Zeyun Yu

Matthias Eisenmann, Annika Reinke, Vivienn Weru et al. · utoronto

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Michael Holst, James Andrew McCammon, Zeyun Yu et al.

We develop an efficient and reliable adaptive finite element method (AFEM) for the nonlinear Poisson-Boltzmann equation (PBE). We first examine the regularization technique of Chen, Holst, and Xu; this technique made possible the first a priori pointwise estimates and the first complete solution and approximation theory for the Poisson-Boltzmann equation. It also made possible the first provably convergent discretization of the PBE, and allowed for the development of a provably convergent AFEM for the PBE. However, in practice the regularization turns out to be numerically ill-conditioned. In this article, we examine a second regularization, and establish a number of basic results to ensure that the new approach produces the same mathematical advantages of the original regularization, without the ill-conditioning property. We then design an AFEM scheme based on the new regularized problem, and show that the resulting AFEM scheme is accurate and reliable, by proving a contraction result for the error. This result, which is one of the first results of this type for nonlinear elliptic problems, is based on using continuous and discrete a priori pointwise estimates to establish quasi-orthogonality. To provide a high-quality geometric model as input to the AFEM algorithm, we also describe a class of feature-preserving adaptive mesh generation algorithms designed specifically for constructing meshes of biomolecular structures, based on the intrinsic local structure tensor of the molecular surface. The stability advantages of the new regularization are demonstrated using an FETK-based implementation, through comparisons with the original regularization approach for a model problem. The convergence and accuracy of the overall AFEM algorithm is also illustrated by numerical approximation of electrostatic solvation energy for an insulin protein.

Yash Patel, Tirth Shah, Mrinal Kanti Dhar et al.

The global burden of acute and chronic wounds presents a compelling case for enhancing wound classification methods, a vital step in diagnosing and determining optimal treatments. Recognizing this need, we introduce an innovative multi-modal network based on a deep convolutional neural network for categorizing wounds into four categories: diabetic, pressure, surgical, and venous ulcers. Our multi-modal network uses wound images and their corresponding body locations for more precise classification. A unique aspect of our methodology is incorporating a body map system that facilitates accurate wound location tagging, improving upon traditional wound image classification techniques. A distinctive feature of our approach is the integration of models such as VGG16, ResNet152, and EfficientNet within a novel architecture. This architecture includes elements like spatial and channel-wise Squeeze-and-Excitation modules, Axial Attention, and an Adaptive Gated Multi-Layer Perceptron, providing a robust foundation for classification. Our multi-modal network was trained and evaluated on two distinct datasets comprising relevant images and corresponding location information. Notably, our proposed network outperformed traditional methods, reaching an accuracy range of 74.79% to 100% for Region of Interest (ROI) without location classifications, 73.98% to 100% for ROI with location classifications, and 78.10% to 100% for whole image classifications. This marks a significant enhancement over previously reported performance metrics in the literature. Our results indicate the potential of our multi-modal network as an effective decision-support tool for wound image classification, paving the way for its application in various clinical contexts.

Hosein Barzekar, Yash Patel, Ling Tong et al.

Cancer is a leading cause of death in many countries. An early diagnosis of cancer based on biomedical imaging ensures effective treatment and a better prognosis. However, biomedical imaging presents challenges to both clinical institutions and researchers. Physiological anomalies are often characterized by slight abnormalities in individual cells or tissues, making them difficult to detect visually. Traditionally, anomalies are diagnosed by radiologists and pathologists with extensive training. This procedure, however, demands the participation of professionals and incurs a substantial cost. The cost makes large-scale biological image classification impractical. In this study, we provide unique deep neural network designs for multiclass classification of medical images, in particular cancer images. We incorporated transformers into a multiclass framework to take advantage of data-gathering capability and perform more accurate classifications. We evaluated models on publicly accessible datasets using various measures to ensure the reliability of the models. Extensive assessment metrics suggest this method can be used for a multitude of classification tasks.

