A Novel Semi-automated Proofreading and Mesh Error Detection Pipeline for Neuron Extension.

The immense scale and complexity of neuronal electron microscopy (EM) datasets pose significant challenges in data processing, validation, and interpretation, necessitating the development of efficient, automated, and scalable error-detection methodologies. This paper proposes a novel approach that employs mesh processing techniques to identify potential error locations near neuronal tips. Error detection at tips is a particularly important challenge since these errors usually indicate that many synapses are falsely split from their parent neuron, injuring the integrity of the connectomic reconstruction. Additionally, we draw implications and results from an implementation of this error detection in a semi-automated proofreading pipeline. Manual proofreading is a laborious, costly, and currently necessary method for identifying the errors in the machine learning based segmentation of neural tissue. This approach streamlines the process of proofreading by systematically highlighting areas likely to contain inaccuracies and guiding proofreaders towards potential continuations, accelerating the rate at which errors are corrected.

Kinematic and Biomechanical Response of Post-Mortem Human Subjects Under Various Pre-Impact Postures to High-Rate Vertical Loading Conditions.

Limited data exist on the injury tolerance and biomechanical response of humans to high-rate, under-body blast (UBB) loading conditions that are commonly seen in current military operations, and there are no data examining the influence of occupant posture on response. Additionally, no anthropomorphic test device (ATD) currently exists that can properly assess the response of humans to high-rate UBB loading. Therefore, the purpose of this research was to examine the response of post-mortem human surrogates (PMHS) in various seated postures to high-rate, vertical loading representative of those conditions seen in theater. In total, six PMHS tests were conducted using loading pulses applied directly to the pelvis and feet of the PMHS: three in an acute posture (foot, knee, and pelvis angles of 75°, 75°, and 36°, respectively), and three in an obtuse posture (15° reclined torso, and foot, knee, and pelvis angles of 105°, 105°, and 49.5°, respectively). Tests were conducted with a seat velocity pulse that peaked at ~4 m/s with a 30-40 ms time to peak velocity (TTP) and a floor velocity that peaked at 6.9-8.0 m/s (2-2.75 ms TTP). Posture condition had no influence on skeletal injuries sustained, but did result in altered leg kinematics, with leg entrapment under the seat occurring in the acute posture, and significant forward leg rotations occurring in the obtuse posture. These data will be used to validate a prototype ATD meant for use in high-rate UBB loading scenarios.

Surgical fiducial segmentation and tracking for pose estimation based on ultrasound B-mode images.

Doppler ultrasound is a non-invasive diagnostic tool for the quantitative measurement of blood flow. However, given that it provides velocity data that is dependent on the location and angle of measurement, repeat measurements to detect problems over time may require an expert to return to the same location. We therefore developed an image-guidance system based on ultrasound B-mode images that enables an inexperienced user to position the ultrasound probe at the same site repeatedly in order to acquire a comparable time series of Doppler readings. The system utilizes a bioresorbable fiducial and complementing software composed of the fiducial detection, key points tracking, probe pose estimation, and graphical user interface (GUI) modules. The fiducial is an echogenic marker that is implanted at the surgical site and can be detected and tracked during ultrasound B-mode screening. The key points on the marker can next be used to determine the pose of the ultrasound probe with respect to the marker. The 3D representation of the probe with its position and orientation are then displayed in the GUI for the user guidance. The fiducial detection has been tested on the data sets collected from three animal studies. The pose estimation algorithm was validated by five data sets collected by a UR5 robot. We tested the system on a plastisol phantom and showed that it can detect and track the fiducial marker while displaying the probe pose in real-time.

In vivo visualization of prostate brachytherapy seeds with photoacoustic imaging.

