Automatic Detection and Reproduction of Natural Head Position in Stereo-Photogrammetry.
Ontology highlight
ABSTRACT: Unlabelled
The aim of this study was to develop an automatic orientation calibration and reproduction method for recording the natural head position (NHP) in stereo-photogrammetry (SP). A board was used as the physical reference carrier for true verticals and NHP alignment mirror orientation. Orientation axes were detected and saved from the digital mesh model of the board. They were used for correcting the pitch, roll and yaw angles of the subsequent captures of patients' facial surfaces, which were obtained without any markings or sensors attached onto the patient. We tested the proposed method on two commercial active (3dMD) and passive (DI3D) SP devices. The reliability of the pitch, roll and yaw for the board placement were within ±0.039904°, ±0.081623°, and ±0.062320°; where standard deviations were 0.020234°, 0.045645° and 0.027211° respectively.Conclusion
Orientation-calibrated stereo-photogrammetry is the most accurate method (angulation deviation within ±0.1°) reported for complete NHP recording with insignificant clinical error.
SUBMITTER: Hsung TC
PROVIDER: S-EPMC4488321 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
Publications
Automatic Detection and Reproduction of Natural Head Position in Stereo-Photogrammetry.
Hsung Tai-Chiu TC Lo John J Li Tik-Shun TS Cheung Lim-Kwong LK
PloS one 20150630 6
<h4>Unlabelled</h4>The aim of this study was to develop an automatic orientation calibration and reproduction method for recording the natural head position (NHP) in stereo-photogrammetry (SP). A board was used as the physical reference carrier for true verticals and NHP alignment mirror orientation. Orientation axes were detected and saved from the digital mesh model of the board. They were used for correcting the pitch, roll and yaw angles of the subsequent captures of patients' facial surface ...[more]
Similar Datasets
Project description:Accurate and timely detection of plant diseases can help mitigate the worldwide losses experienced by the horticulture and agriculture industries each year. Thermal imaging provides a fast and non-destructive way of scanning plants for diseased regions and has been used by various researchers to study the effect of disease on the thermal profile of a plant. However, thermal image of a plant affected by disease has been known to be affected by environmental conditions which include leaf angles and depth of the canopy areas accessible to the thermal imaging camera. In this paper, we combine thermal and visible light image data with depth information and develop a machine learning system to remotely detect plants infected with the tomato powdery mildew fungus Oidium neolycopersici. We extract a novel feature set from the image data using local and global statistics and show that by combining these with the depth information, we can considerably improve the accuracy of detection of the diseased plants. In addition, we show that our novel feature set is capable of identifying plants which were not originally inoculated with the fungus at the start of the experiment but which subsequently developed disease through natural transmission.
| S-EPMC4393321 | biostudies-literature
Project description:Obtaining morphometric data on free-ranging marine megafauna is difficult, as traditional methods rely on post-mortem or live-capture techniques. We linked stereo-laser photogrammetry with long-term demographic data to compare length-at-age (LaA) growth curves of two well-studied populations of Indo-Pacific bottlenose dolphins (Tursiops aduncus) in south-western (SW) and Shark Bay (SB), mid-western Australia. First, we determined the relationship between total length (TL) and blowhole-to-dorsal fin (BH-DF) length from post-mortem subjects (R2?=?0.99, n?=?12). We then predicted TL from laser-derived BH-DF measurements of 129 and 74 known-age individuals in SW and SB, respectively. Richards growth models best described our LaA data. While birth length (103-110?cm) was similar between study regions, TL estimates at 1, 3, 12, and 25 years differed significantly (p?<?0.001). Asymptotic length of adult males (SW?=?246?cm, SB?=?201?cm) and females (SW?=?244?cm, SB?=?200?cm) also differed significantly. Morphotypic variations likely reflect regional adaptations to local water temperatures, with the temperate SW having cooler waters than sub-tropical SB. We demonstrate the effectiveness of a non-invasive technique to understand ecological, demographic and life-history characteristics of long-lived marine megafauna, which are critical parameters for informing conservation and management actions.
