess the hypothesized additive effects of angiographically-evident macrovascular stenoses when intersecting microangiopathic WMH.

Prediction of bird-beak configuration in thoracic endovascular aortic repair preoperatively using patient-specific finite element simulations

Objectives

Formation of bird-beak configuration in thoracic endovascular aortic repair (TEVAR) has been shown to be correlated with the risk of complications such as type Ia endoleaks, stent graft migration, and collapse. The aim of this study was to use patient-specific computational simulations of TEVAR to predict the formation of bird-beak configuration preoperatively.

Methods

Patient-specific TEVAR computational simulations are developed using a retrospective cohort of patients treated for thoracic aortic aneurysm. The preoperative computed tomography images were segmented to develop three-dimensional geometry of the thoracic aorta. These geometries were used in finite element simulations of stent graft deployment during TEVAR. Simulated results were compared against the postoperative computed tomography images to assess the accuracy of simulations in predicting the proximal position of a deployed stent graft and presence of bird-beak. In cases with a bird-beak configuration, the length and angle of the bird-beak were measured and compared between the simulated and postoperative results.

Results

Twelve TEVAR patient cases were simulated. Computational simulations were able to accurately predict whether the proximal stent graft was fully apposed, proximal bare stents were protruded, or bird-beak configuration was present. In three cases with bird-beak configuration, simulations predicted the length and angle of the bird-beak with less than 10% and 24% error, respectively. Other factors such as a small aortic arch angle, small oversizing value, and landing zones close to the arch apex may have played a role in formation of bird-beak in these patients.

Conclusions

Computational simulations of TEVAR accurately predicted the proximal position of a deployed stent graft and the presence of bird-beak preoperatively. The computational models were able to predict the length and angle of bird-beak configurations with good accuracy. These simulations can provide insight into the surgical planning process with the goal of minimizing bird-beak occurrence.

Efficacy and volume stability of a customized allogeneic bone block for the reconstruction of advanced alveolar ridge deficiencies at the anterior maxillary region: a retrospective radiographic evaluation

OBJECTIVES

The aim of this retrospective case series was to evaluate the efficacy and volume stability of a customized allogeneic bone block (CABB) for the hard tissue reconstruction of severely atrophied anterior maxillary ridges.

MATERIALS AND METHODS

Hard tissue alterations between baseline (T1), 2-month follow-up (T2), and 6-month follow-up (T3) cone-beam computed tomography scans were evaluated with semi-automatic segmentation. Following automatic spatial alignment of the datasets, 3D subtraction analysis was performed. The volume stability of the inserted allogeneic bone block was determined on the basis of the ratio of the T3 and T2 hard tissue volumes.

RESULTS

The newly formed hard tissue volume at T2 averaged at of 0.75 cm³ ± 0.57 cm³, whereas at T3, an average of 0.52 cm³ ± 0.42 cm³ volumetric hard tissue gain could be detected. The T3/T2 ratio was found to be 67.83% ± 18.72% on average. The dice similarity coefficient between the T2 and T3 hard tissue models averaged at 0.73 ± 0.15.

CONCLUSIONS

Cancellous CABBs are a reliable option for the reconstruction of severely atrophied alveolar ridges. The resorption rates of these grafts are similar to those found in the literature; however, with precise manufacturing and proper intraoperative flap management, the resorption rates may be reduced.

CLINICAL RELEVANCE

With precise knowledge of the resorption patterns, the shape of blocks can be altered in the future to compensate for the volumetric loss.

Data Provenance in Biomedical Research: Scoping Review

BACKGROUND

Data provenance refers to the origin, processing, and movement of data. Reliable and precise knowledge about data provenance has great potential to improve reproducibility as well as quality in biomedical research and, therefore, to foster good scientific practice. However, despite the increasing interest on data provenance technologies in the literature and their implementation in other disciplines, these technologies have not yet been widely adopted in biomedical research.

OBJECTIVE

The aim of this scoping review was to provide a structured overview of the body of knowledge on provenance methods in biomedical research by systematizing articles covering data provenance technologies developed for or used in this application area; describing and comparing the functionalities as well as the design of the provenance technologies used; and identifying gaps in the literature, which could provide opportunities for future research on technologies that could receive more widespread adoption.

