Alzayat Saleh

Alzayat Saleh, Marcus Sheaves, Dean Jerry et al.

One of the main challenges in deep learning-based underwater image enhancement is the limited availability of high-quality training data. Underwater images are difficult to capture and are often of poor quality due to the distortion and loss of colour and contrast in water. This makes it difficult to train supervised deep learning models on large and diverse datasets, which can limit the model's performance. In this paper, we explore an alternative approach to supervised underwater image enhancement. Specifically, we propose a novel unsupervised underwater image enhancement framework that employs a conditional variational autoencoder (cVAE) to train a deep learning model with probabilistic adaptive instance normalization (PAdaIN) and statistically guided multi-colour space stretch that produces realistic underwater images. The resulting framework is composed of a U-Net as a feature extractor and a PAdaIN to encode the uncertainty, which we call UDnet. To improve the visual quality of the images generated by UDnet, we use a statistically guided multi-colour space stretch module that ensures visual consistency with the input image and provides an alternative to training using a ground truth image. The proposed model does not need manual human annotation and can learn with a limited amount of data and achieves state-of-the-art results on underwater images. We evaluated our proposed framework on eight publicly-available datasets. The results show that our proposed framework yields competitive performance compared to other state-of-the-art approaches in quantitative as well as qualitative metrics. Code available at https://github.com/alzayats/UDnet .

Alzayat Saleh, Marcus Sheaves, Mostafa Rahimi Azghadi

Marine scientists use remote underwater video recording to survey fish species in their natural habitats. This helps them understand and predict how fish respond to climate change, habitat degradation, and fishing pressure. This information is essential for developing sustainable fisheries for human consumption, and for preserving the environment. However, the enormous volume of collected videos makes extracting useful information a daunting and time-consuming task for a human. A promising method to address this problem is the cutting-edge Deep Learning (DL) technology.DL can help marine scientists parse large volumes of video promptly and efficiently, unlocking niche information that cannot be obtained using conventional manual monitoring methods. In this paper, we provide an overview of the key concepts of DL, while presenting a survey of literature on fish habitat monitoring with a focus on underwater fish classification. We also discuss the main challenges faced when developing DL for underwater image processing and propose approaches to address them. Finally, we provide insights into the marine habitat monitoring research domain and shed light on what the future of DL for underwater image processing may hold. This paper aims to inform a wide range of readers from marine scientists who would like to apply DL in their research to computer scientists who would like to survey state-of-the-art DL-based underwater fish habitat monitoring literature.

Alzayat Saleh, Marcus Sheaves, Dean Jerry et al.

Marine ecosystems and their fish habitats are becoming increasingly important due to their integral role in providing a valuable food source and conservation outcomes. Due to their remote and difficult to access nature, marine environments and fish habitats are often monitored using underwater cameras. These cameras generate a massive volume of digital data, which cannot be efficiently analysed by current manual processing methods, which involve a human observer. DL is a cutting-edge AI technology that has demonstrated unprecedented performance in analysing visual data. Despite its application to a myriad of domains, its use in underwater fish habitat monitoring remains under explored. In this paper, we provide a tutorial that covers the key concepts of DL, which help the reader grasp a high-level understanding of how DL works. The tutorial also explains a step-by-step procedure on how DL algorithms should be developed for challenging applications such as underwater fish monitoring. In addition, we provide a comprehensive survey of key deep learning techniques for fish habitat monitoring including classification, counting, localization, and segmentation. Furthermore, we survey publicly available underwater fish datasets, and compare various DL techniques in the underwater fish monitoring domains. We also discuss some challenges and opportunities in the emerging field of deep learning for fish habitat processing. This paper is written to serve as a tutorial for marine scientists who would like to grasp a high-level understanding of DL, develop it for their applications by following our step-by-step tutorial, and see how it is evolving to facilitate their research efforts. At the same time, it is suitable for computer scientists who would like to survey state-of-the-art DL-based methodologies for fish habitat monitoring.

Alzayat Saleh, Md Mehedi Hasan, Herman W Raadsma et al.