We conducted a canine study to investigate the in vivo feasibility of photoacoustic imaging for intraoperative updates to brachytherapy treatment plans. A fiber coupled to a 1064-nm Nd:YAG laser was inserted into high-dose-rate brachytherapy needles, which diffused light spherically. These needles were inserted through the perineum into the prostate for interstitial light delivery and the resulting acoustic waves were detected with a transrectal ultrasound probe. Postoperative computed tomography images and ex vivo photoacoustic images confirmed seed locations. Limitations with insufficient light delivery were mitigated with short-lag spatial coherence (SLSC) beamforming, providing a 10-20 dB contrast improvement over delay-and-sum (DAS) beamforming for pulse energies ranging from 6.8 to 10.5 mJ with a fiber-seed distance as large as 9.5 mm. For the same distance and the same range of energy densities, signal-to-noise ratios (SNRs) were similar while the contrast-to-noise ratio (CNR) was higher in SLSC compared to DAS images. Challenges included visualization of signals associated with the interstitial fiber tip and acoustic reverberations between seeds separated by ≤ 2 mm. Results provide insights into the potential for clinical translation to humans.

An image-guidance system for dynamic dose calculation in prostate brachytherapy using ultrasound and fluoroscopy.

PURPOSE: Brachytherapy is a standard option of care for prostate cancer patients but may be improved by dynamic dose calculation based on localized seed positions. The American Brachytherapy Society states that the major current limitation of intraoperative treatment planning is the inability to localize the seeds in relation to the prostate. An image-guidance system was therefore developed to localize seeds for dynamic dose calculation. METHODS: The proposed system is based on transrectal ultrasound (TRUS) and mobile C-arm fluoroscopy, while using a simple fiducial with seed-like markers to compute pose from the nonencoded C-arm. Three or more fluoroscopic images and an ultrasound volume are acquired and processed by a pipeline of algorithms: (1) seed segmentation, (2) fiducial detection with pose estimation, (3) seed matching with reconstruction, and (4) fluoroscopy-to-TRUS registration. RESULTS: The system was evaluated on ten phantom cases, resulting in an overall mean error of 1.3 mm. The system was also tested on 37 patients and each algorithm was evaluated. Seed segmentation resulted in a 1% false negative rate and 2% false positive rate. Fiducial detection with pose estimation resulted in a 98% detection rate. Seed matching with reconstruction had a mean error of 0.4 mm. Fluoroscopy-to-TRUS registration had a mean error of 1.3 mm. Moreover, a comparison of dose calculations between the authors' intraoperative method and an independent postoperative method shows a small difference of 7% and 2% forD90 and V100, respectively. Finally, the system demonstrated the ability to detect cold spots and required a total processing time of approximately 1 min. CONCLUSIONS: The proposed image-guidance system is the first practical approach to dynamic dose calculation, outperforming earlier solutions in terms of robustness, ease of use, and functional completeness.

Short-lag spatial coherence beamforming of photoacoustic images for enhanced visualization of prostate brachytherapy seeds.

Prostate brachytherapy, administered by implanting tiny radioactive seeds to treat prostate cancer, currently relies on transrectal ultrasound imaging for intraoperative visualization of the metallic seeds. Photoacoustic (PA) imaging has been suggested as a feasible alternative to ultrasound imaging due to its superior sensitivity to metal surrounded by tissue. However, PA images suffer from poor contrast when seeds are distant from the light source. We propose a transperineal light delivery method and investigate the application of a short-lag spatial coherence (SLSC) beamformer to enhance low-contrast photoacoustic signals that are distant from this type of light source. Performance is compared to a conventional delay-and-sum beamformer. A pure gelatin phantom was implanted with black ink-coated brachytherapy seeds and the mean contrast was improved by 3-25 dB with the SLSC beamformer for fiber-seed distances ranging 0.6-6.3 cm, when approximately 10% of the receive aperture elements were included in the short-lag sum. For fiber-seed distances greater than 3-4 cm, the mean contrast-to-noise ratio (CNR) was approximately doubled with the SLSC beamformer, while mean signal-to-noise ratios (SNR) were mostly similar with both beamformers. Lateral resolution was decreased by 2 mm, but improved with larger short-lag values at the expense of poorer CNR and SNR. Similar contrast and CNR improvements were achieved with an uncoated brachytherapy seed implanted in ex vivo tissue. Results indicate that the SLSC beamformer has potential to enhance the visualization of prostate brachytherapy seeds that are distant from the light source.

A Dynamic Dosimetry System for Prostate Brachytherapy.

