4.6 Review

A comprehensive review of image analysis methods for microorganism counting: from classical image processing to deep learning approaches

Related references

Note: Only part of the references are listed.
Review Biology

The impact of pre- and post-image processing techniques on deep learning frameworks: A comprehensive review for digital pathology image analysis

Massimo Salvi et al.

Summary: Deep learning frameworks have become the main methodology for analyzing medical images, especially in digital pathology. These frameworks can handle various image analysis tasks, such as classification, detection, and segmentation. Recent studies have shown that integrating traditional image processing methods for pre- and post-processing within a deep learning pipeline can improve model performance significantly.

COMPUTERS IN BIOLOGY AND MEDICINE (2021)

Article Biology

DeepCervix: A deep learning-based framework for the classification of cervical cells using hybrid deep feature fusion techniques

Md Mamunur Rahaman et al.

Summary: Cervical cancer can be prevented and treated through manual screening and deep learning techniques. The proposed hybrid deep feature fusion technology achieved good results in classifying cervical cells.

COMPUTERS IN BIOLOGY AND MEDICINE (2021)

Article Computer Science, Artificial Intelligence

LCU-Net: A novel low-cost U-Net for environmental microorganism image segmentation *

Jinghua Zhang et al.

Summary: In this paper, a novel Low-cost U-Net (LCU-Net) is proposed for environmental microorganism image segmentation task. The LCU-Net addresses the memory cost issue of traditional U-Net and demonstrates effectiveness and potential in practical application.

PATTERN RECOGNITION (2021)

Review Computer Science, Artificial Intelligence

A review for cervical histopathology image analysis using machine vision approaches

Chen Li et al.

ARTIFICIAL INTELLIGENCE REVIEW (2020)

Editorial Material Infectious Diseases

The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health - The latest 2019 novel coronavirus outbreak in Wuhan, China

David S. Hui et al.

INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES (2020)

Letter Biochemistry & Molecular Biology

The proximal origin of SARS-CoV-2

Kristian G. Andersen et al.

NATURE MEDICINE (2020)

Proceedings Paper Computer Science, Artificial Intelligence

Reverse Perspective Network for Perspective-Aware Object Counting

Yifan Yang et al.

2020 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR) (2020)

Article Multidisciplinary Sciences

A convolutional neural network segments yeast microscopy images with high accuracy

Nicola Dietler et al.

NATURE COMMUNICATIONS (2020)

Article Computer Science, Information Systems

Automated Counting of Colony Forming Units Using Deep Transfer Learning From a Model for Congested Scenes Analysis

Somayah A. Albaradei et al.

IEEE ACCESS (2020)

Article Environmental Sciences

Vision improvement system using image processing technique for adverse weather condition of opencast mines

Debashis Chatterjee et al.

INTERNATIONAL JOURNAL OF MINING RECLAMATION AND ENVIRONMENT (2019)

Article Biochemical Research Methods

Automated image analysis with ImageJ of yeast colony forming units from cannabis flowers

Nicholas Stolze et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2019)

Article Automation & Control Systems

Automatic segmentation method for CFU counting in single plate-serial dilution

Dimitria T. Boukouvalas et al.

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS (2019)

Article Automation & Control Systems

Simultaneously Detecting and Counting Dense Vehicles From Drone Images

Wei Li et al.

IEEE TRANSACTIONS ON INDUSTRIAL ELECTRONICS (2019)

Review Microbiology

Origin and evolution of pathogenic coronaviruses

Jie Cui et al.

NATURE REVIEWS MICROBIOLOGY (2019)

Review Chemistry, Analytical

A review of methods for the detection of pathogenic microorganisms

P. Rajapaksha et al.

ANALYST (2019)

Review Microbiology

Quantitative Methods for Single-Cell Analysis of Microorganisms

E. O. Puchkov

MICROBIOLOGY (2019)

Proceedings Paper Materials Science, Multidisciplinary

Analysis of the Microhardness of Metals Using Digital Metallographic Images

Denis Privezentsev et al.

MATERIALS TODAY-PROCEEDINGS (2019)

Article Computer Science, Artificial Intelligence

A survey for the applications of content-based microscopic image analysis in microorganism classification domains

Chen Li et al.

ARTIFICIAL INTELLIGENCE REVIEW (2019)

Article Computer Science, Artificial Intelligence

Environmental microorganism classification using conditional random fields and deep convolutional neural networks

Sergey Kosov et al.

PATTERN RECOGNITION (2018)

Article Biochemical Research Methods

Automated counting of bacterial colonies on agar plates based on images captured at near-infrared light

Guozhen Zhu et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2018)

Review Materials Science, Multidisciplinary

A review of deep learning in the study of materials degradation

Will Nash et al.

NPJ MATERIALS DEGRADATION (2018)

Article Biotechnology & Applied Microbiology

A smart device application for the automated determination of E-coli colonies on agar plates

Jonas Austerjost et al.

