AeroPath: An airway segmentation benchmark dataset with challenging pathology

To improve the prognosis of patients suffering from pulmonary diseases, such as lung cancer, early diagnosis and treatment are crucial. The analysis of CT images is invaluable for diagnosis, whereas high quality segmentation of the airway tree are required for intervention planning and live guidance during bronchoscopy. Recently, the Multi-domain Airway Tree Modeling (ATM'22) challenge released a large dataset, both enabling training of deep-learning based models and bringing substantial improvement of the state-of-the-art for the airway segmentation task. However, the ATM'22 dataset includes few patients with severe pathologies affecting the airway tree anatomy. In this study, we introduce a new public benchmark dataset (AeroPath), consisting of 27 CT images from patients with pathologies ranging from emphysema to large tumors, with corresponding trachea and bronchi annotations. Second, we present a multiscale fusion design for automatic airway segmentation. Models were trained on the ATM'22 dataset, tested on the AeroPath dataset, and further evaluated against competitive open-source methods. The same performance metrics as used in the ATM'22 challenge were used to benchmark the different considered approaches. Lastly, an open web application is developed, to easily test the proposed model on new data. The results demonstrated that our proposed architecture predicted topologically correct segmentations for all the patients included in the AeroPath dataset. The proposed method is robust and able to handle various anomalies, down to at least the fifth airway generation. In addition, the AeroPath dataset, featuring patients with challenging pathologies, will contribute to development of new state-of-the-art methods. The AeroPath dataset and the web application are made openly available.Comment: 13 pages, 5 figures, submitted to Scientific Report

Open source airway navigation: initial experiences with CustusX and Anser EMT

Electromagnetic tracking (EMT) is a common navigation technology used in image guided applications. EMT is particularly useful in procedures where line-of-sight of the operating field is not feasible. We present a major update of the open source electromagnetic tracking platform Anser EMT [1] and present its results when performing bronchoscopy in a pre-clinical setting using the CustusX navigation suite [2]. The updated system design is open source and free to use and modify under the Berkeley Standard Distribution (BSD) license

Mechanical catheter navigation with electromagnetic tracking to peripheral airway targets

Lung cancer remains the single most deadly cancer in men and women due to low rates of early detection and treatment. Since non-small cell lung cancer usually starts in the outer airways, targeted minimally invasive biopsy which limits radiation exposure and avoids surgery is highly desirable. Current commercial solutions such as the superDimension (Medtronic Inc., Dublin, Ireland), and SpIN (Veran Medical, St. Louis, USA) systems rely on electromagnetic tracking for virtual navigation. However, clinical outcomes have been unconvincing due to poor accuracy, limitations in instrumentation and the lack of tracked catheters. This work proposes a novel mechanical catheter design with embedded electromagnetic tracking to facilitate tip-tracked navigation without the need for proprietary instruments or probe exchange. The catheter was used to reach peripheral airway targets by multiple users in pre-clinical studies

Peripheral tumour targeting using open-source virtual bronchoscopy with electromagnetic tracking: a multi-user pre-clinical study

Objectives: The goal was to demonstrate the utility of open-source tracking and visualisation tools in the targeting of lung cancer. Material and methods: The study demonstrates the first deployment of the Anser electromagnetic (EM) tracking system with the CustusX image-guided interventional research platform to navigate using an endobronchial catheter to injected tumour targets. Live animal investigations validated the deployment and targeting of peripheral tumour models using an innovative tumour marking routine. Results: Novel tumour model deployment was successfully achieved at all eight target sites across two live animal investigations without pneumothorax. Virtual bronchoscopy with tracking successfully guided the tracked catheter to 2–12 mm from the target tumour site. Deployment of a novel marker was achieved at all eight sites providing a reliable measure of targeting accuracy. Targeting accuracy within 10 mm was achieved in 7/8 sites and in all cases, the virtual target distance at marker deployment was within the range subsequently measured with x-ray. Conclusions: Endobronchial targeting of peripheral airway targets is feasible using existing open-source technology. Notwithstanding the shortcomings of current commercial platforms, technological improvements in EM tracking and registration accuracy fostered by open-source technology may provide the impetus for widespread clinical uptake of electromagnetic navigation in bronchoscopy

An open electromagnetic tracking framework applied to targeted liver tumour ablation

Purpose: Electromagnetic tracking is a core platform technology in the navigation and visualisation of image-guided procedures. The technology provides high tracking accuracy in non-line-of-sight environments, allowing instrument navigation in locations where optical tracking is not feasible. EMT can be beneficial in applications such as percutaneous radiofrequency ablation for the treatment of hepatic lesions where the needle tip may be obscured due to difficult liver environments (e.g subcutaneous fat or ablation artefacts). Advances in the field of EMT include novel methods of improving tracking system accuracy, precision and error compensation capabilities, though such system-level improvements cannot be readily incorporated in current therapy applications due to the ‘blackbox’ nature of commercial tracking solving algorithms. Methods: This paper defines a software framework to allow novel EMT designs, and improvements become part of the global design process for image-guided interventions. An exemplary framework is implemented in the Python programming language and demonstrated with the open-source Anser EMT system. The framework is applied in the preclinical setting though targeted liver ablation therapy on an animal model. Results: The developed framework was tested with the Anser EMT electromagnetic tracking platform. Liver tumour targeting was performed using the tracking framework with the CustusX navigation platform using commercially available electromagnetically tracked needles. Ablation of two tumours was performed with a commercially available ablation system. Necropsy of the tumours indicated ablations within 5 mm of the tumours. Conclusions: An open-source framework for electromagnetic tracking was presented and effectively demonstrated in the preclinical setting. We believe that this framework provides a structure for future advancement in EMT system in and customised instrument design

