arXiv subjects

Jonathan Shapey

Publications and source records attributed to Jonathan Shapey.

32 records · Page 2Linked to original sources

arXiv2023

A comparative study of analytical models of diffuse reflectance in homogeneous biological tissues: Gelatin based phantoms and Monte Carlo experiments

Information about tissue oxygen saturation ($StO_2$) and other related important physiological parameters can be extracted from diffuse reflectance spectra measured through non-contact imaging. Three analytical optical reflectance models for homogeneous, semi-infinite, tissue have been proposed (Modified Beer-Lambert, Jacques 1999, Yudovsky 2009) but these have not been directly compared for tissue parameter extraction purposes. We compare these analytical models using Monte Carlo simulated diffuse reflectance spectra and controlled gelatin-based phantoms with measured diffuse reflectance spectra and known ground truth composition parameters. The Yudovsky model performed best against Monte Carlo simulations and measured spectra of tissue phantoms in terms of goodness of fit and parameter extraction accuracy followed closely by Jacques' model. In this study, Yudovsky's model appeared most robust, however our results demonstrated that both Yudovsky and Jacques models are suitable for modelling tissue that can be approximated as a single, homogeneous, semi-infinite slab.

physics.med-ph↗

arXiv2023

MedShapeNet -- A Large-Scale Dataset of 3D Medical Shapes for Computer Vision

Prior to the deep learning era, shape was commonly used to describe the objects. Nowadays, state-of-the-art (SOTA) algorithms in medical imaging are predominantly diverging from computer vision, where voxel grids, meshes, point clouds, and implicit surface models are used. This is seen from numerous shape-related publications in premier vision conferences as well as the growing popularity of ShapeNet (about 51,300 models) and Princeton ModelNet (127,915 models). For the medical domain, we present a large collection of anatomical shapes (e.g., bones, organs, vessels) and 3D models of surgical instrument, called MedShapeNet, created to facilitate the translation of data-driven vision algorithms to medical applications and to adapt SOTA vision algorithms to medical problems. As a unique feature, we directly model the majority of shapes on the imaging data of real patients. As of today, MedShapeNet includes 23 dataset with more than 100,000 shapes that are paired with annotations (ground truth). Our data is freely accessible via a web interface and a Python application programming interface (API) and can be used for discriminative, reconstructive, and variational benchmarks as well as various applications in virtual, augmented, or mixed reality, and 3D printing. Exemplary, we present use cases in the fields of classification of brain tumors, facial and skull reconstructions, multi-class anatomy completion, education, and 3D printing. In future, we will extend the data and improve the interfaces. The project pages are: https://medshapenet.ikim.nrw/ and https://github.com/Jianningli/medshapenet-feedback

cs.CV↗

arXiv2023

A Clinical Guideline Driven Automated Linear Feature Extraction for Vestibular Schwannoma

Vestibular Schwannoma is a benign brain tumour that grows from one of the balance nerves. Patients may be treated by surgery, radiosurgery or with a conservative "wait-and-scan" strategy. Clinicians typically use manually extracted linear measurements to aid clinical decision making. This work aims to automate and improve this process by using deep learning based segmentation to extract relevant clinical features through computational algorithms. To the best of our knowledge, our study is the first to propose an automated approach to replicate local clinical guidelines. Our deep learning based segmentation provided Dice-scores of 0.8124 +- 0.2343 and 0.8969 +- 0.0521 for extrameatal and whole tumour regions respectively for T2 weighted MRI, whereas 0.8222 +- 0.2108 and 0.9049 +- 0.0646 were obtained for T1 weighted MRI. We propose a novel algorithm to choose and extract the most appropriate maximum linear measurement from the segmented regions based on the size of the extrameatal portion of the tumour. Using this tool, clinicians will be provided with a visual guide and related metrics relating to tumour progression that will function as a clinical decision aid. In this study, we utilize 187 scans obtained from 50 patients referred to a tertiary specialist neurosurgical service in the United Kingdom. The measurements extracted manually by an expert neuroradiologist indicated a significant correlation with the automated measurements (p < 0.0001).