D. M. Anisuzzaman, Yash Patel, Jeffrey Niezgoda et al.

The classification of wound severity is a critical step in wound diagnosis. An effective classifier can help wound professionals categorize wound conditions more quickly and affordably, allowing them to choose the best treatment option. This study used wound photos to construct a deep neural network-based wound severity classifier that classified them into one of three classes: green, yellow, or red. The green class denotes wounds still in the early stages of healing and are most likely to recover with adequate care. Wounds in the yellow category require more attention and treatment than those in the green category. Finally, the red class denotes the most severe wounds that require prompt attention and treatment. A dataset containing different types of wound images is designed with the help of wound specialists. Nine deep learning models are used with applying the concept of transfer learning. Several stacked models are also developed by concatenating these transfer learning models. The maximum accuracy achieved on multi-class classification is 68.49%. In addition, we achieved 78.79%, 81.40%, and 77.57% accuracies on green vs. yellow, green vs. red, and yellow vs. red classifications for binary classifications.

Varun Kumar Dasoju, Qingsu Cheng, Zeyun Yu

Annotating medical images demands significant time and expertise, often requiring pathologists to invest hundreds of hours in labeling mammary epithelial nuclei datasets. We address this critical challenge by achieving 95.5% Dice score using just 599 training images for breast cell segmentation, where just 4% of pixels represent breast tissue and 60% of images contain no breast regions. Our framework uses quantum-inspired edge enhancement via multi-scale Gabor filters creating a fourth input channel, enhancing boundary detection where inter-annotator variations reach +/- 3 pixels. We present a stabilized multi-component loss function that integrates adaptive Dice loss with boundary-aware terms and automatic positive weighting to effectively address severe class imbalance, where mammary epithelial cell regions comprise only 0.1%-20% of the total image area. Additionally, a complexity-based weighted sampling strategy is introduced to prioritize the challenging mammary epithelial cell regions. The model employs an EfficientNet-B7/UNet++ architecture with a 4-to-3 channel projection, enabling the use of pretrained weights despite limited medical imaging data. Finally, robust validation is achieved through exponential moving averaging and statistical outlier detection, ensuring reliable performance estimates on a small validation set (129 images). Our framework achieves a Dice score of 95.5% +/- 0.3% and an IoU of 91.2% +/- 0.4%. Notably, quantum-based enhancement contributes to a 2.1% improvement in boundary accuracy, while weighted sampling increases small lesion detection by 3.8%. By achieving groundbreaking performance with limited annotations, our approach significantly reduces the medical expert time required for dataset creation, addressing a fundamental bottleneck in clinical perception AI development.

E. O. Asante-Asamani, Lei Wang, Zeyun Yu

Numerical solutions of partial differential equations (PDEs) on manifolds continues to generate a lot of interest among scientists in the natural and applied sciences. On the other hand, recent developments of 3D scanning and computer vision technologies have produced a large number of 3D surface models represented as point clouds. Herein, we develop a simple and efficient method for solving PDEs on closed surfaces represented as point clouds. By projecting the radial vector of standard radial basis function(RBF) kernels onto the local tangent plane, we are able to produce a representation of functions that permits the replacement of surface differential operators with their Cartesian equivalent. We demonstrate, numerically, the efficiency of the method in discretizing the Laplace Beltrami operator.

Mrinal Kanti Dhar, Chuanbo Wang, Yash Patel et al.

Identifying individual tissues, so-called tissue segmentation, in diabetic foot ulcer (DFU) images is a challenging task and little work has been published, largely due to the limited availability of a clinical image dataset. To address this gap, we have created a DFUTissue dataset for the research community to evaluate wound tissue segmentation algorithms. The dataset contains 110 images with tissues labeled by wound experts and 600 unlabeled images. Additionally, we conducted a pilot study on segmenting wound characteristics including fibrin, granulation, and callus using deep learning. Due to the limited amount of annotated data, our framework consists of both supervised learning (SL) and semi-supervised learning (SSL) phases. In the SL phase, we propose a hybrid model featuring a Mix Transformer (MiT-b3) in the encoder and a CNN in the decoder, enhanced by the integration of a parallel spatial and channel squeeze-and-excitation (P-scSE) module known for its efficacy in improving boundary accuracy. The SSL phase employs a pseudo-labeling-based approach, iteratively identifying and incorporating valuable unlabeled images to enhance overall segmentation performance. Comparative evaluations with state-of-the-art methods are conducted for both SL and SSL phases. The SL achieves a Dice Similarity Coefficient (DSC) of 84.89%, which has been improved to 87.64% in the SSL phase. Furthermore, the results are benchmarked against two widely used SSL approaches: Generative Adversarial Networks and Cross-Consistency Training. Additionally, our hybrid model outperforms the state-of-the-art methods with a 92.99% DSC in performing binary segmentation of DFU wound areas when tested on the Chronic Wound dataset. Codes and data are available at https://github.com/uwm-bigdata/DFUTissueSegNet.

