# A Comprehensive Review of Image Analysis Methods for Microorganism Counting: From Classical Image Processing to Deep Learning Approaches

arXiv: https://arxiv.org/abs/2103.13625 · HTML: https://mlsanity.com/paper/2103.13625/

## Key facts

- Cited by 20 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 25 Mar 2021.

## Built on by (most cited first, 20 of 20)

- [EBHI-Seg: A Novel Enteroscope Biopsy Histopathological Haematoxylin and Eosin Image Dataset for Image Segmentation Tasks](https://mlsanity.com/paper/2212.00532/) (2022)
- [Applications of Artificial Neural Networks in Microorganism Image Analysis: A Comprehensive Review from Conventional Multilayer Perceptron to Popular Convolutional Neural Network and Potential Visual Transformer](https://mlsanity.com/paper/2108.00358/) (2021)
- [A State-of-the-art Survey of Object Detection Techniques in Microorganism Image Analysis: From Classical Methods to Deep Learning Approaches](https://mlsanity.com/paper/2105.03148/) (2021)
- [EMDS-6: Environmental Microorganism Image Dataset Sixth Version for Image Denoising, Segmentation, Feature Extraction, Classification and Detection Methods Evaluation](https://mlsanity.com/paper/2112.07111/) (2021)
- [Transfer learning with generative models for object detection on limited datasets](https://mlsanity.com/paper/2402.06784/) (2024)
- [Deep Learning Innovations for Underwater Waste Detection: An In-Depth Analysis](https://mlsanity.com/paper/2405.18299/) (2024)
- [EMDS-7: Environmental Microorganism Image Dataset Seventh Version for Multiple Object Detection Evaluation](https://mlsanity.com/paper/2110.07723/) (2021)
- [TOD-CNN: An Effective Convolutional Neural Network for Tiny Object Detection in Sperm Videos](https://mlsanity.com/paper/2204.08166/) (2022)
- [AATCT-IDS: A Benchmark Abdominal Adipose Tissue CT Image Dataset for Image Denoising, Semantic Segmentation, and Radiomics Evaluation](https://mlsanity.com/paper/2308.08172/) (2023)
- [PHE-SICH-CT-IDS: A Benchmark CT Image Dataset for Evaluation Semantic Segmentation, Object Detection and Radiomic Feature Extraction of Perihematomal Edema in Spontaneous Intracerebral Hemorrhage](https://mlsanity.com/paper/2308.10521/) (2023)
- [A Comprehensive Survey with Quantitative Comparison of Image Analysis Methods for Microorganism Biovolume Measurements](https://mlsanity.com/paper/2202.09020/) (2022)
- [An application of Pixel Interval Down-sampling (PID) for dense tiny microorganism counting on environmental microorganism images](https://mlsanity.com/paper/2204.01341/) (2022)
- [ECPC-IDS:A benchmark endometrail cancer PET/CT image dataset for evaluation of semantic segmentation and detection of hypermetabolic regions](https://mlsanity.com/paper/2308.08313/) (2023)
- [A State-of-the-art Survey of U-Net in Microscopic Image Analysis: from Simple Usage to Structure Mortification](https://mlsanity.com/paper/2202.06465/) (2022)
- [Application of Graph Based Features in Computer Aided Diagnosis for Histopathological Image Classification of Gastric Cancer](https://mlsanity.com/paper/2205.08467/) (2022)
- [A Pseudo-Boolean Polynomials Approach for Image Edge Detection](https://mlsanity.com/paper/2308.15557/) (2023)
- [Vision Transformers for Weakly-Supervised Microorganism Enumeration](https://mlsanity.com/paper/2412.02250/) (2024)
- [Refining CNN-based Heatmap Regression with Gradient-based Corner Points for Electrode Localization](https://mlsanity.com/paper/2412.17105/) (2024)
- [Performance Evaluation of Transfer Learning Based Medical Image Classification Techniques for Disease Detection](https://mlsanity.com/paper/2512.04397/) (2025)
- [Energy-Efficient Eimeria Parasite Detection Using a Two-Stage Spiking Neural Network Architecture](https://mlsanity.com/paper/2601.00806/) (2025)

## Abstract (arXiv)

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.