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Fulltext Robust video content analysis schemes for human action recognition

Aly CA, Abas FS, Ann GH

Sci Prog, 2021;104(2):368504211005480.
PMID: 33913378 DOI: 10.1177/00368504211005480

INTRODUCTION: Action recognition is a challenging time series classification task that has received much attention in the recent past due to its importance in critical applications, such as surveillance, visual behavior study, topic discovery, security, and content retrieval.
OBJECTIVES: The main objective of the research is to develop a robust and high-performance human action recognition techniques. A combination of local and holistic feature extraction methods used through analyzing the most effective features to extract to reach the objective, followed by using simple and high-performance machine learning algorithms.
METHODS: This paper presents three robust action recognition techniques based on a series of image analysis methods to detect activities in different scenes. The general scheme architecture consists of shot boundary detection, shot frame rate re-sampling, and compact feature vector extraction. This process is achieved by emphasizing variations and extracting strong patterns in feature vectors before classification.
RESULTS: The proposed schemes are tested on datasets with cluttered backgrounds, low- or high-resolution videos, different viewpoints, and different camera motion conditions, namely, the Hollywood-2, KTH, UCF11 (YouTube actions), and Weizmann datasets. The proposed schemes resulted in highly accurate video analysis results compared to those of other works based on four widely used datasets. The First, Second, and Third Schemes provides recognition accuracies of 57.8%, 73.6%, and 52.0% on Hollywood2, 94.5%, 97.0%, and 59.3% on KTH, 94.5%, 95.6%, and 94.2% on UCF11, and 98.9%, 97.8% and 100% on Weizmann.
CONCLUSION: Each of the proposed schemes provides high recognition accuracy compared to other state-of-art methods. Especially, the Second Scheme as it gives excellent comparable results to other benchmarked approaches.
Fulltext Front-end deep learning web apps development and deployment: a review

Goh HA, Ho CK, Abas FS

Appl Intell (Dordr), 2023;53(12):15923-15945.
PMID: 36466774 DOI: 10.1007/s10489-022-04278-6

Machine learning and deep learning models are commonly developed using programming languages such as Python, C++, or R and deployed as web apps delivered from a back-end server or as mobile apps installed from an app store. However, recently front-end technologies and JavaScript libraries, such as TensorFlow.js, have been introduced to make machine learning more accessible to researchers and end-users. Using JavaScript, TensorFlow.js can define, train, and run new or existing, pre-trained machine learning models entirely in the browser from the client-side, which improves the user experience through interaction while preserving privacy. Deep learning models deployed on front-end browsers must be small, have fast inference, and ideally be interactive in real-time. Therefore, the emphasis on development and deployment is different. This paper aims to review the development and deployment of these deep-learning web apps to raise awareness of the recent advancements and encourage more researchers to take advantage of this technology for their own work. First, the rationale behind the deployment stack (front-end, JavaScript, and TensorFlow.js) is discussed. Then, the development approach for obtaining deep learning models that are optimized and suitable for front-end deployment is then described. The article also provides current web applications divided into seven categories to show deep learning potential on the front end. These include web apps for deep learning playground, pose detection and gesture tracking, music and art creation, expression detection and facial recognition, video segmentation, image and signal analysis, healthcare diagnosis, recognition, and identification.
Fulltext Computer-assisted quantification of CD3+ T cells in follicular lymphoma

Abas FS, Shana'ah A, Christian B, Hasserjian R, Louissaint A, Pennell M, et al.