| S-EPMC6706378 | biostudies-literature
Project description:Alfalfa is the most widely cultivated forage legume, with approximately 30 million hectares planted worldwide. Genetic improvements in alfalfa have been highly successful in developing cultivars with exceptional winter hardiness and disease resistance traits. However, genetic improvements have been limited for complex economically important traits such as biomass. One of the major bottlenecks is the labor-intensive phenotyping burden for biomass selection. In this study, we employed two alfalfa fields to pave a path to overcome the challenge by using UAV images with fully automatic field plot segmentation for high-throughput phenotyping. The first field was used to develop the prediction model and the second field to validate the predictions. The first and second fields had 808 and 1025 plots, respectively. The first field had three harvests with biomass measured in May, July, and September of 2019. The second had one harvest with biomass measured in September of 2019. These two fields were imaged one day before harvesting with a DJI Phantom 4 pro UAV carrying an additional Sentera multispectral camera. Alfalfa plot images were extracted by GRID software to quantify vegetative area based on the Normalized Difference Vegetation Index. The prediction model developed from the first field explained 50-70% (R Square) of biomass variation in the second field by incorporating four features from UAV images: vegetative area, plant height, Normalized Green-Red Difference Index, and Normalized Difference Red Edge Index. This result suggests that UAV-based, high-throughput phenotyping could be used to improve the efficiency of the biomass selection process in alfalfa breeding programs.
| S-EPMC7870825 | biostudies-literature
Project description:Local depth variation is a distinctive property of natural scenes, but its effects on perception have only recently begun to be investigated. Depth variation in natural scenes is due to depth edges between objects and surface nonuniformities within objects. Here, we demonstrate how natural depth variation impacts performance in two fundamental tasks related to stereopsis: half-occlusion detection and disparity detection. We report the results of a computational study that uses a large database of natural stereo-images and coregistered laser-based distance measurements. First, we develop a procedure for precisely sampling stereo-image patches from the stereo-images and then quantify the local depth variation in each patch by its disparity contrast. Next, we show that increased disparity contrast degrades half-occlusion detection and disparity detection performance and changes the size and shape of the spatial integration areas ("receptive fields") that optimize performance. Then, we show that a simple image-computable binocular statistic predicts disparity contrast in natural scenes. Finally, we report the most likely spatial patterns of disparity variation and disparity discontinuities (half-occlusions) in natural scenes. Our findings motivate computational and psychophysical investigations of the mechanisms that underlie stereo processing tasks in local regions of natural scenes.
| S-EPMC6005632 | biostudies-literature
Project description:Properly constructed stereoscopic images are aligned vertically on the display screen, so on-screen binocular disparities are strictly horizontal. If the viewer's inter-ocular axis is also horizontal, he/she makes horizontal vergence eye movements to fuse the stereoscopic image. However, if the viewer's head is rolled to the side, the on-screen disparities now have horizontal and vertical components at the eyes. Thus, the viewer must make horizontal and vertical vergence movements to binocularly fuse the two images. Vertical vergence movements occur naturally, but they are usually quite small. Much larger movements are required when viewing stereoscopic images with the head rotated to the side. We asked whether the vertical vergence eye movements required to fuse stereoscopic images when the head is rolled cause visual discomfort. We also asked whether the ability to see stereoscopic depth is compromised with head roll. To answer these questions, we conducted behavioral experiments in which we simulated head roll by rotating the stereo display clockwise or counter-clockwise while the viewer's head remained upright relative to gravity. While viewing the stimulus, subjects performed a psychophysical task. Visual discomfort increased significantly with the amount of stimulus roll and with the magnitude of on-screen horizontal disparity. The ability to perceive stereoscopic depth also declined with increasing roll and on-screen disparity. The magnitude of both effects was proportional to the magnitude of the induced vertical disparity. We conclude that head roll is a significant cause of viewer discomfort and that it also adversely affects the perception of depth from stereoscopic displays.
