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General General

Learning from irregularly sampled data for endomicroscopy super-resolution: a comparative study of sparse and dense approaches.

In International journal of computer assisted radiology and surgery

PURPOSE : Probe-based confocal laser endomicroscopy (pCLE) enables performing an optical biopsy via a probe. pCLE probes consist of multiple optical fibres arranged in a bundle, which taken together generate signals in an irregularly sampled pattern. Current pCLE reconstruction is based on interpolating irregular signals onto an over-sampled Cartesian grid, using a naive linear interpolation. It was shown that convolutional neural networks (CNNs) could improve pCLE image quality. Yet classical CNNs may be suboptimal in regard to irregular data.

METHODS : We compare pCLE reconstruction and super-resolution (SR) methods taking irregularly sampled or reconstructed pCLE images as input. We also propose to embed a Nadaraya-Watson (NW) kernel regression into the CNN framework as a novel trainable CNN layer. We design deep learning architectures allowing for reconstructing high-quality pCLE images directly from the irregularly sampled input data. We created synthetic sparse pCLE images to evaluate our methodology.

RESULTS : The results were validated through an image quality assessment based on a combination of the following metrics: peak signal-to-noise ratio and the structural similarity index. Our analysis indicates that both dense and sparse CNNs outperform the reconstruction method currently used in the clinic.

CONCLUSION : The main contributions of our study are a comparison of sparse and dense approach in pCLE image reconstruction. We also implement trainable generalised NW kernel regression as a novel sparse approach. We also generated synthetic data for training pCLE SR.

Szczotka Agnieszka Barbara, Shakir Dzhoshkun Ismail, Ravì Daniele, Clarkson Matthew J, Pereira Stephen P, Vercauteren Tom


CNN, Nadaraya–Watson kernel regression, Super-resolution, pCLE reconstruction

Radiology Radiology

Automated detection and classification of shoulder arthroplasty models using deep learning.

In Skeletal radiology

OBJECTIVE : To develop and evaluate the performance of deep convolutional neural networks (DCNN) to detect and identify specific total shoulder arthroplasty (TSA) models.

MATERIALS AND METHODS : We included 482 radiography studies obtained from publicly available image repositories with native shoulders, reverse TSA (RTSA) implants, and five different TSA models. We trained separate ResNet DCNN-based binary classifiers to (1) detect the presence of shoulder arthroplasty implants, (2) differentiate between TSA and RTSA, and (3) differentiate between the five TSA models, using five individual classifiers for each model, respectively. Datasets were divided into training, validation, and test datasets. Training and validation datasets were 20-fold augmented. Test performances were assessed with area under the receiver-operating characteristic curves (AUC-ROC) analyses. Class activation mapping was used to identify distinguishing imaging features used for DCNN classification decisions.

RESULTS : The DCNN for the detection of the presence of shoulder arthroplasty implants achieved an AUC-ROC of 1.0, whereas the AUC-ROC for differentiation between TSA and RTSA was 0.97. Class activation map analysis demonstrated the emphasis on the characteristic arthroplasty components in decision-making. DCNNs trained to distinguish between the five TSA models achieved AUC-ROCs ranging from 0.86 for Stryker Solar to 1.0 for Zimmer Bigliani-Flatow with class activation map analysis demonstrating an emphasis on unique implant design features.

CONCLUSION : DCNNs can accurately identify the presence of and distinguish between TSA & RTSA, and classify five specific TSA models with high accuracy. The proof of concept of these DCNNs may set the foundation for an automated arthroplasty atlas for rapid and comprehensive model identification.

Yi Paul H, Kim Tae Kyung, Wei Jinchi, Li Xinning, Hager Gregory D, Sair Haris I, Fritz Jan


Artificial intelligence, Deep learning, Implant identification, Shoulder arthroplasty

Surgery Surgery

Osteoarthritis of the Temporomandibular Joint can be diagnosed earlier using biomarkers and machine learning.

In Scientific reports ; h5-index 158.0

After chronic low back pain, Temporomandibular Joint (TMJ) disorders are the second most common musculoskeletal condition affecting 5 to 12% of the population, with an annual health cost estimated at $4 billion. Chronic disability in TMJ osteoarthritis (OA) increases with aging, and the main goal is to diagnosis before morphological degeneration occurs. Here, we address this challenge using advanced data science to capture, process and analyze 52 clinical, biological and high-resolution CBCT (radiomics) markers from TMJ OA patients and controls. We tested the diagnostic performance of four machine learning models: Logistic Regression, Random Forest, LightGBM, XGBoost. Headaches, Range of mouth opening without pain, Energy, Haralick Correlation, Entropy and interactions of TGF-β1 in Saliva and Headaches, VE-cadherin in Serum and Angiogenin in Saliva, VE-cadherin in Saliva and Headaches, PA1 in Saliva and Headaches, PA1 in Saliva and Range of mouth opening without pain; Gender and Muscle Soreness; Short Run Low Grey Level Emphasis and Headaches, Inverse Difference Moment and Trabecular Separation accurately diagnose early stages of this clinical condition. Our results show the XGBoost + LightGBM model with these features and interactions achieves the accuracy of 0.823, AUC 0.870, and F1-score 0.823 to diagnose the TMJ OA status. Thus, we expect to boost future studies into osteoarthritis patient-specific therapeutic interventions, and thereby improve the health of articular joints.