ENGINEERING IN LIFE SCIENCES (2017)

Article Computer Science, Information Systems

MicroCount: Free Software For Automated Microorganism Colony Counting By Computer

Alisson Amorim Siqueira et al.

IEEE Latin America Transactions (2017)

Article Computer Science, Artificial Intelligence

Bacterial colony counting with Convolutional Neural Networks in Digital Microbiology Imaging

Alessandro Ferrari et al.

PATTERN RECOGNITION (2017)

Article Biotechnology & Applied Microbiology

Modification of a High-Throughput Automatic Microbial Cell Enumeration System for Shipboard Analyses

Christin M. Bennke et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)

Article Biology

Automatic image classification for the urinoculture screening

Paolo Andreini et al.

COMPUTERS IN BIOLOGY AND MEDICINE (2016)

Editorial Material Computer Science, Artificial Intelligence

Image analysis and machine learning in digital pathology: Challenges and opportunities

Anant Madabhushi et al.

MEDICAL IMAGE ANALYSIS (2016)

Article Multidisciplinary Sciences

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

Valentina Cappello et al.

SCIENTIFIC REPORTS (2016)

Article Food Science & Technology

Automatic Counting and Classification of Bacterial Colonies Using Hyperspectral Imaging

Seung-Chul Yoon et al.

FOOD AND BIOPROCESS TECHNOLOGY (2015)

Article Biochemical Research Methods

Automated counting of bacterial colonies by image analysis

Pei-Ju Chiang et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2015)

Proceedings Paper Computer Science, Artificial Intelligence

Automatic Image Analysis and Classification for Urinary Bacteria Infection Screening

Paolo Andreini et al.

IMAGE ANALYSIS AND PROCESSING - ICIAP 2015, PT I (2015)

Article Biochemical Research Methods

An automated method for the quantification of moving predators such as rotifers in biofilms by image analysis

T. Saur et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2014)

Proceedings Paper Computer Science, Artificial Intelligence

Automated Video Imaging System for Counting Deep-sea Bioluminescence Organisms Events

Luca Mazzei et al.

2014 ICPR WORKSHOP ON COMPUTER VISION FOR ANALYSIS OF UNDERWATER IMAGERY (CVAUI 2014) (2014)

Article Computer Science, Information Systems

An Algorithm for Counting Microorganisms in Digital Images

J. G. A. Barbedo

IEEE LATIN AMERICA TRANSACTIONS (2013)

Article Computer Science, Information Systems

A Review on Methods for Automatic Counting of Objects in Digital Images

J. G. A. Barbedo

IEEE LATIN AMERICA TRANSACTIONS (2012)

Article Biochemical Research Methods

Noise-free accurate count of microbial colonies by time-lapse shadow image analysis

Hiroyuki Ogawa et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2012)

Article Multidisciplinary Sciences

Automated Counting of Bacterial Colony Forming Units on Agar Plates

Silvio D. Brugger et al.

PLOS ONE (2012)

Article Computer Science, Artificial Intelligence

Characteristic analysis of Otsu threshold and its applications

Xiangyang Xu et al.

PATTERN RECOGNITION LETTERS (2011)

Article Biotechnology & Applied Microbiology

Automated Quantification and Sizing of Unbranched Filamentous Cyanobacteria by Model-Based Object-Oriented Image Analysis

Michael Zeder et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)

Article Biochemical Research Methods

Low-Cost, High-Throughput, Automated Counting of Bacterial Colonies

Matthew L. Clarke et al.

CYTOMETRY PART A (2010)

Article Computer Science, Artificial Intelligence

Optimal MLP neural network classifier for fault detection of three phase induction motor

Vilas N. Ghate et al.

EXPERT SYSTEMS WITH APPLICATIONS (2010)

Article Biochemical Research Methods

Single-cell bacteria growth monitoring by automated DEP-facilitated image analysis

Ingmar Peitz et al.

LAB ON A CHIP (2010)

Article Computer Science, Information Systems

An automated bacterial colony counting and classification system

Wei-Bang Chen et al.

INFORMATION SYSTEMS FRONTIERS (2009)

Proceedings Paper Computer Science, Information Systems

An Image-Processing Based Automated Bacteria Colony Counter

Huesyin Ates et al.

2009 24TH INTERNATIONAL SYMPOSIUM ON COMPUTER AND INFORMATION SCIENCES (2009)

Article Computer Science, Artificial Intelligence

Image segmentation evaluation: A survey of unsupervised methods

Hui Zhang et al.

COMPUTER VISION AND IMAGE UNDERSTANDING (2008)

Article Fisheries

Automatic counting of FISH-labeled microbes by an LED illuminated detecting apparatus

Masahiko Nishimura et al.