Mrinal Kanti Dhar, Taiyu Zhang, Yash Patel et al.

This paper presents FUSegNet, a new model for foot ulcer segmentation in diabetes patients, which uses the pre-trained EfficientNet-b7 as a backbone to address the issue of limited training samples. A modified spatial and channel squeeze-and-excitation (scSE) module called parallel scSE or P-scSE is proposed that combines additive and max-out scSE. A new arrangement is introduced for the module by fusing it in the middle of each decoder stage. As the top decoder stage carries a limited number of feature maps, max-out scSE is bypassed there to form a shorted P-scSE. A set of augmentations, comprising geometric, morphological, and intensity-based augmentations, is applied before feeding the data into the network. The proposed model is first evaluated on a publicly available chronic wound dataset where it achieves a data-based dice score of 92.70%, which is the highest score among the reported approaches. The model outperforms other scSE-based UNet models in terms of Pratt's figure of merits (PFOM) scores in most categories, which evaluates the accuracy of edge localization. The model is then tested in the MICCAI 2021 FUSeg challenge, where a variation of FUSegNet called x-FUSegNet is submitted. The x-FUSegNet model, which takes the average of outputs obtained by FUSegNet using 5-fold cross-validation, achieves a dice score of 89.23%, placing it at the top of the FUSeg Challenge leaderboard. The source code for the model is available on https://github.com/mrinal054/FUSegNet.

Farnaz H. Foomani, Shahzad Mirza, Sahjid Mukhida et al.

Skin and soft tissue infections (SSTIs) are among the most frequently observed diseases in ambulatory and hospital settings. Resistance of diverse bacterial pathogens to antibiotics is a significant cause of severe SSTIs, and treatment failure results in morbidity, mortality, and increased cost of hospitalization. Therefore, antimicrobial surveillance is essential to predict antibiotic resistance trends and monitor the results of medical interventions. To address this, we developed machine learning (ML) models (deep and conventional algorithms) to predict antimicrobial resistance using antibiotic susceptibility testing (ABST) data collected from patients clinically diagnosed with primary and secondary pyoderma over a period of one year. We trained an individual ML algorithm on each antimicrobial family to determine whether a Gram-Positive Cocci (GPC) or Gram-Negative Bacilli (GNB) bacteria will resist the corresponding antibiotic. For this purpose, clinical and demographic features from the patient and data from ABST were employed in training. We achieved an Area Under the Curve (AUC) of 0.68-0.98 in GPC and 0.56-0.93 in GNB bacteria, depending on the antimicrobial family. We also conducted a correlation analysis to determine the linear relationship between each feature and antimicrobial families in different bacteria. ML techniques suggest that a predictable nonlinear relationship exists between patients' clinical-demographic characteristics and antibiotic resistance; however, the accuracy of this prediction depends on the type of the antimicrobial family.

Chuanbo Wang, Amirreza Mahbod, Isabella Ellinger et al.

Acute and chronic wounds with varying etiologies burden the healthcare systems economically. The advanced wound care market is estimated to reach $22 billion by 2024. Wound care professionals provide proper diagnosis and treatment with heavy reliance on images and image documentation. Segmentation of wound boundaries in images is a key component of the care and diagnosis protocol since it is important to estimate the area of the wound and provide quantitative measurement for the treatment. Unfortunately, this process is very time-consuming and requires a high level of expertise. Recently automatic wound segmentation methods based on deep learning have shown promising performance but require large datasets for training and it is unclear which methods perform better. To address these issues, we propose the Foot Ulcer Segmentation challenge (FUSeg) organized in conjunction with the 2021 International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI). We built a wound image dataset containing 1,210 foot ulcer images collected over 2 years from 889 patients. It is pixel-wise annotated by wound care experts and split into a training set with 1010 images and a testing set with 200 images for evaluation. Teams around the world developed automated methods to predict wound segmentations on the testing set of which annotations were kept private. The predictions were evaluated and ranked based on the average Dice coefficient. The FUSeg challenge remains an open challenge as a benchmark for wound segmentation after the conference.