Accurate weight estimation and morphometric analyses are useful in aquaculture for optimizing feeding, predicting harvest yields, identifying desirable traits for selective breeding, grading processes, and monitoring the health status of production animals. However, the collection of phenotypic data through traditional manual approaches at industrial scales and in real-time is time-consuming, labour-intensive, and prone to errors. Digital imaging of individuals and subsequent training of prediction models using Deep Learning (DL) has the potential to rapidly and accurately acquire phenotypic data from aquaculture species. In this study, we applied a novel DL approach to automate weight estimation and morphometric analysis using the black tiger prawn (Penaeus monodon) as a model crustacean. The DL approach comprises two main components: a feature extraction module that efficiently combines low-level and high-level features using the Kronecker product operation; followed by a landmark localization module that then uses these features to predict the coordinates of key morphological points (landmarks) on the prawn body. Once these landmarks were extracted, weight was estimated using a weight regression module based on the extracted landmarks using a fully connected network. For morphometric analyses, we utilized the detected landmarks to derive five important prawn traits. Principal Component Analysis (PCA) was also used to identify landmark-derived distances, which were found to be highly correlated with shape features such as body length, and width. We evaluated our approach on a large dataset of 8164 images of the Black tiger prawn (Penaeus monodon) collected from Australian farms. Our experimental results demonstrate that the novel DL approach outperforms existing DL methods in terms of accuracy, robustness, and efficiency.

Alzayat Saleh, Marcus Sheaves, Dean Jerry et al.

Tracking fish movements and sizes of fish is crucial to understanding their ecology and behaviour. Knowing where fish migrate, how they interact with their environment, and how their size affects their behaviour can help ecologists develop more effective conservation and management strategies to protect fish populations and their habitats. Deep learning is a promising tool to analyze fish ecology from underwater videos. However, training deep neural networks (DNNs) for fish tracking and segmentation requires high-quality labels, which are expensive to obtain. We propose an alternative unsupervised approach that relies on spatial and temporal variations in video data to generate noisy pseudo-ground-truth labels. We train a multitask DNN using these pseudo-labels. Our framework consists of three stages: (1) an optical flow model generates the pseudo labels using spatial and temporal consistency between frames, (2) a self-supervised model refines the pseudo-labels incrementally, and (3) a segmentation network uses the refined labels for training. Consequently, we perform extensive experiments to validate our method on three public underwater video datasets and demonstrate its effectiveness for video annotation and segmentation. We also evaluate its robustness to different imaging conditions and discuss its limitations.

Alzayat Saleh, Marcus Sheaves, Dean Jerry et al.

Accurate fish segmentation in underwater videos is challenging due to low visibility, variable lighting, and dynamic backgrounds, making fully-supervised methods that require manual annotation impractical for many applications. This paper introduces a novel self-supervised learning approach for fish segmentation using Deep Learning. Our model, trained without manual annotation, learns robust and generalizable representations by aligning features across augmented views and enforcing spatial-temporal consistency. We demonstrate its effectiveness on three challenging underwater video datasets: DeepFish, Seagrass, and YouTube-VOS, surpassing existing self-supervised methods and achieving segmentation accuracy comparable to fully-supervised methods without the need for costly annotations. Trained on DeepFish, our model exhibits strong generalization, achieving high segmentation accuracy on the unseen Seagrass and YouTube-VOS datasets. Furthermore, our model is computationally efficient due to its parallel processing and efficient anchor sampling technique, making it suitable for real-time applications and potential deployment on edge devices. We present quantitative results using Jaccard Index and Dice coefficient, as well as qualitative comparisons, showcasing the accuracy, robustness, and efficiency of our approach for advancing underwater video analysis

Alzayat Saleh, David Jones, Dean Jerry et al.

Transformer-based models, such as the Vision Transformer (ViT), can outperform onvolutional Neural Networks (CNNs) in some vision tasks when there is sufficient training data. However, (CNNs) have a strong and useful inductive bias for vision tasks (i.e. translation equivariance and locality). In this work, we developed a novel model architecture that we call a Mobile fish landmark detection network (MFLD-net). We have made this model using convolution operations based on ViT (i.e. Patch embeddings, Multi-Layer Perceptrons). MFLD-net can achieve competitive or better results in low data regimes while being lightweight and therefore suitable for embedded and mobile devices. Furthermore, we show that MFLD-net can achieve keypoint (landmark) estimation accuracies on-par or even better than some of the state-of-the-art (CNNs) on a fish image dataset. Additionally, unlike ViT, MFLD-net does not need a pre-trained model and can generalise well when trained on a small dataset. We provide quantitative and qualitative results that demonstrate the model's generalisation capabilities. This work will provide a foundation for future efforts in developing mobile, but efficient fish monitoring systems and devices.

