Microorganisms such as bacteria and fungi play essential roles in many application fields, like biotechnique, medical technique and industrial domain. Microorganism counting techniques are crucial in microorganism analysis, helping biologists and related researchers quantitatively analyze the microorganisms and calculate their characteristics, such as biomass concentration and biological activity. However, traditional microorganism manual counting methods, such as plate counting method, hemocytometry and turbidimetry, are time-consuming, subjective and need complex operations, which are difficult to be applied in large-scale applications. In order to improve this situation, image analysis is applied for microorganism counting since the 1980s, which consists of digital image processing, image segmentation, image classification and suchlike. Image analysis-based microorganism counting methods are efficient comparing with traditional plate counting methods. In this article, we have studied the development of microorganism counting methods using digital image analysis. Firstly, the microorganisms are grouped as bacteria and other microorganisms. Then, the related articles are summarized based on image segmentation methods. Each part of the article is reviewed by methodologies. Moreover, commonly used image processing methods for microorganism counting are summarized and analyzed to find common technological points. More than 144 papers are outlined in this article. In conclusion, this paper provides new ideas for the future development trend of microorganism counting, and provides systematic suggestions for implementing integrated microorganism counting systems in the future. Researchers in other fields can refer to the techniques analyzed in this paper.

Microorganisms play a vital role in human life. Therefore, microorganism detection is of great significance to human beings. However, the traditional manual microscopic detection methods have the disadvantages of long detection cycle, low detection accuracy in large orders, and great difficulty in detecting uncommon microorganisms. Therefore, it is meaningful to apply computer image analysis technology to the field of microorganism detection. Computer image analysis can realize high-precision and high-efficiency detection of microorganisms. In this review, first,we analyse the existing microorganism detection methods in chronological order, from traditional image processing and traditional machine learning to deep learning methods. Then, we analyze and summarize these existing methods and introduce some potential methods, including visual transformers. In the end, the future development direction and challenges of microorganism detection are discussed. In general, we have summarized 142 related technical papers from 1985 to the present. This review will help researchers have a more comprehensive understanding of the development process, research status, and future trends in the field of microorganism detection and provide a reference for researchers in other fields.

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This paper proposes a novel Squeeze-and-excitation-based Mask Region Convolutional Neural Network (SEM-RCNN) for Environmental Microorganisms (EM) detection tasks. Mask RCNN, one of the most applied object detection models, uses ResNet for feature extraction. However, ResNet cannot combine the features of different image channels. To further optimize the feature extraction ability of the network, SEM-RCNN is proposed to combine the different features extracted by SENet and ResNet. The addition of SENet can allocate weight information when extracting features and increase the proportion of useful information. SEM-RCNN achieves a mean average precision (mAP) of 0.511 on EMDS-6. We further apply SEM-RCNN for blood-cell detection tasks on an open source database (more than 17,000 microscopic images of blood cells) to verify the robustness and transferability of the proposed model. By comparing with other detectors based on deep learning, we demonstrate the superiority of SEM-RCNN in EM detection tasks. All experimental results show that the proposed SEM-RCNN exhibits excellent performances in EM detection.

Environmental microorganisms (EMs) are ubiquitous around us and have an important impact on the survival and development of human society. However, the high standards and strict requirements for the preparation of environmental microorganism (EM) data have led to the insufficient of existing related datasets, not to mention the datasets with ground truth (GT) images. This problem seriously affects the progress of related experiments. Therefore, This study develops the Environmental Microorganism Dataset Sixth Version (EMDS-6), which contains 21 types of EMs. Each type of EM contains 40 original and 40 GT images, in total 1680 EM images. In this study, in order to test the effectiveness of EMDS-6. We choose the classic algorithms of image processing methods such as image denoising, image segmentation and object detection. The experimental result shows that EMDS-6 can be used to evaluate the performance of image denoising, image segmentation, image feature extraction, image classification, and object detection methods. EMDS-6 is available at the https://figshare.com/articles/dataset/EMDS6/17125025/1.