Mrinal Kanti Dhar, Zeyun Yu

There is an increasing demand in medical industries to have automated systems for detection and localization which are manually inefficient otherwise. In dentistry, it bears great interest to trace the pathway of mandibular canals accurately. Proper localization of the position of the mandibular canals, which surrounds the inferior alveolar nerve (IAN), reduces the risk of damaging it during dental implantology. Manual detection of canal paths is not an efficient way in terms of time and labor. Here, we propose a deep learning-based framework to detect mandibular canals from CBCT data. It is a 3-stage process fully automatic end-to-end. Ground truths are generated in the preprocessing stage. Instead of using commonly used fixed diameter tubular-shaped ground truth, we generate centerlines of the mandibular canals and used them as ground truths in the training process. A 3D U-Net architecture is used for model training. An efficient post-processing stage is developed to rectify the initial prediction. The precision, recall, F1-score, and IoU are measured to analyze the voxel-level segmentation performance. However, to analyze the distance-based measurements, mean curve distance (MCD) both from ground truth to prediction and prediction to ground truth is calculated. Extensive experiments are conducted to demonstrate the effectiveness of the model.

D. M. Anisuzzaman, Yash Patel, Behrouz Rostami et al.

Wound classification is an essential step of wound diagnosis. An efficient classifier can assist wound specialists in classifying wound types with less financial and time costs and help them decide an optimal treatment procedure. This study developed a deep neural network-based multi-modal classifier using wound images and their corresponding locations to categorize wound images into multiple classes, including diabetic, pressure, surgical, and venous ulcers. A body map is also developed to prepare the location data, which can help wound specialists tag wound locations more efficiently. Three datasets containing images and their corresponding location information are designed with the help of wound specialists. The multi-modal network is developed by concatenating the image-based and location-based classifier's outputs with some other modifications. The maximum accuracy on mixed-class classifications (containing background and normal skin) varies from 77.33% to 100% on different experiments. The maximum accuracy on wound-class classifications (containing only diabetic, pressure, surgical, and venous) varies from 72.95% to 98.08% on different experiments. The proposed multi-modal network also shows a significant improvement in results from the previous works of literature.

Farnaz H. Foomani, D. M. Anisuzzaman, Jeffrey Niezgoda et al.

Wound prognostic models not only provide an estimate of wound healing time to motivate patients to follow up their treatments but also can help clinicians to decide whether to use a standard care or adjuvant therapies and to assist them with designing clinical trials. However, collecting prognosis factors from Electronic Medical Records (EMR) of patients is challenging due to privacy, sensitivity, and confidentiality. In this study, we developed time series medical generative adversarial networks (GANs) to generate synthetic wound prognosis factors using very limited information collected during routine care in a specialized wound care facility. The generated prognosis variables are used in developing a predictive model for chronic wound healing trajectory. Our novel medical GAN can produce both continuous and categorical features from EMR. Moreover, we applied temporal information to our model by considering data collected from the weekly follow-ups of patients. Conditional training strategies were utilized to enhance training and generate classified data in terms of healing or non-healing. The ability of the proposed model to generate realistic EMR data was evaluated by TSTR (test on the synthetic, train on the real), discriminative accuracy, and visualization. We utilized samples generated by our proposed GAN in training a prognosis model to demonstrate its real-life application. Using the generated samples in training predictive models improved the classification accuracy by 6.66-10.01% compared to the previous EMR-GAN. Additionally, the suggested prognosis classifier has achieved the area under the curve (AUC) of 0.975, 0.968, and 0.849 when training the network using data from the first three visits, first two visits, and first visit, respectively. These results indicate a significant improvement in wound healing prediction compared to the previous prognosis models.