Cytometry A, 2017 06;91(6):609-621.
PMID: 28110507 DOI: 10.1002/cyto.a.23049

The advance of high resolution digital scans of pathology slides allowed development of computer based image analysis algorithms that may help pathologists in IHC stains quantification. While very promising, these methods require further refinement before they are implemented in routine clinical setting. Particularly critical is to evaluate algorithm performance in a setting similar to current clinical practice. In this article, we present a pilot study that evaluates the use of a computerized cell quantification method in the clinical estimation of CD3 positive (CD3+) T cells in follicular lymphoma (FL). Our goal is to demonstrate the degree to which computerized quantification is comparable to the practice of estimation by a panel of expert pathologists. The computerized quantification method uses entropy based histogram thresholding to separate brown (CD3+) and blue (CD3-) regions after a color space transformation. A panel of four board-certified hematopathologists evaluated a database of 20 FL images using two different reading methods: visual estimation and manual marking of each CD3+ cell in the images. These image data and the readings provided a reference standard and the range of variability among readers. Sensitivity and specificity measures of the computer's segmentation of CD3+ and CD- T cell are recorded. For all four pathologists, mean sensitivity and specificity measures are 90.97 and 88.38%, respectively. The computerized quantification method agrees more with the manual cell marking as compared to the visual estimations. Statistical comparison between the computerized quantification method and the pathologist readings demonstrated good agreement with correlation coefficient values of 0.81 and 0.96 in terms of Lin's concordance correlation and Spearman's correlation coefficient, respectively. These values are higher than most of those calculated among the pathologists. In the future, the computerized quantification method may be used to investigate the relationship between the overall architectural pattern (i.e., interfollicular vs. follicular) and outcome measures (e.g., overall survival, and time to treatment). © 2017 International Society for Advancement of Cytometry.
Fulltext Allred Scoring of ER-IHC Stained Whole-Slide Images for Hormone Receptor Status in Breast Carcinoma

Ahmad Fauzi MF, Wan Ahmad WSHM, Jamaluddin MF, Lee JTH, Khor SY, Looi LM, et al.

Diagnostics (Basel), 2022 Dec 08;12(12).
PMID: 36553102 DOI: 10.3390/diagnostics12123093

Hormone receptor status is determined primarily to identify breast cancer patients who may benefit from hormonal therapy. The current clinical practice for the testing using either Allred score or H-score is still based on laborious manual counting and estimation of the amount and intensity of positively stained cancer cells in immunohistochemistry (IHC)-stained slides. This work integrates cell detection and classification workflow for breast carcinoma estrogen receptor (ER)-IHC-stained images and presents an automated evaluation system. The system first detects all cells within the specific regions and classifies them into negatively, weakly, moderately, and strongly stained, followed by Allred scoring for ER status evaluation. The generated Allred score relies heavily on accurate cell detection and classification and is compared against pathologists' manual estimation. Experiments on 40 whole-slide images show 82.5% agreement on hormonal treatment recommendation, which we believe could be further improved with an advanced learning model and enhancement to address the cases with 0% ER status. This promising system can automate the exhaustive exercise to provide fast and reliable assistance to pathologists and medical personnel. The system has the potential to improve the overall standards of prognostic reporting for cancer patients, benefiting pathologists, patients, and also the public at large.
Fulltext Nuclear IHC enumeration: A digital phantom to evaluate the performance of automated algorithms in digital pathology

Niazi MKK, Abas FS, Senaras C, Pennell M, Sahiner B, Chen W, et al.

PLoS One, 2018;13(5):e0196547.
PMID: 29746503 DOI: 10.1371/journal.pone.0196547

Automatic and accurate detection of positive and negative nuclei from images of immunostained tissue biopsies is critical to the success of digital pathology. The evaluation of most nuclei detection algorithms relies on manually generated ground truth prepared by pathologists, which is unfortunately time-consuming and suffers from inter-pathologist variability. In this work, we developed a digital immunohistochemistry (IHC) phantom that can be used for evaluating computer algorithms for enumeration of IHC positive cells. Our phantom development consists of two main steps, 1) extraction of the individual as well as nuclei clumps of both positive and negative nuclei from real WSI images, and 2) systematic placement of the extracted nuclei clumps on an image canvas. The resulting images are visually similar to the original tissue images. We created a set of 42 images with different concentrations of positive and negative nuclei. These images were evaluated by four board certified pathologists in the task of estimating the ratio of positive to total number of nuclei. The resulting concordance correlation coefficients (CCC) between the pathologist and the true ratio range from 0.86 to 0.95 (point estimates). The same ratio was also computed by an automated computer algorithm, which yielded a CCC value of 0.99. Reading the phantom data with known ground truth, the human readers show substantial variability and lower average performance than the computer algorithm in terms of CCC. This shows the limitation of using a human reader panel to establish a reference standard for the evaluation of computer algorithms, thereby highlighting the usefulness of the phantom developed in this work. Using our phantom images, we further developed a function that can approximate the true ratio from the area of the positive and negative nuclei, hence avoiding the need to detect individual nuclei. The predicted ratios of 10 held-out images using the function (trained on 32 images) are within ±2.68% of the true ratio. Moreover, we also report the evaluation of a computerized image analysis method on the synthetic tissue dataset.