| S-EPMC3777229 | biostudies-other
Project description:Acute Intracranial hemorrhage (ICH) is a life-threatening disease that requires emergency medical attention, which is routinely diagnosed using non-contrast head CT imaging. The diagnostic accuracy of acute ICH on CT varies greatly among radiologists due to the difficulty of interpreting subtle findings and the time pressure associated with the ever-increasing workload. The use of artificial intelligence technology may help automate the process and assist radiologists for more prompt and better decision-making. In this work, we design a deep learning approach that mimics the interpretation process of radiologists, and combines a 2D CNN model and two sequence models to achieve accurate acute ICH detection and subtype classification. Being developed using the extensive 2019-RSNA Brain CT Hemorrhage Challenge dataset with over 25000 CT scans, our deep learning algorithm can accurately classify the acute ICH and its five subtypes with AUCs of 0.988 (ICH), 0.984 (EDH), 0.992 (IPH), 0.996 (IVH), 0.985 (SAH), and 0.983 (SDH), respectively, reaching the accuracy level of expert radiologists. Our method won 1st place among 1345 teams from 75 countries in the RSNA challenge. We have further evaluated our algorithm on two independent external validation datasets with 75 and 491 CT scans, respectively, and our method maintained high AUCs of 0.964 and 0.949 for acute ICH detection. These results have demonstrated the high performance and robust generalization ability of our proposed method, which makes it a useful second-read or triage tool that can facilitate routine clinical applications.
| S-EPMC8377493 | biostudies-literature
Project description:X-ray computed tomography (CT) imaging of the brain is commonly used in diagnostic settings. Although CT scans are primarily used in clinical practice, they are increasingly used in research. A fundamental processing step in brain imaging research is brain extraction - the process of separating the brain tissue from all other tissues. Methods for brain extraction have either been 1) validated but not fully automated, or 2) fully automated and informally proposed, but never formally validated.To systematically analyze and validate the performance of FSL's brain extraction tool (BET) on head CT images of patients with intracranial hemorrhage. This was done by comparing the manual gold standard with the results of several versions of automatic brain extraction and by estimating the reliability of automated segmentation of longitudinal scans. The effects of the choice of BET parameters and data smoothing is studied and reported.All images were thresholded using a 0-100 Hounsfield unit (HU) range. In one variant of the pipeline, data were smoothed using a 3-dimensional Gaussian kernel (?=1mm(3)) and re-thresholded to 0-100HU; in the other, data were not smoothed. BET was applied using 1 of 3 fractional intensity (FI) thresholds: 0.01, 0.1, or 0.35 and any holes in the brain mask were filled. For validation against a manual segmentation, 36 images from patients with intracranial hemorrhage were selected from 19 different centers from the MISTIE (Minimally Invasive Surgery plus recombinant-tissue plasminogen activator for Intracerebral Evacuation) stroke trial. Intracranial masks of the brain were manually created by one expert CT reader. The resulting brain tissue masks were quantitatively compared to the manual segmentations using sensitivity, specificity, accuracy, and the Dice Similarity Index (DSI). Brain extraction performance across smoothing and FI thresholds was compared using the Wilcoxon signed-rank test. The intracranial volume (ICV) of each scan was estimated by multiplying the number of voxels in the brain mask by the dimensions of each voxel for that scan. From this, we calculated the ICV ratio comparing manual and automated segmentation: ICVautomated/ICVmanual. To estimate the performance in a large number of scans, brain masks were generated from the 6 BET pipelines for 1095 longitudinal scans from 129 patients. Failure rates were estimated from visual inspection. ICV of each scan was estimated and an intraclass correlation (ICC) was estimated using a one-way ANOVA.Smoothing images improves brain extraction results using BET for all measures except specificity (all p<0.01, uncorrected), irrespective of the FI threshold. Using an FI of 0.01 or 0.1 performed better than 0.35. Thus, all reported results refer only to smoothed data using an FI of 0.01 or 0.1. Using an FI of 0.01 had a higher median sensitivity (0.9901) than an FI of 0.1 (0.9884, median difference: 0.0014, p<0.001), accuracy (0.9971 vs. 0.9971; median difference: 0.0001, p<0.001), and DSI (0.9895 vs. 0.9894; median difference: 0.0004, p<0.001) and lower specificity (0.9981 vs. 0.9982; median difference: -0.0001, p<0.001). These measures are all very high indicating that a range of FI values may produce visually indistinguishable brain extractions. Using smoothed data and an FI of 0.01, the mean (SD) ICV ratio was 1.002 (0.008); the mean being close to 1 indicates the ICV estimates are similar for automated and manual segmentation. In the 1095 longitudinal scans, this pipeline had a low failure rate (5.2%) and the ICC estimate was high (0.929, 95% CI: 0.91, 0.945) for successfully extracted brains.BET performs well at brain extraction on thresholded, 1mm(3) smoothed CT images with an FI of 0.01 or 0.1. Smoothing before applying BET is an important step not previously discussed in the literature. Analysis code is provided.