Behrouz Rostami, Jeffrey Niezgoda, Sandeep Gopalakrishnan et al.

Millions of people are affected by acute and chronic wounds yearly across the world. Continuous wound monitoring is important for wound specialists to allow more accurate diagnosis and optimization of management protocols. Machine Learning-based classification approaches provide optimal care strategies resulting in more reliable outcomes, cost savings, healing time reduction, and improved patient satisfaction. In this study, we use a deep learning-based method to classify burn wound images into two or three different categories based on the wound conditions. A pre-trained deep convolutional neural network, AlexNet, is fine-tuned using a burn wound image dataset and utilized as the classifier. The classifier's performance is evaluated using classification metrics such as accuracy, precision, and recall as well as confusion matrix. A comparison with previous works that used the same dataset showed that our designed classifier improved the classification accuracy by more than 8%.

D M Anisuzzaman, Hosein Barzekar, Ling Tong et al.

In the U.S, 5-10\% of new pediatric cases of cancer are primary bone tumors. The most common type of primary malignant bone tumor is osteosarcoma. The intention of the present work is to improve the detection and diagnosis of osteosarcoma using computer-aided detection (CAD) and diagnosis (CADx). Such tools as convolutional neural networks (CNNs) can significantly decrease the surgeon's workload and make a better prognosis of patient conditions. CNNs need to be trained on a large amount of data in order to achieve a more trustworthy performance. In this study, transfer learning techniques, pre-trained CNNs, are adapted to a public dataset on osteosarcoma histological images to detect necrotic images from non-necrotic and healthy tissues. First, the dataset was preprocessed, and different classifications are applied. Then, Transfer learning models including VGG19 and Inception V3 are used and trained on Whole Slide Images (WSI) with no patches, to improve the accuracy of the outputs. Finally, the models are applied to different classification problems, including binary and multi-class classifiers. Experimental results show that the accuracy of the VGG19 has the highest, 96\%, performance amongst all binary classes and multiclass classification. Our fine-tuned model demonstrates state-of-the-art performance on detecting malignancy of Osteosarcoma based on histologic images.

Hosein Barzekar, Zeyun Yu

Cancers are the leading cause of death in many countries. Early diagnosis plays a crucial role in having proper treatment for this debilitating disease. The automated classification of the type of cancer is a challenging task since pathologists must examine a huge number of histopathological images to detect infinitesimal abnormalities. In this study, we propose a novel convolutional neural network (CNN) architecture composed of a Concatenation of multiple Networks, called C-Net, to classify biomedical images. The model incorporates multiple CNNs including Outer, Middle, and Inner. The first two parts of the architecture contain six networks that serve as feature extractors to feed into the Inner network to classify the images in terms of malignancy and benignancy. The C-Net is applied for histopathological image classification on two public datasets, including BreakHis and Osteosarcoma. To evaluate the performance, the model is tested using several evaluation metrics for its reliability. The C-Net model outperforms all other models on the individual metrics for both datasets and achieves zero misclassification. This approach has the potential to be extended to additional classification tasks, as experimental results demonstrate utilizing extensive evaluation metrics.

Behrouz Rostami, D. M. Anisuzzaman, Chuanbo Wang et al.

Acute and chronic wounds are a challenge to healthcare systems around the world and affect many people's lives annually. Wound classification is a key step in wound diagnosis that would help clinicians to identify an optimal treatment procedure. Hence, having a high-performance classifier assists the specialists in the field to classify the wounds with less financial and time costs. Different machine learning and deep learning-based wound classification methods have been proposed in the literature. In this study, we have developed an ensemble Deep Convolutional Neural Network-based classifier to classify wound images including surgical, diabetic, and venous ulcers, into multi-classes. The output classification scores of two classifiers (patch-wise and image-wise) are fed into a Multi-Layer Perceptron to provide a superior classification performance. A 5-fold cross-validation approach is used to evaluate the proposed method. We obtained maximum and average classification accuracy values of 96.4% and 94.28% for binary and 91.9\% and 87.7\% for 3-class classification problems. The results show that our proposed method can be used effectively as a decision support system in classification of wound images or other related clinical applications.

Chuanbo Wang, DM Anisuzzaman, Victor Williamson et al.

