•Research of navigation technology in medical interventions requires significant engineering efforts.•Platforms allow rapid implementation of applications.•We discuss the most popular platforms, and ...show how to use them through an example.
Navigation technology is changing the clinical standards in medical interventions by making existing procedures more accurate, and new procedures possible. Navigation is based on preoperative or intraoperative imaging combined with 3-dimensional position tracking of interventional tools registered to the images. Research of navigation technology in medical interventions requires significant engineering efforts. The difficulty of developing such complex systems has been limiting the clinical translation of new methods and ideas. A key to the future success of this field is to provide researchers with platforms that allow rapid implementation of applications with minimal resources spent on reimplementing existing system features. A number of platforms have been already developed that can share data in real time through standard interfaces. Complete navigation systems can be built using these platforms using a layered software architecture. In this paper, we review the most popular platforms, and show an effective way to take advantage of them through an example surgical navigation application.
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Purpose:
Interest in adaptive radiation therapy research is constantly growing, but software tools available for researchers are mostly either expensive, closed proprietary applications, or free ...open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we propose SlicerRT, a customizable, free, and open-source radiation therapy research toolkit. SlicerRT aspires to be an open-source toolkit for RT research, providing fast computations, convenient workflows for researchers, and a general image-guided therapy infrastructure to assist clinical translation of experimental therapeutic approaches. It is a medium into which RT researchers can integrate their methods and algorithms, and conduct comparative testing.
Methods:
SlicerRT was implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. SlicerRT provides functionality specifically designed for radiation therapy research, in addition to the powerful tools that 3D Slicer offers for visualization, registration, segmentation, and data management. The feature set of SlicerRT was defined through consensus discussions with a large pool of RT researchers, including both radiation oncologists and medical physicists. The development processes used were similar to those of 3D Slicer to ensure software quality. Standardized mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The testing and validation environment was configured to automatically launch a regression test upon each software change and to perform comparison with ground truth results provided by other RT applications.
Results:
Modules have been created for importing and loading DICOM-RT data, computing and displaying dose volume histograms, creating accumulated dose volumes, comparing dose volumes, and visualizing isodose lines and surfaces. The effectiveness of using 3D Slicer with the proposed SlicerRT extension for radiation therapy research was demonstrated on multiple use cases.
Conclusions:
A new open-source software toolkit has been developed for radiation therapy research. SlicerRT can import treatment plans from various sources into 3D Slicer for visualization, analysis, comparison, and processing. The provided algorithms are extensively tested and they are accessible through a convenient graphical user interface as well as a flexible application programming interface.
•A software library called PolySeg is developed to facilitate dynamic management of segmented structures in different representations.•PolySeg provides automatic conversions between numerous ...representations (e.g. labelmap, surface) to support analysis workflows or interactive editing.•Segment Editor in the open-source 3D Slicer platform provides easy-to-use manual and semi-automatic segmentation features.
Segmentation is a ubiquitous operation in medical image computing. Various data representations can describe segmentation results, such as labelmap volumes or surface models. Conversions between them are often required, which typically include complex data processing steps. We identified four challenges related to managing multiple representations: conversion method selection, data provenance, data consistency, and coherence of in-memory objects.
A complex data container preserves identity and provenance of the contained representations and ensures data coherence. Conversions are executed automatically on-demand. A graph containing the implemented conversion algorithms determines each execution, ensuring consistency between various representations. The design and implementation of a software library are proposed, in order to provide a readily usable software tool to manage segmentation data in multiple data representations. A low-level core library called PolySeg implemented in the Visualization Toolkit (VTK) manages the data objects and conversions. It is used by a high-level application layer, which has been implemented in the medical image visualization and analysis platform 3D Slicer. The application layer provides advanced visualization, transformation, interoperability, and other functions.
The core conversion algorithms comprising the graph were validated. Several applications were implemented based on the library, demonstrating advantages in terms of usability and ease of software development in each case. The Segment Editor application provides fast, comprehensive, and easy-to-use manual and semi-automatic segmentation workflows. Clinical applications for gel dosimetry, external beam planning, and MRI-ultrasound image fusion in brachytherapy were rapidly prototyped resulting robust applications that are already in use in clinical research. The conversion algorithms were found to be accurate and reliable using these applications.