Alzayat Saleh, Mostafa Rahimi Azghadi

Satellite sea surface temperature (SST) products underpin global coral bleaching monitoring, yet they measure only the ocean skin. Corals inhabit depths from the shallows to beyond 20 metres, where temperatures can be 1-3°C cooler than the surface; applying satellite SST uniformly to all depths therefore overestimates subsurface thermal stress. We present a physics-informed neural network (PINN) that fuses NOAA Coral Reef Watch SST with sparse in-situ temperature loggers within the one-dimensional vertical heat equation, enforcing SST as a hard surface boundary condition and jointly learning effective thermal diffusivity (\k{appa}) and light attenuation (Kd). Validated across four Great Barrier Reef sites (30 holdout experiments), the PINN achieves 0.25-1.38°C RMSE at unseen depths. Under extreme sparsity (three training depths), the PINN maintains 0.27°C RMSE at the 5 metre holdout and 0.32°C at the 9.1 metre holdout, where statistical baselines collapse to >1.8°C; it outperforms a physics-only finite-difference baseline in 90% of experiments. Depth-resolved Degree Heating Day (DHD) profiles show that thermal stress attenuates with depth: at Davies Reef, DHD drops from 0.29 at the surface to zero by 10.7 metres, consistent with logger observations, while satellite DHD remains constant at 0.31 across all depths. However, the PINN underestimates absolute DHD at shallow depths because its smooth predictions attenuate the short-duration peaks that drive threshold exceedances; PINN DHD values should be interpreted as conservative lower bounds on depth-resolved stress. These results demonstrate that physics-constrained fusion of satellite SST with sparse loggers can extend bleaching assessment to the depth dimension using existing observational infrastructure.

Alzayat Saleh, Alex Olsen, Jake Wood et al.

Image classification is a crucial task in modern weed management and crop intervention technologies. However, the limited size, diversity, and balance of existing weed datasets hinder the development of deep learning models for generalizable weed identification. In addition, the expensive labelling requirements of mainstream fully-supervised weed classifiers make them cost- and time-prohibitive to deploy widely, for new weed species, and in site-specific weed management. This paper proposes a novel method for Weed Contrastive Learning through visual Representations (WeedCLR), that uses class-optimized loss with Von Neumann Entropy of deep representation for weed classification in long-tailed datasets. WeedCLR leverages self-supervised learning to learn rich and robust visual features without any labels and applies a class-optimized loss function to address the class imbalance problem in long-tailed datasets. WeedCLR is evaluated on two public weed datasets: CottonWeedID15, containing 15 weed species, and DeepWeeds, containing 8 weed species. WeedCLR achieves an average accuracy improvement of 4.3\% on CottonWeedID15 and 5.6\% on DeepWeeds over previous methods. It also demonstrates better generalization ability and robustness to different environmental conditions than existing methods without the need for expensive and time-consuming human annotations. These significant improvements make WeedCLR an effective tool for weed classification in long-tailed datasets and allows for more rapid and widespread deployment of site-specific weed management and crop intervention technologies.

Issam Laradji, Alzayat Saleh, Pau Rodriguez et al.

Aquaculture industries rely on the availability of accurate fish body measurements, e.g., length, width and mass. Manual methods that rely on physical tools like rulers are time and labour intensive. Leading automatic approaches rely on fully-supervised segmentation models to acquire these measurements but these require collecting per-pixel labels -- also time consuming and laborious: i.e., it can take up to two minutes per fish to generate accurate segmentation labels, almost always requiring at least some manual intervention. We propose an automatic segmentation model efficiently trained on images labeled with only point-level supervision, where each fish is annotated with a single click. This labeling process requires significantly less manual intervention, averaging roughly one second per fish. Our approach uses a fully convolutional neural network with one branch that outputs per-pixel scores and another that outputs an affinity matrix. We aggregate these two outputs using a random walk to obtain the final, refined per-pixel segmentation output. We train the entire model end-to-end with an LCFCN loss, resulting in our A-LCFCN method. We validate our model on the DeepFish dataset, which contains many fish habitats from the north-eastern Australian region. Our experimental results confirm that A-LCFCN outperforms a fully-supervised segmentation model at fixed annotation budget. Moreover, we show that A-LCFCN achieves better segmentation results than LCFCN and a standard baseline. We have released the code at \url{https://github.com/IssamLaradji/affinity_lcfcn}.