Acute and chronic wounds have varying etiologies and are an economic burden to healthcare systems around the world. The advanced wound care market is expected to exceed $22 billion by 2024. Wound care professionals rely heavily on images and image documentation for proper diagnosis and treatment. Unfortunately lack of expertise can lead to improper diagnosis of wound etiology and inaccurate wound management and documentation. Fully automatic segmentation of wound areas in natural images is an important part of the diagnosis and care protocol since it is crucial to measure the area of the wound and provide quantitative parameters in the treatment. Various deep learning models have gained success in image analysis including semantic segmentation. Particularly, MobileNetV2 stands out among others due to its lightweight architecture and uncompromised performance. This manuscript proposes a novel convolutional framework based on MobileNetV2 and connected component labelling to segment wound regions from natural images. We build an annotated wound image dataset consisting of 1,109 foot ulcer images from 889 patients to train and test the deep learning models. We demonstrate the effectiveness and mobility of our method by conducting comprehensive experiments and analyses on various segmentation neural networks.

Chuanbo Wang, Ye Guo, Wei Chen et al.

Intervertebral discs (IVDs), as small joints lying between adjacent vertebrae, have played an important role in pressure buffering and tissue protection. The fully-automatic localization and segmentation of IVDs have been discussed in the literature for many years since they are crucial to spine disease diagnosis and provide quantitative parameters in the treatment. Traditionally hand-crafted features are derived based on image intensities and shape priors to localize and segment IVDs. With the advance of deep learning, various neural network models have gained great success in image analysis including the recognition of intervertebral discs. Particularly, U-Net stands out among other approaches due to its outstanding performance on biomedical images with a relatively small set of training data. This paper proposes a novel convolutional framework based on 3D U-Net to segment IVDs from multi-modality MRI images. We first localize the centers of intervertebral discs in each spine sample and then train the network based on the cropped small volumes centered at the localized intervertebral discs. A detailed comprehensive analysis of the results using various combinations of multi-modalities is presented. Furthermore, experiments conducted on 2D and 3D U-Nets with augmented and non-augmented datasets are demonstrated and compared in terms of Dice coefficient and Hausdorff distance. Our method has proved to be effective with a mean segmentation Dice coefficient of 89.0% and a standard deviation of 1.4%.

D. M. Anisuzzaman, Chuanbo Wang, Behrouz Rostami et al.

Efficient and effective assessment of acute and chronic wounds can help wound care teams in clinical practice to greatly improve wound diagnosis, optimize treatment plans, ease the workload and achieve health related quality of life to the patient population. While artificial intelligence (AI) has found wide applications in health-related sciences and technology, AI-based systems remain to be developed clinically and computationally for high-quality wound care. To this end, we have carried out a systematic review of intelligent image-based data analysis and system developments for wound assessment. Specifically, we provide an extensive review of research methods on wound measurement (segmentation) and wound diagnosis (classification). We also reviewed recent work on wound assessment systems (including hardware, software, and mobile apps). More than 250 articles were retrieved from various publication databases and online resources, and 115 of them were carefully selected to cover the breadth and depth of most recent and relevant work to convey the current review to its fulfillment.

D. M. Anisuzzaman, Yash Patel, Jeffrey Niezgoda et al.

We present an automated wound localizer from 2D wound and ulcer images by using deep neural network, as the first step towards building an automated and complete wound diagnostic system. The wound localizer has been developed by using YOLOv3 model, which is then turned into an iOS mobile application. The developed localizer can detect the wound and its surrounding tissues and isolate the localized wounded region from images, which would be very helpful for future processing such as wound segmentation and classification due to the removal of unnecessary regions from wound images. For Mobile App development with video processing, a lighter version of YOLOv3 named tiny-YOLOv3 has been used. The model is trained and tested on our own image dataset in collaboration with AZH Wound and Vascular Center, Milwaukee, Wisconsin. The YOLOv3 model is compared with SSD model, showing that YOLOv3 gives a mAP value of 93.9%, which is much better than the SSD model (86.4%). The robustness and reliability of these models are also tested on a publicly available dataset named Medetec and shows a very good performance as well.

Fereshteh S. Bashiri, Reihaneh Rostami, Peggy Peissig et al.

