Multimodal surface defect detection from wooden logs for sawing optimization

We propose a novel, good-quality, and less demanding method for detecting knots on the surface of wooden logs using multimodal data fusion. Knots are a primary factor affecting the quality of sawn timber, making their detection fundamental to any timber grading or cutting optimization system. While X-ray computed tomography provides accurate knot locations and internal structures, it is often too slow or expensive for practical use. An attractive alternative is to use fast and cost-effective log surface measurements, such as laser scanners or RGB cameras, to detect surface knots and estimate the internal structure of wood. However, due to the small size of knots and noise caused by factors, such as bark and other natural variations, detection accuracy often remains low when only one measurement modality is used. In this paper, we demonstrate that by using a data fusion pipeline consisting of separate streams for RGB and point cloud data, combined by a late fusion module, higher knot detection accuracy can be achieved compared to using either modality alone. We further propose a simple yet efficient sawing angle optimization method that utilizes surface knot detections and cross-correlation to minimize the amount of unwanted arris knots, demonstrating its benefits over randomized sawing angles.

Towards synthetic generation of realistic wooden logs

In this work, we propose a novel method to synthetically generate realistic 3D representations of wooden logs. Efficient sawmilling heavily relies on accurate measurement of logs and the distribution of knots inside them. Computed Tomography (CT) can be used to obtain accurate information about the knots but is often not feasible in a sawmill environment. A promising alternative is to utilize surface measurements and machine learning techniques to predict the inner structure of the logs. However, obtaining enough training data remains a challenge. We focus mainly on two aspects of log generation: the modeling of knot growth inside the tree, and the realistic synthesis of the surface including the regions, where the knots reach the surface. This results in the first log synthesis approach capable of generating both the internal knot and external surface structures of wood. We demonstrate that the proposed mathematical log model accurately fits to real data obtained from CT scans and enables the generation of realistic logs.

Deep Unsupervised Segmentation of Log Point Clouds

In sawmills, it is essential to accurately measure the raw material, i.e. wooden logs, to optimise the sawing process. Earlier studies have shown that accurate predictions of the inner structure of the logs can be obtained using just surface point clouds produced by a laser scanner. This provides a cost-efficient and fast alternative to the X-ray CT-based measurement devices. The essential steps in analysing log point clouds is segmentation, as it forms the basis for finding the fine surface details that provide the cues about the inner structure of the log. We propose a novel Point Transformer-based point cloud segmentation technique that learns to find the points belonging to the log surface in unsupervised manner. This is obtained using a loss function that utilises the geometrical properties of a cylinder while taking into account the shape variation common in timber logs. We demonstrate the accuracy of the method on wooden logs, but the approach could be utilised also on other cylindrical objects.

Self-Supervised Pretraining for Fine-Grained Plankton Recognition

Plankton recognition is an important computer vision problem due to plankton's essential role in ocean food webs and carbon capture, highlighting the need for species-level monitoring. However, this task is challenging due to its fine-grained nature and dataset shifts caused by different imaging instruments and varying species distributions. As new plankton image datasets are collected at an increasing pace, there is a need for general plankton recognition models that require minimal expert effort for data labeling. In this work, we study large-scale self-supervised pretraining for fine-grained plankton recognition. We first employ masked autoencoding and a large volume of diverse plankton image data to pretrain a general-purpose plankton image encoder. Then we utilize fine-tuning to obtain accurate plankton recognition models for new datasets with a very limited number of labeled training images. Our experiments show that self-supervised pretraining with diverse plankton data clearly increases plankton recognition accuracy compared to standard ImageNet pretraining when the amount of training data is limited. Moreover, the accuracy can be further improved when unlabeled target data is available and utilized during the pretraining.

Open-Set Plankton Recognition

This paper considers open-set recognition (OSR) of plankton images. Plankton include a diverse range of microscopic aquatic organisms that have an important role in marine ecosystems as primary producers and as a base of food webs. Given their sensitivity to environmental changes, fluctuations in plankton populations offer valuable information about oceans' health and climate change motivating their monitoring. Modern automatic plankton imaging devices enable the collection of large-scale plankton image datasets, facilitating species-level analysis. Plankton species recognition can be seen as an image classification task and is typically solved using deep learning-based image recognition models. However, data collection in real aquatic environments results in imaging devices capturing a variety of non-plankton particles and plankton species not present in the training set. This creates a challenging fine-grained OSR problem, characterized by subtle differences between taxonomically close plankton species. We address this challenge by conducting extensive experiments on three OSR approaches using both phyto- and zooplankton images analyzing also on the effect of the rejection thresholds for OSR. The results demonstrate that high OSR accuracy can be obtained promoting the use of these methods in operational plankton research. We have made the data publicly available to the research community.

Mineral segmentation using electron microscope images and spectral sampling through multimodal graph neural networks

We propose a novel Graph Neural Network-based method for segmentation based on data fusion of multimodal Scanning Electron Microscope (SEM) images. In most cases, Backscattered Electron (BSE) images obtained using SEM do not contain sufficient information for mineral segmentation. Therefore, imaging is often complemented with point-wise Energy-Dispersive X-ray Spectroscopy (EDS) spectral measurements that provide highly accurate information about the chemical composition but that are time-consuming to acquire. This motivates the use of sparse spectral data in conjunction with BSE images for mineral segmentation. The unstructured nature of the spectral data makes most traditional image fusion techniques unsuitable for BSE-EDS fusion. We propose using graph neural networks to fuse the two modalities and segment the mineral phases simultaneously. Our results demonstrate that providing EDS data for as few as 1% of BSE pixels produces accurate segmentation, enabling rapid analysis of mineral samples. The proposed data fusion pipeline is versatile and can be adapted to other domains that involve image data and point-wise measurements.

Understanding the Impact of Training Set Size on Animal Re-identification

Recent advancements in the automatic re-identification of animal individuals from images have opened up new possibilities for studying wildlife through camera traps and citizen science projects. Existing methods leverage distinct and permanent visual body markings, such as fur patterns or scars, and typically employ one of two strategies: local features or end-to-end learning. In this study, we delve into the impact of training set size by conducting comprehensive experiments across six different methods and five animal species. While it is well known that end-to-end learning-based methods surpass local feature-based methods given a sufficient amount of good-quality training data, the challenge of gathering such datasets for wildlife animals means that local feature-based methods remain a more practical approach for many species. We demonstrate the benefits of both local feature and end-to-end learning-based approaches and show that species-specific characteristics, particularly intra-individual variance, have a notable effect on training data requirements.

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.