Alzayat Saleh, Issam H. Laradji, Dmitry A. Konovalov et al.

Visual analysis of complex fish habitats is an important step towards sustainable fisheries for human consumption and environmental protection. Deep Learning methods have shown great promise for scene analysis when trained on large-scale datasets. However, current datasets for fish analysis tend to focus on the classification task within constrained, plain environments which do not capture the complexity of underwater fish habitats. To address this limitation, we present DeepFish as a benchmark suite with a large-scale dataset to train and test methods for several computer vision tasks. The dataset consists of approximately 40 thousand images collected underwater from 20 \green{habitats in the} marine-environments of tropical Australia. The dataset originally contained only classification labels. Thus, we collected point-level and segmentation labels to have a more comprehensive fish analysis benchmark. These labels enable models to learn to automatically monitor fish count, identify their locations, and estimate their sizes. Our experiments provide an in-depth analysis of the dataset characteristics, and the performance evaluation of several state-of-the-art approaches based on our benchmark. Although models pre-trained on ImageNet have successfully performed on this benchmark, there is still room for improvement. Therefore, this benchmark serves as a testbed to motivate further development in this challenging domain of underwater computer vision. Code is available at: https://github.com/alzayats/DeepFish

Alzayat Saleh, Alex Olsen, Jake Wood et al.

Shadows significantly hinder computer vision tasks in outdoor environments, particularly in field robotics, where varying lighting conditions complicate object detection and localisation. We present FieldNet, a novel deep learning framework for real-time shadow removal, optimised for resource-constrained hardware. FieldNet introduces a probabilistic enhancement module and a novel loss function to address challenges of inconsistent shadow boundary supervision and artefact generation, achieving enhanced accuracy and simplicity without requiring shadow masks during inference. Trained on a dataset of 10,000 natural images augmented with synthetic shadows, FieldNet outperforms state-of-the-art methods on benchmark datasets (ISTD, ISTD+, SRD), with up to $9$x speed improvements (66 FPS on Nvidia 2080Ti) and superior shadow removal quality (PSNR: 38.67, SSIM: 0.991). Real-world case studies in precision agriculture robotics demonstrate the practical impact of FieldNet in enhancing weed detection accuracy. These advancements establish FieldNet as a robust, efficient solution for real-time vision tasks in field robotics and beyond.

Alzayat Saleh, Alex Olsen, Jake Wood et al.

Weeds present a significant challenge in agriculture, causing yield loss and requiring expensive control measures. Automatic weed detection using computer vision and deep learning offers a promising solution. However, conventional deep learning methods often require large amounts of labelled training data, which can be costly and time-consuming to acquire. This paper introduces a novel method for semi-supervised weed detection, comprising two main components. Firstly, a multi-scale feature representation technique is employed to capture distinctive weed features across different scales. Secondly, we propose an adaptive pseudo-label assignment strategy, leveraging a small set of labelled images during training. This strategy dynamically assigns confidence scores to pseudo-labels generated from unlabeled data. Additionally, our approach integrates epoch-corresponding and mixed pseudo-labels to further enhance the learning process. Experimental results on the COCO dataset and five prominent weed datasets -- CottonWeedDet12, CropAndWeed, Palmer amaranth, RadishWheat, and RoboWeedMap -- illustrate that our method achieves state-of-the-art performance in weed detection, even with significantly less labelled data compared to existing techniques. This approach holds the potential to alleviate the labelling burden and enhance the feasibility and deployment speed of deep learning for weed detection in real-world agricultural scenarios.