A generic software library has been designed and developed for automatic management of multiple data formats in segmentation tasks. It enhances both user and developer experience, enabling fast and convenient manual workflows and quicker and more robust software prototyping. The software’s BSD-style open-source license allows complete freedom of use of the library.
A prototype of a navigation system to fuse two image modalities is presented. The standard inter-modality registration is replaced with a tracker-based image registration of calibrated imaging ...devices. Intra-procedure transrectal US (TRUS) images were merged with pre-procedure magnetic resonance (MR) images for prostate biopsy. The registration between MR and TRUS images was performed by an additional abdominal 3D-US (ab-3D-US), which enables replacing the inter-modal MR/TRUS registration by an intra-modal ab-3D-US/3D-TRUS registration. Calibration procedures were carried out using an optical tracking system (OTS) for the pre-procedure image fusion of the ab-3D-US with the MR. Inter-modal ab-3D-US/MR image fusion was evaluated using a multi-cone phantom for the target registration error (TRE) and a prostate phantom for the Dice score and the Hausdorff distance of lesions . Finally, the pre-procedure ab- 3D-US was registered with the TRUS images and the errors for the transformation from the MR to the TRUS were determined. The TRE of the ab-3D-US/MR image registration was 1.81 mm. The Dice-score and the Hausdorff distance for ab-3D-US and MR were found to be 0.67 and 3.19 mm. The Dice score and the Hausdorff distance for TRUS and MR were 0.67 and 3.18 mm. The hybrid navigation system showed sufficient accuracy for fusion guided biopsy procedures with prostate phantoms. The system might provide intra-procedure fusion for most US-guided biopsy and ablation interventions.
Background
Suturing is a fundamental skill in undergraduate medical education. It can be taught by faculty-led, peer tutor-led, and holography-augmented methods; however, the most educationally ...effective and cost-efficient method for proficiency-based teaching of suturing is yet to be determined.
Methods
We conducted a randomized controlled trial comparing faculty-led, peer tutor-led, and holography-augmented proficiency-based suturing training in pre-clerkship medical students. Holography-augmented training provided holographic, voice-controlled instructional material. Technical skill was assessed using hand motion analysis every ten sutures and used to construct learning curves. Proficiency was defined by one standard deviation within average faculty surgeon performance. Intervention arms were compared using one-way ANOVA of the number of sutures placed, full-length sutures used, time to proficiency, and incremental costs incurred. Surveys were used to evaluate participant preferences.
Results
Forty-four students were randomized to the faculty-led (
n
= 16), peer tutor-led (
n
= 14), and holography-augmented (
n
= 14) intervention arms. At proficiency, there were no differences between groups in the number of sutures placed, full-length sutures used, and time to achieve proficiency. The incremental costs of the holography-augmented method were greater than faculty-led and peer tutor-led instruction ($247.00 ± $12.05,
p
< 0.001) due to the high cost of the equipment. Faculty-led teaching was the most preferred method (78.0%), while holography-augmented was the least preferred (0%). 90.6% of students reported high confidence in performing simple interrupted sutures, which did not differ between intervention arms (faculty-led 100.0%, peer tutor-led 90.0%, holography-augmented 83.3%,
p
= 0.409). 93.8% of students felt the program should be offered in the future.
Conclusion
Faculty-led and peer tutor-led instructional methods of proficiency-based suturing teaching were superior to holography-augmented method with respect to costs and participants’ preferences despite being educationally equivalent.
We hypothesized that the use of an interactive 3D digital anatomy model can improve the quality of communication with patients about prostate disease.
A 3D digital anatomy model of the prostate was ...created from an MRI scan, according to McNeal's zonal anatomy classification. During urological consultation, the physician presented the digital model on a computer and used it to explain the disease and available management options. The experience of patients and physicians was recorded in questionnaires.
The main findings were as follows: 308 patients and 47 physicians participated in the study. In the patient group, 96.8% reported an improved level of understanding of prostate disease and 90.6% reported an improved ability to ask questions during consultation. Among the physicians, 91.5% reported improved communication skills and 100% reported an improved ability to obtain patient consent for subsequent treatment. At the same time, 76.6% of physicians noted that using the computer model lengthened the consultation.
This exploratory study found that the use of a 3D digital anatomy model in urology consultations was received overwhelmingly favorably by both patients and physicians, and it was perceived to improve the quality of communication between patient and physician. A randomized study is needed to confirm the preliminary findings and further quantify the improvements in the quality of patient-physician communication.