The lack of dynamic dosimetry tools for permanent prostate brachytherapy causes otherwise avoidable problems in prostate cancer patient care. The goal of this work is to satisfy this need in a readily adoptable manner. Using the ubiquitous ultrasound scanner and mobile non-isocentric C-arm, we show that dynamic dosimetry is now possible with only the addition of an arbitrarily configured marker-based fiducial. Not only is the system easily configured from accessible hardware, but it is also simple and convenient, requiring little training from technicians. Furthermore, the proposed system is built upon robust algorithms of seed segmentation, fiducial detection, seed reconstruction, and image registration. All individual steps of the pipeline have been thoroughly tested, and the system as a whole has been validated on a study of 25 patients. The system has shown excellent results of accurately computing dose, and does so with minimal manual intervention, therefore showing promise for widespread adoption of dynamic dosimetry.

Ultrasound-fluoroscopy registration for prostate brachytherapy dosimetry.

Prostate brachytherapy is a treatment for prostate cancer using radioactive seeds that are permanently implanted in the prostate. The treatment success depends on adequate coverage of the target gland with a therapeutic dose, while sparing the surrounding tissue. Since seed implantation is performed under transrectal ultrasound (TRUS) imaging, intraoperative localization of the seeds in ultrasound can provide physicians with dynamic dose assessment and plan modification. However, since all the seeds cannot be seen in the ultrasound images, registration between ultrasound and fluoroscopy is a practical solution for intraoperative dosimetry. In this manuscript, we introduce a new image-based nonrigid registration method that obviates the need for manual seed segmentation in TRUS images and compensates for the prostate displacement and deformation due to TRUS probe pressure. First, we filter the ultrasound images for subsequent registration using thresholding and Gaussian blurring. Second, a computationally efficient point-to-volume similarity metric, an affine transformation and an evolutionary optimizer are used in the registration loop. A phantom study showed final registration errors of 0.84 ± 0.45 mm compared to ground truth. In a study on data from 10 patients, the registration algorithm showed overall seed-to-seed errors of 1.7 ± 1.0 mm and 1.5 ± 0.9 mm for rigid and nonrigid registration methods, respectively, performed in approximately 30s per patient.

Real-time photoacoustic imaging of prostate brachytherapy seeds using a clinical ultrasound system.

Prostate brachytherapy is a popular prostate cancer treatment option that involves the permanent implantation of radioactive seeds into the prostate. However, contemporary brachytherapy procedure is limited by the lack of an imaging system that can provide real-time seed-position feedback. While many other imaging systems have been proposed, photoacoustic imaging has emerged as a potential ideal modality to address this need, since it could easily be incorporated into the current ultrasound system used in the operating room. We present such a photoacoustic imaging system built around a clinical ultrasound system to achieve the task of visualizing and localizing seeds. We performed several experiments to analyze the effects of various parameters on the appearance of brachytherapy seeds in photoacoustic images. We also imaged multiple seeds in an ex vivo dog prostate phantom to demonstrate the possibility of using this system in a clinical setting. Although still in its infancy, these initial results of a photoacoustic imaging system for the application of prostate brachytherapy seed localization are highly promising.

Automatic segmentation of radiographic fiducial and seeds from X-ray images in prostate brachytherapy.

Prostate brachytherapy guided by transrectal ultrasound is a common treatment option for early stage prostate cancer. Prostate cancer accounts for 28% of cancer cases and 11% of cancer deaths in men with 217,730 estimated new cases and 32,050 estimated deaths in 2010 in the United States alone. The major current limitation is the inability to reliably localize implanted radiation seeds spatially in relation to the prostate. Multimodality approaches that incorporate X-ray for seed localization have been proposed, but they require both accurate tracking of the imaging device and segmentation of the seeds. Some use image-based radiographic fiducials to track the X-ray device, but manual intervention is needed to select proper regions of interest for segmenting both the tracking fiducial and the seeds, to evaluate the segmentation results, and to correct the segmentations in the case of segmentation failure, thus requiring a significant amount of extra time in the operating room. In this paper, we present an automatic segmentation algorithm that simultaneously segments the tracking fiducial and brachytherapy seeds, thereby minimizing the need for manual intervention. In addition, through the innovative use of image processing techniques such as mathematical morphology, Hough transforms, and RANSAC, our method can detect and separate overlapping seeds that are common in brachytherapy implant images. Our algorithm was validated on 55 phantom and 206 patient images, successfully segmenting both the fiducial and seeds with a mean seed segmentation rate of 96% and sub-millimeter accuracy.