eess.IV↗

arXiv2023

Synthetic white balancing for intra-operative hyperspectral imaging

Hyperspectral imaging shows promise for surgical applications to non-invasively provide spatially-resolved, spectral information. For calibration purposes, a white reference image of a highly-reflective Lambertian surface should be obtained under the same imaging conditions. Standard white references are not sterilizable, and so are unsuitable for surgical environments. We demonstrate the necessity for in situ white references and address this by proposing a novel, sterile, synthetic reference construction algorithm. The use of references obtained at different distances and lighting conditions to the subject were examined. Spectral and color reconstructions were compared with standard measurements qualitatively and quantitatively, using $ΔE$ and normalised RMSE respectively. The algorithm forms a composite image from a video of a standard sterile ruler, whose imperfect reflectivity is compensated for. The reference is modelled as the product of independent spatial and spectral components, and a scalar factor accounting for gain, exposure, and light intensity. Evaluation of synthetic references against ideal but non-sterile references is performed using the same metrics alongside pixel-by-pixel errors. Finally, intraoperative integration is assessed though cadaveric experiments. Improper white balancing leads to increases in all quantitative and qualitative errors. Synthetic references achieve median pixel-by-pixel errors lower than 6.5% and produce similar reconstructions and errors to an ideal reference. The algorithm integrated well into surgical workflow, achieving median pixel-by-pixel errors of 4.77%, while maintaining good spectral and color reconstruction.

eess.IV↗

arXiv2023

Deep Reinforcement Learning Based System for Intraoperative Hyperspectral Video Autofocusing

Hyperspectral imaging (HSI) captures a greater level of spectral detail than traditional optical imaging, making it a potentially valuable intraoperative tool when precise tissue differentiation is essential. Hardware limitations of current optical systems used for handheld real-time video HSI result in a limited focal depth, thereby posing usability issues for integration of the technology into the operating room. This work integrates a focus-tunable liquid lens into a video HSI exoscope, and proposes novel video autofocusing methods based on deep reinforcement learning. A first-of-its-kind robotic focal-time scan was performed to create a realistic and reproducible testing dataset. We benchmarked our proposed autofocus algorithm against traditional policies, and found our novel approach to perform significantly ($p<0.05$) better than traditional techniques ($0.070\pm.098$ mean absolute focal error compared to $0.146\pm.148$). In addition, we performed a blinded usability trial by having two neurosurgeons compare the system with different autofocus policies, and found our novel approach to be the most favourable, making our system a desirable addition for intraoperative HSI.

cs.CV↗

arXiv2023

Spatial gradient consistency for unsupervised learning of hyperspectral demosaicking: Application to surgical imaging

Hyperspectral imaging has the potential to improve intraoperative decision making if tissue characterisation is performed in real-time and with high-resolution. Hyperspectral snapshot mosaic sensors offer a promising approach due to their fast acquisition speed and compact size. However, a demosaicking algorithm is required to fully recover the spatial and spectral information of the snapshot images. Most state-of-the-art demosaicking algorithms require ground-truth training data with paired snapshot and high-resolution hyperspectral images, but such imagery pairs with the exact same scene are physically impossible to acquire in intraoperative settings. In this work, we present a fully unsupervised hyperspectral image demosaicking algorithm which only requires exemplar snapshot images for training purposes. We regard hyperspectral demosaicking as an ill-posed linear inverse problem which we solve using a deep neural network. We take advantage of the spectral correlation occurring in natural scenes to design a novel inter spectral band regularisation term based on spatial gradient consistency. By combining our proposed term with standard regularisation techniques and exploiting a standard data fidelity term, we obtain an unsupervised loss function for training deep neural networks, which allows us to achieve real-time hyperspectral image demosaicking. Quantitative results on hyperspetral image datasets show that our unsupervised demosaicking approach can achieve similar performance to its supervised counter-part, and significantly outperform linear demosaicking. A qualitative user study on real snapshot hyperspectral surgical images confirms the results from the quantitative analysis. Our results suggest that the proposed unsupervised algorithm can achieve promising hyperspectral demosaicking in real-time thus advancing the suitability of the modality for intraoperative use.

eess.IV↗

arXiv2022

CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwannoma and Cochlea Segmentation

Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice - VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice - VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image.