Bianchi Jonas, de Oliveira Ruellas Antônio Carlos, Gonçalves João Roberto, Paniagua Beatriz, Prieto Juan Carlos, Styner Martin, Li Tengfei, Zhu Hongtu, Sugai James, Giannobile William, Benavides Erika, Soki Fabiana, Yatabe Marilia, Ashman Lawrence, Walker David, Soroushmehr Reza, Najarian Kayvan, Cevidanes Lucia Helena Soares


General General

AxoNet: A deep learning-based tool to count retinal ganglion cell axons.

In Scientific reports ; h5-index 158.0

In this work, we develop a robust, extensible tool to automatically and accurately count retinal ganglion cell axons in optic nerve (ON) tissue images from various animal models of glaucoma. We adapted deep learning to regress pixelwise axon count density estimates, which were then integrated over the image area to determine axon counts. The tool, termed AxoNet, was trained and evaluated using a dataset containing images of ON regions randomly selected from whole cross sections of both control and damaged rat ONs and manually annotated for axon count and location. This rat-trained network was then applied to a separate dataset of non-human primate (NHP) ON images. AxoNet was compared to two existing automated axon counting tools, AxonMaster and AxonJ, using both datasets. AxoNet outperformed the existing tools on both the rat and NHP ON datasets as judged by mean absolute error, R2 values when regressing automated vs. manual counts, and Bland-Altman analysis. AxoNet does not rely on hand-crafted image features for axon recognition and is robust to variations in the extent of ON tissue damage, image quality, and species of mammal. Therefore, AxoNet is not species-specific and can be extended to quantify additional ON characteristics in glaucoma and potentially other neurodegenerative diseases.

Ritch Matthew D, Hannon Bailey G, Read A Thomas, Feola Andrew J, Cull Grant A, Reynaud Juan, Morrison John C, Burgoyne Claude F, Pardue Machelle T, Ethier C Ross


oncology Oncology

An Automated Segmentation Pipeline for Intratumoural Regions in Animal Xenografts Using Machine Learning and Saturation Transfer MRI.

In Scientific reports ; h5-index 158.0

Saturation transfer MRI can be useful in the characterization of different tumour types. It is sensitive to tumour metabolism, microstructure, and microenvironment. This study aimed to use saturation transfer to differentiate between intratumoural regions, demarcate tumour boundaries, and reduce data acquisition times by identifying the imaging scheme with the most impact on segmentation accuracy. Saturation transfer-weighted images were acquired over a wide range of saturation amplitudes and frequency offsets along with T1 and T2 maps for 34 tumour xenografts in mice. Independent component analysis and Gaussian mixture modelling were used to segment the images and identify intratumoural regions. Comparison between the segmented regions and histopathology indicated five distinct clusters: three corresponding to intratumoural regions (active tumour, necrosis/apoptosis, and blood/edema) and two extratumoural (muscle and a mix of muscle and connective tissue). The fraction of tumour voxels segmented as necrosis/apoptosis quantitatively matched those calculated from TUNEL histopathological assays. An optimal protocol was identified providing reasonable qualitative agreement between MRI and histopathology and consisting of T1 and T2 maps and 22 magnetization transfer (MT)-weighted images. A three-image subset was identified that resulted in a greater than 90% match in positive and negative predictive value of tumour voxels compared to those found using the entire 24-image dataset. The proposed algorithm can potentially be used to develop a robust intratumoural segmentation method.

Lam Wilfred W, Oakden Wendy, Karami Elham, Koletar Margaret M, Murray Leedan, Liu Stanley K, Sadeghi-Naini Ali, Stanisz Greg J


General General

Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth.

In Nature communications ; h5-index 260.0

The current trends of crop yield improvements are not expected to meet the projected rise in demand. Genomic selection uses molecular markers and machine learning to identify superior genotypes with improved traits, such as growth. Plant growth directly depends on rates of metabolic reactions which transform nutrients into the building blocks of biomass. Here, we predict growth of Arabidopsis thaliana accessions by employing genomic prediction of reaction rates estimated from accession-specific metabolic models. We demonstrate that, comparing to classical genomic selection on the available data sets for 67 accessions, our approach improves the prediction accuracy for growth within and across nitrogen environments by 32.6% and 51.4%, respectively, and from optimal nitrogen to low carbon environment by 50.4%. Therefore, integration of molecular markers into metabolic models offers an approach to predict traits directly related to metabolism, and its usefulness in breeding can be examined by gathering matching datasets in crops.

Tong Hao, Küken Anika, Nikoloski Zoran