Point-to-volume registration of prostate implants to ultrasound.

Ultrasound-Fluoroscopy fusion is a key step toward intraoperative dosimetry for prostate brachytherapy. We propose a method for intensity-based registration of fluoroscopy to ultrasound that obviates the need for seed segmentation required for seed-based registration. We employ image thresholding and morphological and Gaussian filtering to enhance the image intensity distribution of ultrasound volume. Finally, we find the registration parameters by maximizing a point-to-volume similarity metric. We conducted an experiment on a ground truth phantom and achieved registration error of 0.7 +/- 0.2 mm. Our clinical results on 5 patient data sets show excellent visual agreement between the registered seeds and the ultrasound volume with a seed-to-seed registration error of 1.8 +/- 0.9mm. With low registration error, high computational speed and no need for manual seed segmentation, our method is promising for clinical application.

Intraoperative 3D reconstruction of prostate brachytherapy implants with automatic pose correction.

The success of prostate brachytherapy critically depends on delivering adequate dose to the prostate gland, and the capability of intraoperatively localizing implanted seeds provides potential for dose evaluation and optimization during therapy. REDMAPS is a recently reported algorithm that carries out seed localization by detecting, matching and reconstructing seeds in only a few seconds from three acquired x-ray images (Lee et al 2011 IEEE Trans. Med. Imaging 29 38-51). In this paper, we present an automatic pose correction (APC) process that is combined with REDMAPS to allow for both more accurate seed reconstruction and the use of images with relatively large pose errors. APC uses a set of reconstructed seeds as a fiducial and corrects the image pose by minimizing the overall projection error. The seed matching and APC are iteratively computed until a stopping condition is met. Simulations and clinical studies show that APC significantly improves the reconstructions with an overall average matching rate of ⩾99.4%, reconstruction error of ⩽0.5 mm, and the matching solution optimality of ⩾99.8%.

MRI-BASED PROSTATE BRACHYTHERAPY SEED LOCALIZATION.

A magnetic resonance imaging (MRI) pulse sequence and a corresponding image processing algorithm to localize prostate brachytherapy seeds during or after therapy are presented. Inversion-Recovery with ON-resonant water suppression (IRON) is an MRI methodology that generates positive contrast in regions of magnetic field susceptibility, as created by prostate brachytherapy seeds. Phantoms comprising of several materials found in brachytherapy seeds were created to assess the usability of the IRON pulse sequence for imaging seeds. Resulting images show that seed materials are clearly visible with high contrast using IRON, agreeing with theoretical predictions. A seed localization algorithm to process IRON images demonstrates the potential of this imaging technique for seed localization and dosimetry.

Automatic segmentation of seeds and fluoroscope tracking (FTRAC) fiducial in prostate brachytherapy x-ray images.

C-arm X-ray fluoroscopy-based radioactive seed localization for intraoperative dosimetry of prostate brachytherapy is an active area of research. The fluoroscopy tracking (FTRAC) fiducial is an image-based tracking device composed of radio-opaque BBs, lines, and ellipses that provides an effective means for pose estimation so that three-dimensional reconstruction of the implanted seeds from multiple X-ray images can be related to the ultrasound-computed prostate volume. Both the FTRAC features and the brachytherapy seeds must be segmented quickly and accurately during the surgery, but current segmentation algorithms are inhibitory in the operating room (OR). The first reason is that current algorithms require operators to manually select a region of interest (ROI), preventing automatic pipelining from image acquisition to seed reconstruction. Secondly, these algorithms fail often, requiring operators to manually correct the errors. We propose a fast and effective ROI-free automatic FTRAC and seed segmentation algorithm to minimize such human intervention. The proposed algorithm exploits recent image processing tools to make seed reconstruction as easy and convenient as possible. Preliminary results on 162 patient images show this algorithm to be fast, effective, and accurate for all features to be segmented. With near perfect success rates and subpixel differences to manual segmentation, our automatic FTRAC and seed segmentation algorithm shows promising results to save crucial time in the OR while reducing errors.