eess.IV↗

arXiv2022

Boundary Distance Loss for Intra-/Extra-meatal Segmentation of Vestibular Schwannoma

Vestibular Schwannoma (VS) typically grows from the inner ear to the brain. It can be separated into two regions, intrameatal and extrameatal respectively corresponding to being inside or outside the inner ear canal. The growth of the extrameatal regions is a key factor that determines the disease management followed by the clinicians. In this work, a VS segmentation approach with subdivision into intra-/extra-meatal parts is presented. We annotated a dataset consisting of 227 T2 MRI instances, acquired longitudinally on 137 patients, excluding post-operative instances. We propose a staged approach, with the first stage performing the whole tumour segmentation and the second stage performing the intra-/extra-meatal segmentation using the T2 MRI along with the mask obtained from the first stage. To improve on the accuracy of the predicted meatal boundary, we introduce a task-specific loss which we call Boundary Distance Loss. The performance is evaluated in contrast to the direct intrameatal extrameatal segmentation task performance, i.e. the Baseline. Our proposed method, with the two-stage approach and the Boundary Distance Loss, achieved a Dice score of 0.8279+-0.2050 and 0.7744+-0.1352 for extrameatal and intrameatal regions respectively, significantly improving over the Baseline, which gave Dice score of 0.7939+-0.2325 and 0.7475+-0.1346 for the extrameatal and intrameatal regions respectively.

eess.IV↗

arXiv2021

Methodology development and evaluation of optical properties characterisation of small size tissue samples

Integrating sphere (IS) techniques combined with an inverse adding doubling (IAD) algorithm have been widely used for determination of optical properties of ex vivo tissues. Semi-infinite samples are required in such cases. The aim of this study is to develop a methodology for calculating the optical absorption and reduced scattering of biological tissues of small size from IS measurements at 400-1800 nm. We propose a two-stage IAD algorithm to mitigate profound cross-talk effects in the estimation of the reduced scattering in the case of very high absorption. We developed a small sample adaptor kit to allow IS measurements of samples with small sizes using a commercial spectrophotometer. Results showed that: The two-stage IAD substantially eliminated the cross-talks in the reduced scattering spectra, thus rectifying absorption accordingly; and the small sized sample measurements led to systematically overestimated absorption values while the spectrum shape well preserved as compared to the normal port size measurements.

physics.optics↗

arXiv2021

Inter Extreme Points Geodesics for End-to-End Weakly Supervised Image Segmentation

We introduce $\textit{InExtremIS}$, a weakly supervised 3D approach to train a deep image segmentation network using particularly weak train-time annotations: only 6 extreme clicks at the boundary of the objects of interest. Our fully-automatic method is trained end-to-end and does not require any test-time annotations. From the extreme points, 3D bounding boxes are extracted around objects of interest. Then, deep geodesics connecting extreme points are generated to increase the amount of "annotated" voxels within the bounding boxes. Finally, a weakly supervised regularised loss derived from a Conditional Random Field formulation is used to encourage prediction consistency over homogeneous regions. Extensive experiments are performed on a large open dataset for Vestibular Schwannoma segmentation. $\textit{InExtremIS}$ obtained competitive performance, approaching full supervision and outperforming significantly other weakly supervised techniques based on bounding boxes. Moreover, given a fixed annotation time budget, $\textit{InExtremIS}$ outperforms full supervision. Our code and data are available online.

cs.CV↗

arXiv2021

Deep Learning Approach for Hyperspectral Image Demosaicking, Spectral Correction and High-resolution RGB Reconstruction

Hyperspectral imaging is one of the most promising techniques for intraoperative tissue characterisation. Snapshot mosaic cameras, which can capture hyperspectral data in a single exposure, have the potential to make a real-time hyperspectral imaging system for surgical decision-making possible. However, optimal exploitation of the captured data requires solving an ill-posed demosaicking problem and applying additional spectral corrections to recover spatial and spectral information of the image. In this work, we propose a deep learning-based image demosaicking algorithm for snapshot hyperspectral images using supervised learning methods. Due to the lack of publicly available medical images acquired with snapshot mosaic cameras, a synthetic image generation approach is proposed to simulate snapshot images from existing medical image datasets captured by high-resolution, but slow, hyperspectral imaging devices. Image reconstruction is achieved using convolutional neural networks for hyperspectral image super-resolution, followed by cross-talk and leakage correction using a sensor-specific calibration matrix. The resulting demosaicked images are evaluated both quantitatively and qualitatively, showing clear improvements in image quality compared to a baseline demosaicking method using linear interpolation. Moreover, the fast processing time of~45\,ms of our algorithm to obtain super-resolved RGB or oxygenation saturation maps per image frame for a state-of-the-art snapshot mosaic camera demonstrates the potential for its seamless integration into real-time surgical hyperspectral imaging applications.