Alzayat Saleh, Shunsuke Hatano, Mostafa Rahimi Azghadi

The automated management of invasive weeds is critical for sustainable agriculture, yet the performance of deep learning models in real-world fields is often compromised by two factors: challenging environmental conditions and the high cost of data annotation. This study tackles both issues through a diagnostic-driven, semi-supervised framework. Using a unique dataset of approximately 975 labeled and 10,000 unlabeled images of Guinea Grass in sugarcane, we first establish strong supervised baselines for classification (ResNet) and detection (YOLO, RF-DETR), achieving F1 scores up to 0.90 and mAP50 scores exceeding 0.82. Crucially, this foundational analysis, aided by interpretability tools, uncovered a pervasive "shadow bias," where models learned to misidentify shadows as vegetation. This diagnostic insight motivated our primary contribution: a semi-supervised pipeline that leverages unlabeled data to enhance model robustness. By training models on a more diverse set of visual information through pseudo-labeling, this framework not only helps mitigate the shadow bias but also provides a tangible boost in recall, a critical metric for minimizing weed escapes in automated spraying systems. To validate our methodology, we demonstrate its effectiveness in a low-data regime on a public crop-weed benchmark. Our work provides a clear and field-tested framework for developing, diagnosing, and improving robust computer vision systems for the complex realities of precision agriculture.

Alzayat Saleh, Issam H. Laradji, Corey Lammie et al.

Health professionals extensively use Two- Dimensional (2D) Ultrasound (US) videos and images to visualize and measure internal organs for various purposes including evaluation of muscle architectural changes. US images can be used to measure abdominal muscles dimensions for the diagnosis and creation of customized treatment plans for patients with Low Back Pain (LBP), however, they are difficult to interpret. Due to high variability, skilled professionals with specialized training are required to take measurements to avoid low intra-observer reliability. This variability stems from the challenging nature of accurately finding the correct spatial location of measurement endpoints in abdominal US images. In this paper, we use a Deep Learning (DL) approach to automate the measurement of the abdominal muscle thickness in 2D US images. By treating the problem as a localization task, we develop a modified Fully Convolutional Network (FCN) architecture to generate blobs of coordinate locations of measurement endpoints, similar to what a human operator does. We demonstrate that using the TrA400 US image dataset, our network achieves a Mean Absolute Error (MAE) of 0.3125 on the test set, which almost matches the performance of skilled ultrasound technicians. Our approach can facilitate next steps for automating the process of measurements in 2D US images, while reducing inter-observer as well as intra-observer variability for more effective clinical outcomes.

Dmitry A. Konovalov, Alzayat Saleh, Dina B. Efremova et al.

Approximately 2,500 weights and corresponding images of harvested Lates calcarifer (Asian seabass or barramundi) were collected at three different locations in Queensland, Australia. Two instances of the LinkNet-34 segmentation Convolutional Neural Network (CNN) were trained. The first one was trained on 200 manually segmented fish masks with excluded fins and tails. The second was trained on 100 whole-fish masks. The two CNNs were applied to the rest of the images and yielded automatically segmented masks. The one-factor and two-factor simple mathematical weight-from-area models were fitted on 1072 area-weight pairs from the first two locations, where area values were extracted from the automatically segmented masks. When applied to 1,400 test images (from the third location), the one-factor whole-fish mask model achieved the best mean absolute percentage error (MAPE), MAPE=4.36%. Direct weight-from-image regression CNNs were also trained, where the no-fins based CNN performed best on the test images with MAPE=4.28%.

Dmitry A. Konovalov, Alzayat Saleh, Michael Bradley et al.

Given a sufficiently large training dataset, it is relatively easy to train a modern convolution neural network (CNN) as a required image classifier. However, for the task of fish classification and/or fish detection, if a CNN was trained to detect or classify particular fish species in particular background habitats, the same CNN exhibits much lower accuracy when applied to new/unseen fish species and/or fish habitats. Therefore, in practice, the CNN needs to be continuously fine-tuned to improve its classification accuracy to handle new project-specific fish species or habitats. In this work we present a labelling-efficient method of training a CNN-based fish-detector (the Xception CNN was used as the base) on relatively small numbers (4,000) of project-domain underwater fish/no-fish images from 20 different habitats. Additionally, 17,000 of known negative (that is, missing fish) general-domain (VOC2012) above-water images were used. Two publicly available fish-domain datasets supplied additional 27,000 of above-water and underwater positive/fish images. By using this multi-domain collection of images, the trained Xception-based binary (fish/not-fish) classifier achieved 0.17% false-positives and 0.61% false-negatives on the project's 20,000 negative and 16,000 positive holdout test images, respectively. The area under the ROC curve (AUC) was 99.94%.