| S-EPMC4446187 | biostudies-other
Project description:Treatment planning is time-consuming and the outcome depends on the person performing the optimization. A system that automates treatment planning could potentially reduce the manual time required for optimization and could also provide a method to reduce the variation between persons performing radiation dose planning (dosimetrist) and potentially improve the overall plan quality. This study evaluates the performance of the Auto-Planning module that has recently become clinically available in the Pinnacle3 radiation therapy treatment planning system. Twenty-six clinically delivered head and neck treatment plans were reoptimized with the Auto-Planning module. Comparison of the two types of treatment plans were performed using DVH metrics and a blinded clinical evaluation by two senior radiation oncologists using a scale from one to six. Both evaluations investigated dose coverage of target and dose to healthy tissues. Auto-Planning was able to produce clinically acceptable treatment plans in all 26 cases. Target coverages in the two types of plans were similar, but automatically generated plans had less irradiation of healthy tissue. In 94% of the evaluations, the autoplans scored at least as high as the previously delivered clinical plans. For all patients, the Auto-Planning tool produced clinically acceptable head and neck treatment plans without any manual intervention, except for the initial target and OAR delineations. The main benefit of the method is the likely improvement in the overall treatment quality since consistent, high-quality plans are generated which even can be further optimized, if necessary. This makes it possible for the dosimetrist to focus more time on difficult dose planning goals and to spend less time on the more tedious parts of the planning process.
| S-EPMC5690191 | biostudies-literature
Project description:BackgroundMounting evidence suggests several diseases and biological processes target transcription termination to misregulate gene expression. Disruption of transcription termination leads to readthrough transcription past the 3' end of genes, which can result in novel transcripts, changes in epigenetic states and altered 3D genome structure.ResultsWe developed Automatic Readthrough Transcription Detection (ARTDeco), a tool to detect and analyze multiple features of readthrough transcription from RNA-seq and other next-generation sequencing (NGS) assays that profile transcriptional activity. ARTDeco robustly quantifies the global severity of readthrough phenotypes, and reliably identifies individual genes that fail to terminate (readthrough genes), are aberrantly transcribed due to upstream termination failure (read-in genes), and novel transcripts created as a result of readthrough (downstream of gene or DoG transcripts). We used ARTDeco to characterize readthrough transcription observed during influenza A virus (IAV) infection, validating its specificity and sensitivity by comparing its performance in samples infected with a mutant virus that fails to block transcription termination. We verify ARTDeco's ability to detect readthrough as well as identify read-in genes from different experimental assays across multiple experimental systems with known defects in transcriptional termination, and show how these results can be leveraged to improve the interpretation of gene expression and downstream analysis. Applying ARTDeco to a gene expression data set from IAV-infected monocytes from different donors, we find strong evidence that read-in gene-associated expression quantitative trait loci (eQTLs) likely regulate genes upstream of read-in genes. This indicates that taking readthrough transcription into account is important for the interpretation of eQTLs in systems where transcription termination is blocked.ConclusionsARTDeco aids researchers investigating readthrough transcription in a variety of systems and contexts.
| S-EPMC7249449 | biostudies-literature
Project description:Computer vision has greatly advanced recently. Since AlexNet was first introduced, many modified deep learning architectures have been developed and they are still evolving. However, there are few studies comparing these architectures in the field of ophthalmology. This study compared the performance of various state-of-the-art deep-learning architectures for detecting the optic nerve head and vertical cup-to-disc ratio in fundus images. Three different architectures were compared: YOLO V3, ResNet, and DenseNet. We compared various aspects of performance, which were not confined to the accuracy of detection but included, as well, the processing time, diagnostic performance, effect of the graphic processing unit (GPU), and image resolution. In general, as the input image resolution increased, the classification accuracy, localization error, and diagnostic performance all improved, but the optimal architecture differed depending on the resolution. The processing time was significantly accelerated with GPU assistance; even at the high resolution of 832 × 832, it was approximately 170 ms, which was at least 26 times slower without GPU. The choice of architecture may depend on the researcher's purpose when balancing between speed and accuracy. This study provides a guideline to determine deep learning architecture, optimal image resolution, and the appropriate hardware.
| S-EPMC7081256 | biostudies-literature