The residual STL volume as a metric to evaluate accuracy and reproducibility of anatomic models for 3D printing: application in the validation of 3D-printable models of maxillofacial bone from reduced radiation dose CT images.

BackgroundThe effects of reduced radiation dose CT for the generation of maxillofacial bone STL models for 3D printing is currently unknown. Images of two full-face transplantation patients scanned with non-contrast 320-detector row CT were reconstructed at fractions of the acquisition radiation dose using noise simulation software and both filtered back-projection (FBP) and Adaptive Iterative Dose Reduction 3D (AIDR3D). The maxillofacial bone STL model segmented with thresholding from AIDR3D images at 100 % dose was considered the reference. For all other dose/reconstruction method combinations, a "residual STL volume" was calculated as the topologic subtraction of the STL model derived from that dataset from the reference and correlated to radiation dose.ResultsThe residual volume decreased with increasing radiation dose and was lower for AIDR3D compared to FBP reconstructions at all doses. As a fraction of the reference STL volume, the residual volume decreased from 2.9 % (20 % dose) to 1.4 % (50 % dose) in patient 1, and from 4.1 % to 1.9 %, respectively in patient 2 for AIDR3D reconstructions. For FBP reconstructions it decreased from 3.3 % (20 % dose) to 1.0 % (100 % dose) in patient 1, and from 5.5 % to 1.6 %, respectively in patient 2. Its morphology resembled a thin shell on the osseous surface with average thickness <0.1 mm.ConclusionThe residual volume, a topological difference metric of STL models of tissue depicted in DICOM images supports that reduction of CT dose by up to 80 % of the clinical acquisition in conjunction with iterative reconstruction yields maxillofacial bone models accurate for 3D printing

Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hopkinson, B. M., King, A. C., Owen, D. P., Johnson-Roberson, M., Long, M. H., & Bhandarkar, S. M. Automated classification of three-dimensional reconstructions of coral reefs using convolutional neural networks. PLoS One, 15(3), (2020): e0230671, doi: 10.1371/journal.pone.0230671.Coral reefs are biologically diverse and structurally complex ecosystems, which have been severally affected by human actions. Consequently, there is a need for rapid ecological assessment of coral reefs, but current approaches require time consuming manual analysis, either during a dive survey or on images collected during a survey. Reef structural complexity is essential for ecological function but is challenging to measure and often relegated to simple metrics such as rugosity. Recent advances in computer vision and machine learning offer the potential to alleviate some of these limitations. We developed an approach to automatically classify 3D reconstructions of reef sections and assessed the accuracy of this approach. 3D reconstructions of reef sections were generated using commercial Structure-from-Motion software with images extracted from video surveys. To generate a 3D classified map, locations on the 3D reconstruction were mapped back into the original images to extract multiple views of the location. Several approaches were tested to merge information from multiple views of a point into a single classification, all of which used convolutional neural networks to classify or extract features from the images, but differ in the strategy employed for merging information. Approaches to merging information entailed voting, probability averaging, and a learned neural-network layer. All approaches performed similarly achieving overall classification accuracies of ~96% and >90% accuracy on most classes. With this high classification accuracy, these approaches are suitable for many ecological applications.This study was funded by grants from the Alfred P. Sloan Foundation (BMH, BR2014-049; https://sloan.org), and the National Science Foundation (MHL, OCE-1657727; https://www.nsf.gov). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript

EchoFusion: Tracking and Reconstruction of Objects in 4D Freehand Ultrasound Imaging without External Trackers

Ultrasound (US) is the most widely used fetal imaging technique. However, US images have limited capture range, and suffer from view dependent artefacts such as acoustic shadows. Compounding of overlapping 3D US acquisitions into a high-resolution volume can extend the field of view and remove image artefacts, which is useful for retrospective analysis including population based studies. However, such volume reconstructions require information about relative transformations between probe positions from which the individual volumes were acquired. In prenatal US scans, the fetus can move independently from the mother, making external trackers such as electromagnetic or optical tracking unable to track the motion between probe position and the moving fetus. We provide a novel methodology for image-based tracking and volume reconstruction by combining recent advances in deep learning and simultaneous localisation and mapping (SLAM). Tracking semantics are established through the use of a Residual 3D U-Net and the output is fed to the SLAM algorithm. As a proof of concept, experiments are conducted on US volumes taken from a whole body fetal phantom, and from the heads of real fetuses. For the fetal head segmentation, we also introduce a novel weak annotation approach to minimise the required manual effort for ground truth annotation. We evaluate our method qualitatively, and quantitatively with respect to tissue discrimination accuracy and tracking robustness.Comment: MICCAI Workshop on Perinatal, Preterm and Paediatric Image analysis (PIPPI), 201

Structured Light-Based 3D Reconstruction System for Plants.

Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance

3D Face Reconstruction by Learning from Synthetic Data

Fast and robust three-dimensional reconstruction of facial geometric structure from a single image is a challenging task with numerous applications. Here, we introduce a learning-based approach for reconstructing a three-dimensional face from a single image. Recent face recovery methods rely on accurate localization of key characteristic points. In contrast, the proposed approach is based on a Convolutional-Neural-Network (CNN) which extracts the face geometry directly from its image. Although such deep architectures outperform other models in complex computer vision problems, training them properly requires a large dataset of annotated examples. In the case of three-dimensional faces, currently, there are no large volume data sets, while acquiring such big-data is a tedious task. As an alternative, we propose to generate random, yet nearly photo-realistic, facial images for which the geometric form is known. The suggested model successfully recovers facial shapes from real images, even for faces with extreme expressions and under various lighting conditions.Comment: The first two authors contributed equally to this wor

On Acquisition and Analysis of a Dataset Comprising of Gait, Ear and Semantic data

In outdoor scenarios such as surveillance where there is very little control over the environments, complex computer vision algorithms are often required for analysis. However constrained environments, such as walkways in airports where the surroundings and the path taken by individuals can be controlled, provide an ideal application for such systems. Figure 1.1 depicts an idealised constrained environment. The path taken by the subject is restricted to a narrow path and once inside is in a volume where lighting and other conditions are controlled to facilitate biometric analysis. The ability to control the surroundings and the flow of people greatly simplifes the computer vision task, compared to typical unconstrained environments. Even though biometric datasets with greater than one hundred people are increasingly common, there is still very little known about the inter and intra-subject variation in many biometrics. This information is essential to estimate the recognition capability and limits of automatic recognition systems. In order to accurately estimate the inter- and the intra- class variance, substantially larger datasets are required [40]. Covariates such as facial expression, headwear, footwear type, surface type and carried items are attracting increasing attention; although considering the potentially large impact on an individuals biometrics, large trials need to be conducted to establish how much variance results. This chapter is the first description of the multibiometric data acquired using the University of Southampton's Multi-Biometric Tunnel [26, 37]; a biometric portal using automatic gait, face and ear recognition for identification purposes. The tunnel provides a constrained environment and is ideal for use in high throughput security scenarios and for the collection of large datasets. We describe the current state of data acquisition of face, gait, ear, and semantic data and present early results showing the quality and range of data that has been collected. The main novelties of this dataset in comparison with other multi-biometric datasets are: 1. gait data exists for multiple views and is synchronised, allowing 3D reconstruction and analysis; 2. the face data is a sequence of images allowing for face recognition in video; 3. the ear data is acquired in a relatively unconstrained environment, as a subject walks past; and 4. the semantic data is considerably more extensive than has been available previously. We shall aim to show the advantages of this new data in biometric analysis, though the scope for such analysis is considerably greater than time and space allows for here