METHODS

Following a methodological framework for scoping studies and the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) guidelines, articles were identified by searching the PubMed, IEEE Xplore, and Web of Science databases and subsequently screened for eligibility. We included original articles covering software-based provenance management for scientific research published between 2010 and 2021. A set of data items was defined along the following five axes: publication metadata, application scope, provenance aspects covered, data representation, and functionalities. The data items were extracted from the articles, stored in a charting spreadsheet, and summarized in tables and figures.

RESULTS

We identified 44 original articles published between 2010 and 2021. We found that the solutions described were heterogeneous along all axes. We also identified relationships among motivations for the use of provenance information, feature sets (capture, storage, retrieval, visualization, and analysis), and implementation details such as the data models and technologies used. The important gap that we identified is that only a few publications address the analysis of provenance data or use established provenance standards, such as PROV.

CONCLUSIONS

The heterogeneity of provenance methods, models, and implementations found in the literature points to the lack of a unified understanding of provenance concepts for biomedical data. Providing a common framework, a biomedical reference, and benchmarking data sets could foster the development of more comprehensive provenance solutions.

3D Ultrasound Reconstructions of the Carotid Artery and Thyroid Gland Using Artificial-Intelligence-Based Automatic Segmentation-Qualitative and Quantitative Evaluation of the Segmentation Results via Comparison with CT Angiography

The aim of this study was to evaluate the feasibility of a noninvasive and low-operator-dependent imaging method for carotid-artery-stenosis diagnosis. A previously developed prototype for 3D ultrasound scans based on a standard ultrasound machine and a pose reading sensor was used for this study. Working in a 3D space and processing data using automatic segmentation lowers operator dependency. Additionally, ultrasound imaging is a noninvasive diagnosis method. Artificial intelligence (AI)-based automatic segmentation of the acquired data was performed for the reconstruction and visualization of the scanned area: the carotid artery wall, the carotid artery circulated lumen, soft plaque, and calcified plaque. A qualitative evaluation was conducted via comparing the US reconstruction results with the CT angiographies of healthy and carotid-artery-disease patients. The overall scores for the automated segmentation using the MultiResUNet model for all segmented classes in our study were 0.80 for the IoU and 0.94 for the Dice. The present study demonstrated the potential of the MultiResUNet-based model for 2D-ultrasound-image automated segmentation for atherosclerosis diagnosis purposes. Using 3D ultrasound reconstructions may help operators achieve better spatial orientation and evaluation of segmentation results.

Characterizing a photoacoustic and fluorescence imaging platform for preclinical murine longitudinal studies

Significance

To effectively study preclinical animal models, medical imaging technology must be developed with a high enough resolution and sensitivity to perform anatomical, functional, and molecular assessments. Photoacoustic (PA) tomography provides high resolution and specificity, and fluorescence (FL) molecular tomography provides high sensitivity; the combination of these imaging modes will enable a wide range of research applications to be studied in small animals.

Aim

We introduce and characterize a dual-modality PA and FL imaging platform using in vivo and phantom experiments.

Approach

The imaging platform's detection limits were characterized through phantom studies that determined the PA spatial resolution, PA sensitivity, optical spatial resolution, and FL sensitivity.

Results

The system characterization yielded a PA spatial resolution of 173 ± 17    μ m in the transverse plane and 640 ± 120    μ m in the longitudinal axis, a PA sensitivity detection limit not less than that of a sample with absorption coefficient μ a = 0.258    cm - 1 , an optical spatial resolution of 70    μ m in the vertical axis and 112    μ m in the horizontal axis, and a FL sensitivity detection limit not < 0.9    μ M concentration of IR-800. The scanned animals displayed in three-dimensional renders showed high-resolution anatomical detail of organs.

Conclusions

The combined PA and FL imaging system has been characterized and has demonstrated its ability to image mice in vivo, proving its suitability for biomedical imaging research applications.

Three-dimensional volumetric assessment of hard tissue alterations following horizontal guided bone regeneration using a split-thickness flap design: A case series

OBJECTIVES

To analyze morphological, volumetric, and linear hard tissue changes following horizontal ridge augmentation using a three-dimensional radiographic method.

METHODS

As part of a larger ongoing prospective study, 10 lower lateral surgical sites were selected for evaluation. Horizontal ridge deficiencies were treated with guided bone regeneration (GBR) using a split-thickness flap design and a resorbable collagen barrier membrane. Following the segmentation of baseline and 6-month follow-up cone-beam computed tomography scans, volumetric, linear, and morphological hard tissue changes and the efficacy of the augmentation were assessed (expressed by the volume-to-surface ratio).