Bronchoscopy using a head-mounted mixed reality device—a phantom study and a first in-patient user experience

Background: Bronchoscopy for peripheral lung lesions may involve image sources such as computed tomography (CT), fluoroscopy, radial endobronchial ultrasound (R-EBUS), and virtual/electromagnetic navigation bronchoscopy. Our objective was to evaluate the feasibility of replacing these multiple monitors with a head-mounted display (HMD), always providing relevant image data in the line of sight of the bronchoscopist.Methods: A total of 17 pulmonologists wearing a HMD (Microsoft® HoloLens 2) performed bronchoscopy with electromagnetic navigation in a lung phantom. The bronchoscopists first conducted an endobronchial inspection and navigation to the target, followed by an endobronchial ultrasound bronchoscopy. The HMD experience was evaluated using a questionnaire. Finally, the HMD was used in bronchoscopy inspection and electromagnetic navigation of two patients presenting with hemoptysis.Results: In the phantom study, the perceived quality of video and ultrasound images was assessed using a visual analog scale, with 100% representing optimal image quality. The score for video quality was 58% (95% confidence interval [CI] 48%–68%) and for ultrasound image quality, the score was 43% (95% CI 30%–56%). Contrast, color rendering, and resolution were all considered suboptimal. Despite adjusting the brightness settings, video image rendering was considered too dark. Navigation to the target for biopsy sampling was accomplished by all participants, with no significant difference in procedure time between experienced and less experienced bronchoscopists. The overall system latency for the image stream was 0.33–0.35 s. Fifteen of the pulmonologists would consider using HoloLens for navigation in the periphery, and two would not consider using HoloLens in bronchoscopy at all. In the human study, bronchoscopy inspection was feasible for both patients.Conclusion: Bronchoscopy using an HMD was feasible in a lung phantom and in two patients. Video and ultrasound image quality was considered inferior to that of video monitors. HoloLens 2 was suboptimal for airway and mucosa inspection but may be adequate for virtual bronchoscopy navigation

Ultrasound Contrast Imaging - Improved Tissue Suppression in Amplitude Modulation

The ability to image myocardial perfusion is very important in order to detect coronary diseases. GE Vingmed Ultrasound uses contrast agent in combination with a pulse inversion (PI) technique to do the imaging. But this technique does not function sufficiently for all patients. Therefore have other techniques been tested out, including transmission of pulses with different amplitude (AM), to enhance the nonlinear signal from contrast bubbles. But a problem achieving sufficient cancellation of linear tissue signal is a feebleness of the method. In this diploma work has an effort been put into enhancing the tissue suppression in amplitude modulation. First the source of the lack of suppression was searched for by measuring electrical and acoustical pulses. The further examination revealed a dissymmetry in between pulses of different amplitude. To reduce this error were several attempts to make a compensation filter performed, which finally resulted in a filter created of echo data acquired from a tissue mimicking phantom. The filter was furthermore tested out on a flow phantom to see how it affected the signal from tissue and contrast bubbles, compared to the former use of a constant instead of the filter. The comparison showed 1.5-3.2 dB increase in tissue suppression (TS). But unfortunately did the filtering process slightly reduce the contrast signal as well, which resulted in a smaller increase of Contrast-to-Tissue-Ratio (CTR) than TS; 1.0-2.8 dB. During the work was the source of another problem concerning tissue suppression discovered. In earlier work by the author cite{prosjekt} the experimental results suffered from low TS around the transmitted frequency, which was found inexplicable at that time. This problem was revealed to be caused by reverberations from one pulse, interfering with the echoes from the next pulse. The solution suggested in this thesis is to transmit pulses in such a way that every pulse used to create an image has a relatively equal pulse in front. For instance, if a technique employs two pulses to create an image, and the first has half the amplitude and opposite polarity of the second. Then, to eliminate the reverberations must the first imaging pulse have a pulse in front which has half the amplitude and opposite polarity of the pulse in front of the second imaging pulse

Versatile robotic probe calibration for position tracking in ultrasound imaging

Within the field of ultrasound-guided procedures, there are a number of methods for ultrasound probe calibration. While these methods are usually developed for a specific probe, they are in principle easily adapted to other probes. In practice, however, the adaptation often proves tedious and this is impractical in a research setting, where new probes are tested regularly. Therefore, we developed a method which can be applied to a large variety of probes without adaptation. The method used a robot arm to move a plastic sphere submerged in water through the ultrasound image plane, providing a slow and precise movement. The sphere was then segmented from the recorded ultrasound images using a MATLAB programme and the calibration matrix was computed based on this segmentation in combination with tracking information. The method was tested on three very different probes demonstrating both great versatility and high accuracy

Versatile robotic probe calibration for position tracking in ultrasound imaging

Within the field of ultrasound-guided procedures, there are a number of methods for ultrasound probe calibration. While these methods are usually developed for a specific probe, they are in principle easily adapted to other probes. In practice, however, the adaptation often proves tedious and this is impractical in a research setting, where new probes are tested regularly. Therefore, we developed a method which can be applied to a large variety of probes without adaptation. The method used a robot arm to move a plastic sphere submerged in water through the ultrasound image plane, providing a slow and precise movement. The sphere was then segmented from the recorded ultrasound images using a MATLAB programme and the calibration matrix was computed based on this segmentation in combination with tracking information. The method was tested on three very different probes demonstrating both great versatility and high accuracy