DAPlankton: Benchmark Dataset for Multi-instrument Plankton Recognition via Fine-grained Domain Adaptation

Plankton recognition provides novel possibilities to study various environmental aspects and an interesting real-world context to develop domain adaptation (DA) methods. Different imaging instruments cause domain shift between datasets hampering the development of general plankton recognition methods. A promising remedy for this is DA allowing to adapt a model trained on one instrument to other instruments. In this paper, we present a new DA dataset called DAPlankton which consists of phytoplankton images obtained with different instruments. Phytoplankton provides a challenging DA problem due to the fine-grained nature of the task and high class imbalance in real-world datasets. DAPlankton consists of two subsets. DAPlankton_LAB contains images of cultured phytoplankton providing a balanced dataset with minimal label uncertainty. DAPlankton_SEA consists of images collected from the Baltic Sea providing challenging real-world data with large intra-class variance and class imbalance. We further present a benchmark comparison of three widely used DA methods.

Combining feature aggregation and geometric similarity for re-identification of patterned animals

Image-based re-identification of animal individuals allows gathering of information such as migration patterns of the animals over time. This, together with large image volumes collected using camera traps and crowdsourcing, opens novel possibilities to study animal populations. For many species, the re-identification can be done by analyzing the permanent fur, feather, or skin patterns that are unique to each individual. In this paper, we address the re-identification by combining two types of pattern similarity metrics: 1) pattern appearance similarity obtained by pattern feature aggregation and 2) geometric pattern similarity obtained by analyzing the geometric consistency of pattern similarities. The proposed combination allows to efficiently utilize both the local and global pattern features, providing a general re-identification approach that can be applied to a wide variety of different pattern types. In the experimental part of the work, we demonstrate that the method achieves promising re-identification accuracies for Saimaa ringed seals and whale sharks.

Survey of Automatic Plankton Image Recognition: Challenges, Existing Solutions and Future Perspectives

Planktonic organisms are key components of aquatic ecosystems and respond quickly to changes in the environment, therefore their monitoring is vital to understand the changes in the environment. Yet, monitoring plankton at appropriate scales still remains a challenge, limiting our understanding of functioning of aquatic systems and their response to changes. Modern plankton imaging instruments can be utilized to sample at high frequencies, enabling novel possibilities to study plankton populations. However, manual analysis of the data is costly, time consuming and expert based, making such approach unsuitable for large-scale application and urging for automatic solutions. The key problem related to the utilization of plankton datasets through image analysis is plankton recognition. Despite the large amount of research done, automatic methods have not been widely adopted for operational use. In this paper, a comprehensive survey on existing solutions for automatic plankton recognition is presented. First, we identify the most notable challenges that that make the development of plankton recognition systems difficult. Then, we provide a detailed description of solutions for these challenges proposed in plankton recognition literature. Finally, we propose a workflow to identify the specific challenges in new datasets and the recommended approaches to address them. For many of the challenges, applicable solutions exist. However, important challenges remain unsolved: 1) the domain shift between the datasets hindering the development of a general plankton recognition system that would work across different imaging instruments, 2) the difficulty to identify and process the images of previously unseen classes, and 3) the uncertainty in expert annotations that affects the training of the machine learning models for recognition. These challenges should be addressed in the future research.

Towards Phytoplankton Parasite Detection Using Autoencoders

Phytoplankton parasites are largely understudied microbial components with a potentially significant ecological impact on phytoplankton bloom dynamics. To better understand their impact, we need improved detection methods to integrate phytoplankton parasite interactions in monitoring aquatic ecosystems. Automated imaging devices usually produce high amount of phytoplankton image data, while the occurrence of anomalous phytoplankton data is rare. Thus, we propose an unsupervised anomaly detection system based on the similarity of the original and autoencoder-reconstructed samples. With this approach, we were able to reach an overall F1 score of 0.75 in nine phytoplankton species, which could be further improved by species-specific fine-tuning. The proposed unsupervised approach was further compared with the supervised Faster R-CNN based object detector. With this supervised approach and the model trained on plankton species and anomalies, we were able to reach the highest F1 score of 0.86. However, the unsupervised approach is expected to be more universal as it can detect also unknown anomalies and it does not require any annotated anomalous data that may not be always available in sufficient quantities. Although other studies have dealt with plankton anomaly detection in terms of non-plankton particles, or air bubble detection, our paper is according to our best knowledge the first one which focuses on automated anomaly detection considering putative phytoplankton parasites or infections.

