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Register a new userDeep Learning Classification of Lake Zooplankton
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Added by
Marco Baity-Jesi
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Plankton are effective indicators of environmental change and ecosystem health in freshwater habitats, but collection of plankton data using manual microscopic methods is extremely labor-intensive and expensive. Automated plankton imaging offers a promising way forward to monitor plankton communities with high frequency and accuracy in real-time. Yet, manual annotation of millions of images proposes a serious challenge to taxonomists. Deep learning classifiers have been successfully applied in various fields and provided encouraging results when used to categorize marine plankton images. Here, we present a set of deep learning models developed for the identification of lake plankton, and study several strategies to obtain optimal performances,which lead to operational prescriptions for users. To this aim, we annotated into 35 classes over 17900 images of zooplankton and large phytoplankton colonies, detected in Lake Greifensee (Switzerland) with the Dual Scripps Plankton Camera. Our best models were based on transfer learning and ensembling, which classified plankton images with 98% accuracy and 93% F1 score. When tested on freely available plankton datasets produced by other automated imaging tools (ZooScan, FlowCytobot and ISIIS), our models performed better than previously used models. Our annotated data, code and classification models are freely available online.
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High-resolution mapping of cells and tissue structures provides a foundation for developing interpretable machine-learning models for computational pathology. Deep learning algorithms can provide accurate mappings given large numbers of labeled instances for training and validation. Generating adequate volume of quality labels has emerged as a critical barrier in computational pathology given the time and effort required from pathologists. In this paper we describe an approach for engaging crowds of medical students and pathologists that was used to produce a dataset of over 220,000 annotations of cell nuclei in breast cancers. We show how suggested annotations generated by a weak algorithm can improve the accuracy of annotations generated by non-experts and can yield useful data for training segmentation algorithms without laborious manual tracing. We systematically examine interrater agreement and describe modifications to the MaskRCNN model to improve cell mapping. We also describe a technique we call Decision Tree Approximation of Learned Embeddings (DTALE) that leverages nucleus segmentations and morphologic features to improve the transparency of nucleus classification models. The annotation data produced in this study are freely available for algorithm development and benchmarking at: https://sites.google.com/view/nucls.
Water quality has a direct impact on industry, agriculture, and public health. Algae species are common indicators of water quality. It is because algal communities are sensitive to changes in their habitats, giving valuable knowledge on variations in water quality. However, water quality analysis requires professional inspection of algal detection and classification under microscopes, which is very time-consuming and tedious. In this paper, we propose a novel multi-target deep learning framework for algal detection and classification. Extensive experiments were carried out on a large-scale colored microscopic algal dataset. Experimental results demonstrate that the proposed method leads to the promising performance on algal detection, class identification and genus identification.
We propose a deep-learning-based classification of data pages used in holographic memory. We numerically investigated the classification performance of a conventional multi-layer perceptron (MLP) and a deep neural network, under the condition that reconstructed page data are contaminated by some noise and are randomly laterally shifted. The MLP was found to have a classification accuracy of 91.58%, whereas the deep neural network was able to classify data pages at an accuracy of 99.98%. The accuracy of the deep neural network is two orders of magnitude better than the MLP.
Learning powerful discriminative features for remote sensing image scene classification is a challenging computer vision problem. In the past, most classification approaches were based on handcrafted features. However, most recent approaches to remote sensing scene classification are based on Convolutional Neural Networks (CNNs). The de facto practice when learning these CNN models is only to use original RGB patches as input with training performed on large amounts of labeled data (ImageNet). In this paper, we show class activation map (CAM) encoded CNN models, codenamed DDRL-AM, trained using original RGB patches and attention map based class information provide complementary information to the standard RGB deep models. To the best of our knowledge, we are the first to investigate attention information encoded CNNs. Additionally, to enhance the discriminability, we further employ a recently developed object function called center loss, which has proved to be very useful in face recognition. Finally, our framework provides attention guidance to the model in an end-to-end fashion. Extensive experiments on two benchmark datasets show that our approach matches or exceeds the performance of other methods.
CNN visualization and interpretation methods, like class-activation maps (CAMs), are typically used to highlight the image regions linked to class predictions. These models allow to simultaneously classify images and extract class-dependent saliency maps, without the need for costly pixel-level annotations. However, they typically yield segmentations with high false-positive rates and, therefore, coarse visualisations, more so when processing challenging images, as encountered in histology. To mitigate this issue, we propose an active learning (AL) framework, which progressively integrates pixel-level annotations during training. Given training data with global image-level labels, our deep weakly-supervised learning model jointly performs supervised image-level classification and active learning for segmentation, integrating pixel annotations by an oracle. Unlike standard AL methods that focus on sample selection, we also leverage large numbers of unlabeled images via pseudo-segmentations (i.e., self-learning at the pixel level), and integrate them with the oracle-annotated samples during training. We report extensive experiments over two challenging benchmarks -- high-resolution medical images (histology GlaS data for colon cancer) and natural images (CUB-200-2011 for bird species). Our results indicate that, by simply using random sample selection, the proposed approach can significantly outperform state-of the-art CAMs and AL methods, with an identical oracle-supervision budget. Our code is publicly available.
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