With the rapid expansion of applied 3D computational vision, shape descriptors have become increasingly important for a wide variety of applications and objects from molecules to planets. Appropriate shape descriptors are critical for accurate (and efficient) shape retrieval and 3D model classification. Several spectral-based shape descriptors have been introduced by solving various physical equations over a 3D surface model. In this paper, for the first time, we incorporate a specific group of techniques in statistics and machine learning, known as manifold learning, to develop a global shape descriptor in the computer graphics domain. The proposed descriptor utilizes the Laplacian Eigenmap technique in which the Laplacian eigenvalue problem is discretized using an exponential weighting scheme. As a result, our descriptor eliminates the limitations tied to the existing spectral descriptors, namely dependency on triangular mesh representation and high intra-class quality of 3D models. We also present a straightforward normalization method to obtain a scale-invariant descriptor. The extensive experiments performed in this study show that the present contribution provides a highly discriminative and robust shape descriptor under the presence of a high level of noise, random scale variations, and low sampling rate, in addition to the known isometric-invariance property of the Laplace-Beltrami operator. The proposed method significantly outperforms state-of-the-art algorithms on several non-rigid shape retrieval benchmarks.

Ahmad Pahlavan Tafti, Hamid Hassannia, Zeyun Yu

Image features detection and description is a longstanding topic in computer vision and pattern recognition areas. The Scale Invariant Feature Transform (SIFT) is probably the most popular and widely demanded feature descriptor which facilitates a variety of computer vision applications such as image registration, object tracking, image forgery detection, and 3D surface reconstruction. This work introduces a Software as a Service (SaaS) based implementation of the SIFT algorithm which is freely available at http://siftservice.com for any academic, educational and research purposes. The service provides application-to-application interaction and aims Rapid Application Development (RAD) and also fast prototyping for computer vision students and researchers all around the world. An Internet connection is all they need!

Ahmadreza Baghaie, Roshan M. D'souza, Zeyun Yu

Optical Coherence Tomography (OCT) is an emerging technique in the field of biomedical imaging, with applications in ophthalmology, dermatology, coronary imaging etc. OCT images usually suffer from a granular pattern, called speckle noise, which restricts the process of interpretation. Therefore the need for speckle noise reduction techniques is of high importance. To the best of our knowledge, use of Independent Component Analysis (ICA) techniques has never been explored for speckle reduction of OCT images. Here, a comparative study of several ICA techniques (InfoMax, JADE, FastICA and SOBI) is provided for noise reduction of retinal OCT images. Having multiple B-scans of the same location, the eye movements are compensated using a rigid registration technique. Then, different ICA techniques are applied to the aggregated set of B-scans for extracting the noise-free image. Signal-to-Noise-Ratio (SNR), Contrast-to-Noise-Ratio (CNR) and Equivalent-Number-of-Looks (ENL), as well as analysis on the computational complexity of the methods, are considered as metrics for comparison. The results show that use of ICA can be beneficial, especially in case of having fewer number of B-scans.

Ahmadreza Baghaie, Roshan M. D'souza, Zeyun Yu

Optical Coherence Tomography (OCT) is an emerging technique in the field of biomedical imaging, with applications in ophthalmology, dermatology, coronary imaging etc. Due to the underlying physics, OCT images usually suffer from a granular pattern, called speckle noise, which restricts the process of interpretation. Here, a sparse and low rank decomposition based method is used for speckle reduction in retinal OCT images. This technique works on input data that consists of several B-scans of the same location. The next step is the batch alignment of the images using a sparse and low-rank decomposition based technique. Finally the denoised image is created by median filtering of the low-rank component of the processed data. Simultaneous decomposition and alignment of the images result in better performance in comparison to simple registration-based methods that are used in the literature for noise reduction of OCT images.