ObjectivesWe hypothesized that the use of an interactive 3D digital anatomy model can improve the quality of communication with patients about prostate disease.MethodsA 3D digital anatomy model of ...the prostate was created from an MRI scan, according to McNeal's zonal anatomy classification. During urological consultation, the physician presented the digital model on a computer and used it to explain the disease and available management options. The experience of patients and physicians was recorded in questionnaires.ResultsThe main findings were as follows: 308 patients and 47 physicians participated in the study. In the patient group, 96.8% reported an improved level of understanding of prostate disease and 90.6% reported an improved ability to ask questions during consultation. Among the physicians, 91.5% reported improved communication skills and 100% reported an improved ability to obtain patient consent for subsequent treatment. At the same time, 76.6% of physicians noted that using the computer model lengthened the consultation.ConclusionThis exploratory study found that the use of a 3D digital anatomy model in urology consultations was received overwhelmingly favorably by both patients and physicians, and it was perceived to improve the quality of communication between patient and physician. A randomized study is needed to confirm the preliminary findings and further quantify the improvements in the quality of patient-physician communication.
We present a needle deflection estimation method to anticipate needle bending during insertion into deformable tissue. Using limited additional sensory information, our approach reduces the ...estimation error caused by uncertainties inherent in the conventional needle deflection estimation methods. We use Kalman filters to combine a kinematic needle deflection model with the position measurements of the base and the tip of the needle taken by electromagnetic (EM) trackers. One EM tracker is installed on the needle base and estimates the needle tip position indirectly using the kinematic needle deflection model. Another EM tracker is installed on the needle tip and estimates the needle tip position through direct, but noisy measurements. Kalman filters are then employed to fuse these two estimates in real time and provide a reliable estimate of the needle tip position, with reduced variance in the estimation error. We implemented this method to compensate for needle deflection during simulated needle insertions and performed sensitivity analysis for various conditions. At an insertion depth of 150 mm, we observed needle tip estimation error reductions in the range of 28% (from 1.8 to 1.3 mm) to 74% (from 4.8 to 1.2 mm), which demonstrates the effectiveness of our method, offering a clinically practical solution.
Purpose
Up to date, there has been a lack of software infrastructure to connect 3D Slicer to any augmented reality (AR) device. This work describes a novel connection approach using Microsoft ...HoloLens 2 and OpenIGTLink, with a demonstration in pedicle screw placement planning.
Methods
We developed an AR application in Unity that is wirelessly rendered onto Microsoft HoloLens 2 using Holographic Remoting. Simultaneously, Unity connects to 3D Slicer using the OpenIGTLink communication protocol. Geometrical transform and image messages are transferred between both platforms in real time. Through the AR glasses, a user visualizes a patient’s computed tomography overlaid onto virtual 3D models showing anatomical structures. We technically evaluated the system by measuring message transference latency between the platforms. Its functionality was assessed in pedicle screw placement planning. Six volunteers planned pedicle screws' position and orientation with the AR system and on a 2D desktop planner. We compared the placement accuracy of each screw with both methods. Finally, we administered a questionnaire to all participants to assess their experience with the AR system.
Results
The latency in message exchange is sufficiently low to enable real-time communication between the platforms. The AR method was non-inferior to the 2D desktop planner, with a mean error of 2.1 ± 1.4 mm. Moreover, 98% of the screw placements performed with the AR system were successful, according to the Gertzbein–Robbins scale. The average questionnaire outcomes were 4.5/5.
Conclusions
Real-time communication between Microsoft HoloLens 2 and 3D Slicer is feasible and supports accurate planning for pedicle screw placement.
Quantitative analysis of clinical image data is an active area of research that holds promise for precision medicine, early assessment of treatment response, and objective characterization of the ...disease. Interoperability, data sharing, and the ability to mine the resulting data are of increasing importance, given the explosive growth in the number of quantitative analysis methods being proposed. The Digital Imaging and Communications in Medicine (DICOM) standard is widely adopted for image and metadata in radiology.
(DICOM for Quantitative Imaging) is a free, open source library that implements conversion of the data stored in commonly used research formats into the standard DICOM representation.
source code is distributed under BSD-style license. It is freely available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. Installation and usage instructions are provided in the GitHub repository at https://github.com/qiicr/dcmqi
.
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