This paper deals with automatic taxa identification based on machine learning methods. The aim is therefore to automatically classify diatoms, in terms of pattern recognition terminology. Diatoms are a kind of algae microorganism with high biodiversity at the species level, which are useful for water quality assessment. The most relevant features for diatom description and classification have been selected using an extensive dataset of 80 taxa with a minimum of 100 samples/taxon augmented to 300 samples/taxon. In addition to published morphological, statistical and textural descriptors, a new textural descriptor, Local Binary Patterns (LBP), to characterize the diatom's valves, and a log Gabor implementation not tested before for this purpose are introduced in this paper. Results show an overall accuracy of 98.11% using bagging decision trees and combinations of descriptors. Finally, some phycological features of diatoms that are still difficult to integrate in computer systems are discussed for future work.

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Currently, microalgae (i.e., diatoms) constitute a generally accepted bioindicator of water quality and therefore provide an index of the status of biological ecosystems. Diatom detection for specimen counting and sample classification are two difficult time-consuming tasks for the few existing expert diatomists. To mitigate this challenge, in this work, we propose a fully operative low-cost automated microscope, integrating algorithms for: (1) stage and focus control, (2) image acquisition (slide scanning, stitching, contrast enhancement), and (3) diatom detection and a prospective specimen classification (among 80 taxa). Deep learning algorithms have been applied to overcome the difficult selection of image descriptors imposed by classical machine learning strategies. With respect to the mentioned strategies, the best results were obtained by deep neural networks with a maximum precision of 86% (with the YOLO network) for detection and 99.51% for classification, among 80 different species (with the AlexNet network). All the developed operational modules are integrated and controlled by the user from the developed graphical user interface running in the main controller. With the developed operative platform, it is noteworthy that this work provides a quite useful toolbox for phycologists in their daily challenging tasks to identify and classify diatoms.

Many biological objects are barely distinguished with the brightfield microscope because they appear transparent, translucent and colourless. One simple way to make such specimens visible without compromising contrast and resolution is by controlling the amount and the directionality of the illumination light. Oblique illumination is an old technique described by many scientists and microscopists that however has been largely neglected in favour of other alternative methods. Oblique lighting is created by illuminating the sample by only a portion of the light coming from the condenser. If properly used it can improve the resolution and contrast of transparent specimens such as diatoms. In this paper a quantitative evaluation of OL in brigthfield microscopy is presented. Several feature descriptors were selected for characterising contrast and sharpness showing that in general OL provides better performance for distinguishing minute details compared to other lighting modalities. Oblique lighting is capable to produce directionally shadowed differential contrast images allowing to observe phase details in a similar way to differential contrast images (DIC) but at lower cost. The main advantage of OL is that the resolution of the light microscope can be increased by effectively doubling the angular aperture. OL appears as a cost-effective technique both for the amateur and professional scientist that can be used as a replacement of DIC or phase contrast when resources are scarce.

Diatom detection has been a challenging task for computer scientist and biologist during past years. In this work, the new state of art techniques based on the deep learning framework have been tested, in order to check whether they are suitable for this purpose. On the one hand, RCNNs (Region based Convolutional Neural Networks), which select candidate regions and applies a convolutional neural network and, on the other hand, YOLO (You Only Look Once), which applies a single neural network over the whole image, have been tested. The first one is able to reach poor results in out experimentation, with an average of 0.68 recall and some tricky aspects, as for example it is needed to apply a bounding box merging algorithm to get stable detections; but the second one gets remarkable results, with an average of 0.84 recall in the evaluation that have been carried out, and less aspects to take into account after the detection has been performed. Future work related to parameter tuning and processing are needed to increase the performance of deep learning in the detection task. However, as for classification it has been probed to provide succesfully performance.

A microscope is an essential tool in biosciences and production quality laboratories for unveiling the secrets of microworlds. This paper describes the development of MicroHikari3D, an affordable DIY optical microscopy platform with automated sample positioning, autofocus and several illumination modalities to provide a high-quality flexible microscopy tool for labs with a short budget. This proposed optical microscope design aims to achieve high customization capabilities to allow whole 2D slide imaging and observation of 3D live specimens. The MicroHikari3D motion control system is based on the entry level 3D printer kit Tronxy X1 controlled from a server running in a Raspberry Pi 4. The server provides services to a client mobile app for video/image acquisition, processing, and a high level classification task by applying deep learning models.

Closed-circuit television (CCTV) systems are essential nowadays to prevent security threats or dangerous situations, in which early detection is crucial. Novel deep learning-based methods have allowed to develop automatic weapon detectors with promising results. However, these approaches are mainly based on visual weapon appearance only. For handguns, body pose may be a useful cue, especially in cases where the gun is barely visible. In this work, a novel method is proposed to combine, in a single architecture, both weapon appearance and human pose information. First, pose keypoints are estimated to extract hand regions and generate binary pose images, which are the model inputs. Then, each input is processed in different subnetworks and combined to produce the handgun bounding box. Results obtained show that the combined model improves the handgun detection state of the art, achieving from 4.23 to 18.9 AP points more than the best previous approach. INDEX TERMSCCTV surveillance, deep learning, handgun detection, human pose estimation.

This article presents a review after an exhaustive search that yielded 23 works carried out in the last decade for the availability of optical microscopes with open hardware as a low‐cost alternative to commercial systems. These works were developed with the aim of covering needs within several areas such as: Bio Sciences research in institutions with limited resources, diagnosis of diseases and health screenings in large populations in developing countries, and training in educational contexts with a need for high availability of equipment and low replacement cost. The analysis of the selected works allows us to classify the analyzed solutions into two main categories, for which their essential characteristics are enumerated: portable field microscopes and multipurpose automated microscopes. Moreover, this work includes a discussion on the degree of maturity of the solutions in terms of the adoption of practices aligned with the development of Open Science. Research Highlights Concise review on low‐cost microscopes for developing Open Science, exposing the role of smartphone‐based microscopy. The work classifies microscopes in two main categories: (1) portable field microscopes, and (2) multipurpose automated microscopes.