RESULTS

Volumetric hard tissue gain averaged 605.32 ± 380.68 mm³. An average of 238.48 ± 127.82 mm³ hard tissue loss was also detected at the lingual aspect of the surgical area. Horizontal hard tissue gain averaged 3.00 ± 1.45 mm. Midcrestal vertical hard tissue loss averaged 1.18 ± 0.81 mm. The volume-to-surface ratio averaged 1.19 ± 0.52 mm³/mm². The three-dimensional analysis showed slight lingual or crestal hard tissue resorption in all cases. In certain instances, the greatest extent of hard tissue gain was observed 2-3 mm apical to the initial level of the marginal crest.

CONCLUSIONS

With the applied method, previously unreported aspects of hard tissue changes following horizontal GBR could be examined. Midcrestal bone resorption was demonstrated, most likely caused by increased osteoclast activity following the elevation of the periosteum. The volume-to-surface ratio expressed the efficacy of the procedure independent of the size of the surgical area.

3D-Printed Tumor Phantoms for Assessment of In Vivo Fluorescence Imaging Analysis Methods

PURPOSE

Interventional fluorescence imaging is increasingly being utilized to quantify cancer biomarkers in both clinical and preclinical models, yet absolute quantification is complicated by many factors. The use of optical phantoms has been suggested by multiple professional organizations for quantitative performance assessment of fluorescence guidance imaging systems. This concept can be further extended to provide standardized tools to compare and assess image analysis metrics.

PROCEDURES

3D-printed fluorescence phantoms based on solid tumor models were developed with representative bio-mimicking optical properties. Phantoms were produced with discrete tumors embedded with an NIR fluorophore of fixed concentration and either zero or 3% non-specific fluorophore in the surrounding material. These phantoms were first imaged by two fluorescence imaging systems using two methods of image segmentation, and four assessment metrics were calculated to demonstrate variability in the quantitative assessment of system performance. The same analysis techniques were then applied to one tumor model with decreasing tumor fluorophore concentrations.

RESULTS

These anatomical phantom models demonstrate the ability to use 3D printing to manufacture anthropomorphic shapes with a wide range of reduced scattering (μ_s': 0.24-1.06 mm^-1) and absorption (μ_a: 0.005-0.14 mm^-1) properties. The phantom imaging and analysis highlight variability in the measured sensitivity metrics associated with tumor visualization.

CONCLUSIONS

3D printing techniques provide a platform for demonstrating complex biological models that introduce real-world complexities for quantifying fluorescence image data. Controlled iterative development of these phantom designs can be used as a tool to advance the field and provide context for consensus-building beyond performance assessment of fluorescence imaging platforms, and extend support for standardizing how quantitative metrics are extracted from imaging data and reported in literature.

Software tool for visualization of a probabilistic map of the epileptogenic zone from seizure semiologies

Around one third of epilepsies are drug-resistant. For these patients, seizures may be reduced or cured by surgically removing the epileptogenic zone (EZ), which is the portion of the brain giving rise to seizures. If noninvasive data are not sufficiently lateralizing or localizing, the EZ may need to be localized by precise implantation of intracranial electroencephalography (iEEG) electrodes. The choice of iEEG targets is influenced by clinicians' experience and personal knowledge of the literature, which leads to substantial variations in implantation strategies across different epilepsy centers. The clinical diagnostic pathway for surgical planning could be supported and standardized by an objective tool to suggest EZ locations, based on the outcomes of retrospective clinical cases reported in the literature. We present an open-source software tool that presents clinicians with an intuitive and data-driven visualization to infer the location of the symptomatogenic zone, that may overlap with the EZ. The likely EZ is represented as a probabilistic map overlaid on the patient's images, given a list of seizure semiologies observed in that specific patient. We demonstrate a case study on retrospective data from a patient treated in our unit, who underwent resective epilepsy surgery and achieved 1-year seizure freedom after surgery. The resected brain structures identified as EZ location overlapped with the regions highlighted by our tool, demonstrating its potential utility.

Role of intratumoral and peritumoral CT radiomics for the prediction of EGFR gene mutation in primary lung cancer

Objectives

To determine the added value of combining intratumoral and peritumoral CT radiomics for the prediction of epidermal growth factor receptor (EGFR) gene mutations in primary lung cancer (PLC).

