Developing deep learning methods for aquaculture applications

Alzayat Saleh developed a computer vision framework that can aid aquaculture experts in analyzing fish habitats. In particular, he developed a labelling efficient method of training a CNN-based fish-detector and also developed a model that estimates the fish weight directly from its image

Novel deep learning architectures for marine and aquaculture applications

Alzayat Saleh's research was in the area of artificial intelligence and machine learning to autonomously recognise fish and their morphological features from digital images. Here he created new deep learning architectures that solved various computer vision problems specific to the marine and aquaculture context. He found that these techniques can facilitate aquaculture management and environmental protection. Fisheries and conservation agencies can use his results for better monitoring strategies and sustainable fishing practices

Underwater Fish Detection with Weak Multi-Domain Supervision

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%.Comment: Published in the 2019 International Joint Conference on Neural Networks (IJCNN-2019), Budapest, Hungary, July 14-19, 2019, https://www.ijcnn.org/ , https://ieeexplore.ieee.org/document/885190

MFLD-net: a lightweight deep learning network for fish morphometry using landmark detection

Monitoring the morphological traits of farmed fish is pivotal in understanding growth, estimating yield, artificial breeding, and population-based investigations. Currently, morphology measurements mostly happen manually and sometimes in conjunction with individual fish imaging, which is a time-consuming and expensive procedure. In addition, extracting useful information such as fish yield and detecting small variations due to growth or deformities, require extra offline processing of the manually collected images and data. Deep learning (DL) and specifically convolutional neural networks (CNNs) have previously demonstrated great promise in estimating fish features such as weight and length from images. However, their use for extracting fish morphological traits through detecting fish keypoints (landmarks) has not been fully explored. In this paper, we developed a novel DL architecture that we call Mobile Fish Landmark Detection network (MFLD-net). We show that MFLD-net can achieve keypoint detection accuracies on par or even better than some of the state-of-the-art CNNs on a fish image dataset. MFLD-net uses convolution operations based on Vision Transformers (i.e. patch embeddings, multi-layer perceptrons). We show that MFLD-net can achieve competitive or better results in low data regimes while being lightweight and therefore suitable for embedded and mobile devices. We also provide quantitative and qualitative results that demonstrate its generalisation capabilities. These features make MFLD-net suitable for future deployment in fish farms and fish harvesting plants

WeedCLR: Weed Contrastive Learning through Visual Representations with Class-Optimized Loss in Long-Tailed Datasets

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.Comment: 24 pages, 10 figures, 8 tables. Submitted to the Computers and Electronics in Agriculture journa

Estimating mass of harvested Asian seabass Lates calcarifer from images

Total of 1072 Asian seabass or barramundi (Lates calcarifer) were harvested at two different locations in Queensland, Australia. Each fish was digitally photographed and weighed. A subsample of 200 images (100 from each location) were manually segmented to extract the fish-body area (S in cm2), excluding all fins. After scaling the segmented images to 1mm per pixel, the fish mass values (M in grams) were fitted by a single-factor model ( M=aS1.5 , a=0.1695 ) achieving the coefficient of determination (R2) and the Mean Absolute Relative Error (MARE) of R2=0.9819 and MARE=5.1% , respectively. A segmentation Convolutional Neural Network (CNN) was trained on the 200 hand-segmented images, and then applied to the rest of the available images. The CNN predicted fish-body areas were used to fit the mass-area estimation models: the single-factor model, M=aS1.5 , a=0.170 , R2=0.9819 , MARE=5.1% ; and the two-factor model, M=aSb , a=0.124 , b=0.155 , R2=0.9834 , MARE=4.5

Weakly supervised underwater fish segmentation using affinity LCFCN

Estimating fish body measurements like length, width, and mass has received considerable research due to its potential in boosting productivity in marine and aquaculture applications. Some methods are based on manual collection of these measurements using tools like a ruler which is time consuming and labour intensive. Others rely on fully-supervised segmentation models to automatically acquire these measurements but require collecting per-pixel labels which are also time consuming. It can take up to 2 minutes per fish to acquire accurate segmentation labels. To address this problem, we propose a segmentation model that can efficiently train on images labeled with point-level supervision, where each fish is annotated with a single click. This labeling scheme takes an average of only 1 second per fish. Our model uses a fully convolutional neural network with one branch that outputs per-pixel scores and another that outputs an affinity matrix. These two outputs are aggregated using a random walk to get the final, refined per-pixel output. The whole model is trained end-to-end using the localization-based counting fully convolutional neural network (LCFCN) loss and thus we call our method Affinity-LCFCN (A-LCFCN). We conduct experiments on the DeepFish dataset, which contains several fish habitats from north-eastern Australia. The results show that A-LCFCN outperforms a fully-supervised segmentation model when the annotation budget is fixed. They also show that A-LCFCN achieves better segmentation results than LCFCN and a standard baseline

A realistic fish-habitat dataset to evaluate algorithms for underwater visual analysis

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 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

Laparoscopy in management of appendicitis in high-, middle-, and low-income countries: a multicenter, prospective, cohort study.

BACKGROUND: Appendicitis is the most common abdominal surgical emergency worldwide. Differences between high- and low-income settings in the availability of laparoscopic appendectomy, alternative management choices, and outcomes are poorly described. The aim was to identify variation in surgical management and outcomes of appendicitis within low-, middle-, and high-Human Development Index (HDI) countries worldwide. METHODS: This is a multicenter, international prospective cohort study. Consecutive sampling of patients undergoing emergency appendectomy over 6 months was conducted. Follow-up lasted 30 days. RESULTS: 4546 patients from 52 countries underwent appendectomy (2499 high-, 1540 middle-, and 507 low-HDI groups). Surgical site infection (SSI) rates were higher in low-HDI (OR 2.57, 95% CI 1.33-4.99, p = 0.005) but not middle-HDI countries (OR 1.38, 95% CI 0.76-2.52, p = 0.291), compared with high-HDI countries after adjustment. A laparoscopic approach was common in high-HDI countries (1693/2499, 67.7%), but infrequent in low-HDI (41/507, 8.1%) and middle-HDI (132/1540, 8.6%) groups. After accounting for case-mix, laparoscopy was still associated with fewer overall complications (OR 0.55, 95% CI 0.42-0.71, p < 0.001) and SSIs (OR 0.22, 95% CI 0.14-0.33, p < 0.001). In propensity-score matched groups within low-/middle-HDI countries, laparoscopy was still associated with fewer overall complications (OR 0.23 95% CI 0.11-0.44) and SSI (OR 0.21 95% CI 0.09-0.45). CONCLUSION: A laparoscopic approach is associated with better outcomes and availability appears to differ by country HDI. Despite the profound clinical, operational, and financial barriers to its widespread introduction, laparoscopy could significantly improve outcomes for patients in low-resource environments. TRIAL REGISTRATION: NCT02179112