eess.IV↗

arXiv2020

Scribble-based Domain Adaptation via Co-segmentation

Although deep convolutional networks have reached state-of-the-art performance in many medical image segmentation tasks, they have typically demonstrated poor generalisation capability. To be able to generalise from one domain (e.g. one imaging modality) to another, domain adaptation has to be performed. While supervised methods may lead to good performance, they require to fully annotate additional data which may not be an option in practice. In contrast, unsupervised methods don't need additional annotations but are usually unstable and hard to train. In this work, we propose a novel weakly-supervised method. Instead of requiring detailed but time-consuming annotations, scribbles on the target domain are used to perform domain adaptation. This paper introduces a new formulation of domain adaptation based on structured learning and co-segmentation. Our method is easy to train, thanks to the introduction of a regularised loss. The framework is validated on Vestibular Schwannoma segmentation (T1 to T2 scans). Our proposed method outperforms unsupervised approaches and achieves comparable performance to a fully-supervised approach.

cs.CV↗

arXiv2020

Manual segmentation versus semi-automated segmentation for quantifying vestibular schwannoma volume on MRI

Management of vestibular schwannoma (VS) is based on tumour size as observed on T1 MRI scans with contrast agent injection. Current clinical practice is to measure the diameter of the tumour in its largest dimension. It has been shown that volumetric measurement is more accurate and more reliable as a measure of VS size. The reference approach to achieve such volumetry is to manually segment the tumour, which is a time intensive task. We suggest that semi-automated segmentation may be a clinically applicable solution to this problem and that it could replace linear measurements as the clinical standard. Using high-quality software available for academic purposes, we ran a comparative study of manual versus semi-automated segmentation of VS on MRI with 5 clinicians and scientists. We gathered both quantitative and qualitative data to compare the two approaches; including segmentation time, segmentation effort and segmentation accuracy. We found that the selected semi-automated segmentation approach is significantly faster (167s versus 479s, p<0.001), less temporally and physically demanding and has approximately equal performance when compared with manual segmentation, with some improvements in accuracy. There were some limitations, including algorithmic unpredictability and error, which produced more frustration and increased mental effort in comparison to manual segmentation. We suggest that semi-automated segmentation could be applied clinically for volumetric measurement of VS on MRI. In future, the generic software could be refined for use specifically for VS segmentation, thereby improving accuracy.

eess.IV↗

arXiv2019

Automatic Segmentation of Vestibular Schwannoma from T2-Weighted MRI by Deep Spatial Attention with Hardness-Weighted Loss

Automatic segmentation of vestibular schwannoma (VS) tumors from magnetic resonance imaging (MRI) would facilitate efficient and accurate volume measurement to guide patient management and improve clinical workflow. The accuracy and robustness is challenged by low contrast, small target region and low through-plane resolution. We introduce a 2.5D convolutional neural network (CNN) able to exploit the different in-plane and through-plane resolutions encountered in standard of care imaging protocols. We use an attention module to enable the CNN to focus on the small target and propose a supervision on the learning of attention maps for more accurate segmentation. Additionally, we propose a hardness-weighted Dice loss function that gives higher weights to harder voxels to boost the training of CNNs. Experiments with ablation studies on the VS tumor segmentation task show that: 1) the proposed 2.5D CNN outperforms its 2D and 3D counterparts, 2) our supervised attention mechanism outperforms unsupervised attention, 3) the voxel-level hardness-weighted Dice loss can improve the performance of CNNs. Our method achieved an average Dice score and ASSD of 0.87 and 0.43~mm respectively. This will facilitate patient management decisions in clinical practice.

eess.IV↗