Methods

This study included 478 patients with PLC (348 adenocarcinomas and 130 other histological types) who underwent surgical resection and EGFR gene testing. Two radiologists performed segmentation of tumors and peritumoral regions using precontrast high-resolution CT images, and 398 radiomic features (212 intra- and 186 peritumoral features) were extracted. The peritumoral region was defined as the lung parenchyma within a distance of 3 mm from the tumor border. Model performance was estimated using Random Forest, a machine-learning algorithm.

Results

EGFR mutations were found in 162 tumors; 161 adenocarcinomas, and one pleomorphic carcinoma. After exclusion of poorly reproducible and redundant features, 32 radiomic features remained (14 intra- and 18 peritumoral features) and were included in the model building. For predicting EGFR mutations, combining intra- and peritumoral radiomics significantly improved the performance compared to intratumoral radiomics alone (AUC [area under the receiver operating characteristic curve], 0.774 vs 0.730; p < 0.001). Even in adenocarcinomas only, adding peritumoral radiomics significantly increased performance (AUC, 0.687 vs 0.630; p < 0.001). The predictive performance using radiomics and clinical features was significantly higher than that of clinical features alone (AUC, 0.826 vs 0.777; p = 0.005).

Conclusions

Combining intra- and peritumoral radiomics improves the predictive accuracy of EGFR mutations and could be used to aid in decision-making of whether to perform biopsy for gene tests.

Advances in knowledge

Adding peritumoral to intratumoral radiomics yields greater accuracy than intratumoral radiomics alone in predicting EGFR mutations and may serve as a non-invasive method of predicting of the gene status in PLC.

Phantom Study on the Robustness of MR Radiomics Features: Comparing the Applicability of 3D Printed and Biological Phantoms

The objectives of our study were to (a) evaluate the feasibility of using 3D printed phantoms in magnetic resonance imaging (MR) in assessing the robustness and repeatability of radiomic parameters and (b) to compare the results obtained from the 3D printed phantoms to metrics obtained in biological phantoms. To this end, three different 3D phantoms were printed: a Hilbert cube (5 × 5 × 5 cm³) and two cubic quick response (QR) code phantoms (a large phantom (large QR) (5 × 5 × 4 cm³) and a small phantom (small QR) (4 × 4 × 3 cm³)). All 3D printed and biological phantoms (kiwis, tomatoes, and onions) were scanned thrice on clinical 1.5 T and 3 T MR with 1 mm and 2 mm isotropic resolution. Subsequent analyses included analyses of several radiomics indices (RI), their repeatability and reliability were calculated using the coefficient of variation (CV), the relative percentage difference (RPD), and the interclass coefficient (ICC) parameters. Additionally, the readability of QR codes obtained from the MR images was examined with several mobile phones and algorithms. The best repeatability (CV ≤ 10%) is reported for the acquisition protocols with the highest spatial resolution. In general, the repeatability and reliability of RI were better in data obtained at 1.5 T (CV = 1.9) than at 3 T (CV = 2.11). Furthermore, we report good agreements between results obtained for the 3D phantoms and biological phantoms. Finally, analyses of the read-out rate of the QR code revealed better texture analyses for images with a spatial resolution of 1 mm than 2 mm. In conclusion, 3D printing techniques offer a unique solution to create textures for analyzing the reliability of radiomic data from MR scans.

SlicerHeart: An open-source computing platform for cardiac image analysis and modeling

Cardiovascular disease is a significant cause of morbidity and mortality in the developed world. 3D imaging of the heart's structure is critical to the understanding and treatment of cardiovascular disease. However, open-source tools for image analysis of cardiac images, particularly 3D echocardiographic (3DE) data, are limited. We describe the rationale, development, implementation, and application of SlicerHeart, a cardiac-focused toolkit for image analysis built upon 3D Slicer, an open-source image computing platform. We designed and implemented multiple Python scripted modules within 3D Slicer to import, register, and view 3DE data, including new code to volume render and crop 3DE. In addition, we developed dedicated workflows for the modeling and quantitative analysis of multi-modality image-derived heart models, including heart valves. Finally, we created and integrated new functionality to facilitate the planning of cardiac interventions and surgery. We demonstrate application of SlicerHeart to a diverse range of cardiovascular modeling and simulation including volume rendering of 3DE images, mitral valve modeling, transcatheter device modeling, and planning of complex surgical intervention such as cardiac baffle creation. SlicerHeart is an evolving open-source image processing platform based on 3D Slicer initiated to support the investigation and treatment of congenital heart disease. The technology in SlicerHeart provides a robust foundation for 3D image-based investigation in cardiovascular medicine.