NORPPA: NOvel Ringed seal re-identification by Pelage Pattern Aggregation

We propose a method for Saimaa ringed seal (Pusa hispida saimensis) re-identification. Access to large image volumes through camera trapping and crowdsourcing provides novel possibilities for animal monitoring and conservation and calls for automatic methods for analysis, in particular, when re-identifying individual animals from the images. The proposed method NOvel Ringed seal re-identification by Pelage Pattern Aggregation (NORPPA) utilizes the permanent and unique pelage pattern of Saimaa ringed seals and content-based image retrieval techniques. First, the query image is preprocessed, and each seal instance is segmented. Next, the seal's pelage pattern is extracted using a U-net encoder-decoder based method. Then, CNN-based affine invariant features are embedded and aggregated into Fisher Vectors. Finally, the cosine distance between the Fisher Vectors is used to find the best match from a database of known individuals. We perform extensive experiments of various modifications of the method on a new challenging Saimaa ringed seals re-identification dataset. The proposed method is shown to produce the best re-identification accuracy on our dataset in comparisons with alternative approaches.

SealID: Saimaa ringed seal re-identification dataset

Wildlife camera traps and crowd-sourced image material provide novel possibilities to monitor endangered animal species. However, massive image volumes that these methods produce are overwhelming for researchers to go through manually which calls for automatic systems to perform the analysis. The analysis task that has gained the most attention is the re-identification of individuals, as it allows, for example, to study animal migration or to estimate the population size. The Saimaa ringed seal (Pusa hispida saimensis) is an endangered subspecies only found in the Lake Saimaa, Finland, and is one of the few existing freshwater seal species. Ringed seals have permanent pelage patterns that are unique to each individual which can be used for the identification of individuals. Large variation in poses further exacerbated by the deformable nature of seals together with varying appearance and low contrast between the ring pattern and the rest of the pelage makes the Saimaa ringed seal re-identification task very challenging, providing a good benchmark to evaluate state-of-the-art re-identification methods. Therefore, we make our Saimaa ringed seal image (SealID) dataset (N=57) publicly available for research purposes. In this paper, the dataset is described, the evaluation protocol for re-identification methods is proposed, and the results for two baseline methods HotSpotter and NORPPA are provided. The SealID dataset has been made publicly available.

EDEN: Deep Feature Distribution Pooling for Saimaa Ringed Seals Pattern Matching

In this paper, pelage pattern matching is considered to solve the individual re-identification of the Saimaa ringed seals. Animal re-identification together with the access to large amount of image material through camera traps and crowd-sourcing provide novel possibilities for animal monitoring and conservation. We propose a novel feature pooling approach that allow aggregating the local pattern features to get a fixed size embedding vector that incorporate global features by taking into account the spatial distribution of features. This is obtained by eigen decomposition of covariances computed for probability mass functions representing feature maps. Embedding vectors can then be used to find the best match in the database of known individuals allowing animal re-identification. The results show that the proposed pooling method outperforms the existing methods on the challenging Saimaa ringed seal image data.

Resolving Overlapping Convex Objects in Silhouette Images by Concavity Analysis and Gaussian Process

Segmentation of overlapping convex objects has various applications, for example, in nanoparticles and cell imaging. Often the segmentation method has to rely purely on edges between the background and foreground making the analyzed images essentially silhouette images. Therefore, to segment the objects, the method needs to be able to resolve the overlaps between multiple objects by utilizing prior information about the shape of the objects. This paper introduces a novel method for segmentation of clustered partially overlapping convex objects in silhouette images. The proposed method involves three main steps: pre-processing, contour evidence extraction, and contour estimation. Contour evidence extraction starts by recovering contour segments from a binarized image by detecting concave points. After this, the contour segments which belong to the same objects are grouped. The grouping is formulated as a combinatorial optimization problem and solved using the branch and bound algorithm. Finally, the full contours of the objects are estimated by a Gaussian process regression method. The experiments on a challenging dataset consisting of nanoparticles demonstrate that the proposed method outperforms three current state-of-art approaches in overlapping convex objects segmentation. The method relies only on edge information and can be applied to any segmentation problems where the objects are partially overlapping and have a convex shape.