Ahmadreza Baghaie, Zeyun Yu, Roshan M. D'souza

In this paper a fast triangular mesh based registration method is proposed. Having Template and Reference images as inputs, the template image is triangulated using a content adaptive mesh generation algorithm. Considering the pixel values at mesh nodes, interpolated using spline interpolation method for both of the images, the energy functional needed for image registration is minimized. The minimization process was achieved using a mesh based discretization of the distance measure and regularization term which resulted in a sparse system of linear equations, which due to the smaller size in comparison to the pixel-wise registration method, can be solved directly. Mean Squared Difference (MSD) is used as a metric for evaluating the results. Using the mesh based technique, higher speed was achieved compared to pixel-based curvature registration technique with fast DCT solver. The implementation was done in MATLAB without any specific optimization. Higher speeds can be achieved using C/C++ implementations.

Ahmadreza Baghaie, Roshan M. D'souza, Zeyun Yu

Optical Coherence Tomography (OCT) is one of the most emerging imaging modalities that has been used widely in the field of biomedical imaging. From its emergence in 1990's, plenty of hardware and software improvements have been made. Its applications range from ophthalmology to dermatology to coronary imaging etc. Here, the focus is on applications of OCT in ophthalmology and retinal imaging. OCT is able to non-invasively produce cross-sectional volume images of the tissues which are further used for analysis of the tissue structure and its properties. Due to the underlying physics, OCT images usually suffer from a granular pattern, called speckle noise, which restricts the process of interpretation, hence requiring specialized noise reduction techniques to remove the noise while preserving image details. Also, given the fact that OCT images are in the $μm$ -level, further analysis in needed to distinguish between the different structures in the imaged volume. Therefore the use of different segmentation techniques are of high importance. The movement of the tissue under imaging or the progression of disease in the tissue also imposes further implications both on the quality and the proper interpretation of the acquired images. Thus, use of image registration techniques can be very helpful. In this work, an overview of such image analysis techniques will be given.

Ke Liu, Ming Xu, Zeyun Yu

The triangulation of images has become an active research area in recent years for its compressive representation and ease of image processing and visualization. However, little work has been done on how to faithfully recover image intensities from a triangulated mesh of an image, a process also known as image restoration or decoding from meshes. The existing methods such as linear interpolation, least-square interpolation, or interpolation based on radial basis functions (RBFs) work to some extent, but often yield blurred features (edges, corners, etc.). The main reason for this problem is due to the isotropically-defined Euclidean distance that is taken into consideration in these methods, without considering the anisotropicity of feature intensities in an image. Moreover, most existing methods use intensities defined at mesh nodes whose intensities are often ambiguously defined on or near image edges (or feature boundaries). In the current paper, a new method of restoring an image from its triangulation representation is proposed, by utilizing anisotropic radial basis functions (ARBFs). This method considers not only the geometrical (Euclidean) distances but also the local feature orientations (anisotropic intensities). Additionally, this method is based on the intensities of mesh faces instead of mesh nodes and thus provides a more robust restoration. The two strategies together guarantee excellent feature-preserving restoration of an image with arbitrary super-resolutions from its triangulation representation, as demonstrated by various experiments provided in the paper.

Ahmadreza Baghaie, Zeyun Yu

Feature preserving image interpolation is an active area in image processing field. In this paper a new direct edge directed image super-resolution algorithm based on structure tensors is proposed. Using an isotropic Gaussian filter, the structure tensor at each pixel of the input image is computed and the pixels are classified to three distinct classes; uniform region, corners and edges, according to the eigenvalues of the structure tensor. Due to application of the isotropic Gaussian filter, the classification is robust to noise presented in image. Based on the tangent eigenvector of the structure tensor, the edge direction is determined and used for interpolation along the edges. In comparison to some previous edge directed image interpolation methods, the proposed method achieves higher quality in both subjective and objective aspects. Also the proposed method outperforms previous methods in case of noisy and JPEG compressed images. Furthermore, without the need for optimization in the process, the algorithm can achieve higher speed.

Ahmadreza Baghaie, Zeyun Yu

Slice interpolation is a fast growing field in medical image processing. Intensity-based interpolation and object-based interpolation are two major groups of methods in the literature. In this paper, we describe an object-oriented, optimization method based on a modified version of curvature-based image registration, in which a displacement field is computed for the missing slice between two known slices and used to interpolate the intensities of the missing slice. The proposed approach is evaluated quantitatively by using the Mean Squared Difference (MSD) as a metric. The produced results also show visual improvement in preserving sharp edges in images.