Open-Full-Jaw: An open-access dataset and pipeline for finite element models of human jaw

BACKGROUND

State-of-the-art finite element studies on human jaws are mostly limited to the geometry of a single patient. In general, developing accurate patient-specific computational models of the human jaw acquired from cone-beam computed tomography (CBCT) scans is labor-intensive and non-trivial, which involves time-consuming human-in-the-loop procedures, such as segmentation, geometry reconstruction, and re-meshing tasks. Therefore, with the current practice, researchers need to spend considerable time and effort to produce finite element models (FEMs) to get to the point where they can use the models to answer clinically-interesting questions. Besides, any manual task involved in the process makes it difficult for the researchers to reproduce identical models generated in the literature. Hence, a quantitative comparison is not attainable due to the lack of surface/volumetric meshes and FEMs.

METHODS

We share an open-access repository composed of 17 patient-specific computational models of human jaws and the utilized pipeline for generating them for reproducibility of our work. The used pipeline minimizes the required time for processing and any potential biases in the model generation process caused by human intervention. It gets the segmented geometries with irregular and dense surface meshes and provides reduced, adaptive, watertight, and conformal surface/volumetric meshes, which can directly be used in finite element (FE) analysis.

RESULTS

We have quantified the variability of our 17 models and assessed the accuracy of the developed models from three different aspects; (1) the maximum deviations from the input meshes using the Hausdorff distance as an error measurement, (2) the quality of the developed volumetric meshes, and (3) the stability of the FE models under two different scenarios of tipping and biting.

CONCLUSIONS

The obtained results indicate that the developed computational models are precise, and they consist of quality meshes suitable for various FE scenarios. We believe the provided dataset of models including a high geometrical variation obtained from 17 different models will pave the way for population studies focusing on the biomechanical behavior of human jaws.

Actuated Reflector-Based 3-D Ultrasound Imaging With Synthetic Aperture Focusing

The 3-D ultrasound (US) imaging addresses the limitation in field-of-view (FOV) in conventional 2-D US imaging by providing 3-D viewing of the anatomy. The 3-D US imaging has been extensively adapted for diagnosis and image-guided surgical intervention. However, conventional approaches to implement 3-D US imaging require either expensive and sophisticated 2-D array transducers or external actuation mechanisms to move a 1-D array mechanically. Here, we propose a 3-D US imaging mechanism using an actuated acoustic reflector instead of the sensor elements for volume acquisition with significantly extended 3-D FOV, which can be implemented with simple hardware and compact size. To improve image quality on the elevation plane, we implemented the synthetic aperture focusing (SAF) method according to the diagonal geometry of the virtual element array in the proposed imaging mechanism for elevation beamforming. We first evaluated the proposed imaging mechanism and SAF with simulated point targets and cyst targets. The results of point targets suggested improved image quality on the elevation plane, and the results of cysts targets demonstrated a potential to improve 3-D visualization of human anatomy. We built a prototype imaging system with a 3-D FOV of 38 mm (lateral) by 38 mm (elevation) by 50 mm (axial) and collected data in imaging experiments with phantoms. Experimental data showed consistency with simulation results. The SAF method enhanced quantifying the cyst volume size in the breast mimicking phantom compared with no elevation beamforming. These results suggested that the proposed 3-D US imaging mechanism could potentially be applied in clinical scenarios.

The transparent minds: methods of creation of 3D digital models from patient specific data

This paper focuses on the method for creating 3-dimensional (3D) digital models extracted from patient- specific scans of the brain. The described approach consists of several cross-platform stages: raw data segmentation, data correction in 3D-modelling software, post-processing of the 3D digital models and their presentation on an interactive web-based platform. This method of data presentation offers a cost and time effective option to present medical data accurately. An important aspect of the process is using real patient data and enriching the traditional slice-based representation of the scans with 3D models that can provide better understanding of the organs' structures. The resulting 3D digital models also form the basis for further processing into different modalities, for example models in Virtual Reality or 3D physical model printouts. The option to make medical data less abstract and more understandable can extend their use beyond diagnosis and into a potential aid in anatomy and patient education. The methods presented in this paper were originally based on the master thesis 'Transparent Minds: Testing for Efficiency of Transparency in 3D Physical and 3D Digital Models', which focussed on creating and comparing the efficiency of transparent 3D physical and 3D digital models from real-patient data.