FISHERIES SCIENCE (2008)

Article Engineering, Biomedical

A novel computational approach for simultaneous tracking and feature extraction of C. elegans populations in fluid environments

Gabriel Tsechpenakis et al.

IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING (2008)

Article Biochemical Research Methods

Rapid and automated enumeration of viable bacteria in compost using a micro-colony auto counting system

Xiaodan Wang et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2007)

Article Medical Laboratory Technology

Urine sediment examination: A comparison of automated urinalysis systems and manual microscopy

Tzu-I Chien et al.

CLINICA CHIMICA ACTA (2007)

Article Computer Science, Artificial Intelligence

Classification-driven watershed segmentation

Ilya Levner et al.

IEEE TRANSACTIONS ON IMAGE PROCESSING (2007)

Review Biotechnology & Applied Microbiology

Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis

Holger Daims et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2007)

Article Oncology

Counting colonies of clonogenic assays by using densitometric software

Maximilian Niyazi et al.

RADIATION ONCOLOGY (2007)

Article Engineering, Biomedical

Automated segmentation, classification, and tracking of cancer cell nuclei in time-lapse microscopy

XW Chen et al.

IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING (2006)

Article Biochemical Research Methods

Simplified method to automatically count bacterial colony forming unit

M Putman et al.

JOURNAL OF IMMUNOLOGICAL METHODS (2005)

Article Biochemical Research Methods

An improved method for the automated enumeration of fluorescently labelled bacteria in human faeces

R Thiel et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2005)

Article Biotechnology & Applied Microbiology

Multicolour digital image analysis system for identification of bacteria and concurrent assessment of their respiratory activity

M Ogawa et al.

JOURNAL OF APPLIED MICROBIOLOGY (2005)

Review Marine & Freshwater Biology

Literature review of Florida red tide: implications for human health effects

B Kirkpatrick et al.

HARMFUL ALGAE (2004)

Article Biochemical Research Methods

High-throughput imaging of bacterial colonies grown on filter plates with application to serum bactericidal assays

X Liu et al.

JOURNAL OF IMMUNOLOGICAL METHODS (2004)

Article Engineering, Chemical

Monitoring flames in an industrial boiler using multivariate image analysis

HL Yu et al.

AICHE JOURNAL (2004)

Article Biotechnology & Applied Microbiology

Modelling the growth of Trichoderma virens with limited sampling of digital images

D Cross et al.

JOURNAL OF APPLIED MICROBIOLOGY (2004)

Review Biochemistry & Molecular Biology

A review of conventional detection and enumeration methods for pathogenic bacteria in food

KS Gracias et al.

CANADIAN JOURNAL OF MICROBIOLOGY (2004)

Article Engineering, Chemical

Softwood lumber grading through on-line multivariate image analysis techniques

MH Bharati et al.

INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH (2003)

Article Marine & Freshwater Biology

Automated counting of phytoplankton by pattern recognition: a comparison with a manual counting method

KV Embleton et al.

JOURNAL OF PLANKTON RESEARCH (2003)

Article Biotechnology & Applied Microbiology

Automated enumeration of groups of marine picoplankton after fluorescence in situ hybridization

J Pernthaler et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2003)

Article Biotechnology & Applied Microbiology

Development of multicolour digital image analysis system to enumerate actively respiring bacteria in natural river water

M Ogawa et al.

JOURNAL OF APPLIED MICROBIOLOGY (2003)

Article Biotechnology & Applied Microbiology

Automated image analysis to improve bead ingestion toxicity test counts in the protozoan Tetrahymena pyriformis

N Dias et al.

LETTERS IN APPLIED MICROBIOLOGY (2003)

Article Biotechnology & Applied Microbiology

Cell identification and sizing using digital image analysis for estimation of cell biomass in High Rate Algal Ponds

AJ Gray et al.

JOURNAL OF APPLIED PHYCOLOGY (2002)

Article Computer Science, Interdisciplinary Applications

Effective object recognition for automated counting of colonies in Petri dishes (automated colony counting)

J Marotz et al.

COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE (2001)

Article Biotechnology & Applied Microbiology

A machine vision system using immuno-fluorescence microscopy for rapid recognition of Salmonella typhimurium

O Trujillo et al.

JOURNAL OF RAPID METHODS AND AUTOMATION IN MICROBIOLOGY (2001)

Article Biochemical Research Methods

A fully automated microscope bacterial enumeration system for studies of oral microbial ecology

S Singleton et al.

JOURNAL OF IMMUNOASSAY & IMMUNOCHEMISTRY (2001)

Article Dentistry, Oral Surgery & Medicine

Automated immunofluorescence for enumeration of selected taxa in supragingival dental plaque

R Gmür et al.

EUROPEAN JOURNAL OF ORAL SCIENCES (2000)

Article Microbiology

Prevalence and risk factors of tinea unguium and tinea pedis in the general population in Spain

S Perea et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2000)