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Colony Counter – Definition, Types, Parts, Principle

What is Colony Counter?

  • A colony counter is a useful equipment in microbiology laboratories for counting bacterial or other microorganism colonies on a plate containing solid growth medium. Manually counting colonies can be difficult and time-consuming, especially when dealing with small or concealed colonies or cultures with distinct colors.
  • Microbiologists must perform colony counting on a frequent basis because it is a necessary step in many studies and analyses. Traditional methods of counting colonies, on the other hand, are prone to inaccuracies and subjectivity. As a result, a more efficient and precise technique of optimizing laboratory procedures is required.
  • A colony counter is a dependable answer for this problem. This device is intended to make colony counts easier and faster. It usually comprises of a viewing area with an integrated light source to improve vision and an agar plate with colonies. The counter has a digital display or software interface that allows the user to enter and monitor the colony count.
  • The colony counting method is concerned with determining the number of colony forming units (CFUs) present in a particular sample. The amount of viable bacterial or mycelial cells in a culture is estimated using CFUs. Viable cells are those that can reproduce under carefully regulated settings via processes such as binary fission.
  • Microbiologists can reliably and efficiently determine the CFU count in a sample by using a colony counter. This information is critical for a variety of applications, including determining the efficacy of antimicrobial medicines, researching microorganism growth features, and monitoring the presence of pathogens in clinical or environmental samples.
  • Aside from increasing accuracy and speed, colony counts frequently include capabilities that improve data administration and analysis. Some types may feature software for automatic counting and data recording, removing the need for manual entry. This not only lowers the possibility of human error, but also speeds up the overall procedure.
  • A colony counter is a specialized equipment used in microbiology laboratories to count bacterial or microorganism colonies on agar plates. It provides an efficient and precise technique of calculating the CFU count, which is essential for a variety of microbiological tests and analysis. Researchers can improve their techniques and gain more dependable results by using a colony counter.

Definition of Colony Counter

A colony counter is a device used in microbiology laboratories to count bacterial or microorganism colonies on a solid growth medium. It simplifies and accelerates the colony counting process, providing an accurate measurement of colony forming units (CFUs) in a given sample.

Purpose of colony counting

The purpose of colony counting in microbiology is to determine the approximate number of viable cells in a sample based on their ability to grow and form colonies under specific conditions. Each colony originates from a single viable cell that undergoes replication and expansion in the presence of suitable environmental factors, such as temperature and the quality of the growth medium.

By counting colonies, researchers can estimate the initial number of cells present in the sample. This information is valuable for various applications:

  1. Quantification: Colony counting provides a quantitative measure of the microbial load in a sample. It allows researchers to determine the population size, which is crucial for understanding the growth characteristics and behavior of microorganisms.
  2. Assessing Microbial Viability: Counting colonies helps assess the viability of microorganisms in a sample. Only viable cells have the ability to replicate and form colonies, indicating their potential to cause infections or carry out desired functions in various fields like biotechnology or fermentation.
  3. Monitoring Microbial Growth: Colony counting is essential for monitoring the growth of microorganisms over time. By counting colonies at different time points, researchers can analyze the growth rate, evaluate the effectiveness of growth-promoting factors or antimicrobial agents, and assess the impact of environmental conditions.
  4. Quality Control: In industrial settings, colony counting is crucial for quality control processes. It allows manufacturers to monitor the microbial contamination levels in products, ensuring compliance with safety and regulatory standards.
  5. Clinical Diagnosis: In clinical microbiology, colony counting is utilized to identify and quantify pathogens in patient samples. By counting and identifying specific colonies, healthcare professionals can diagnose infections and determine appropriate treatment strategies.

Overall, colony counting serves the purpose of providing quantitative information about the number and viability of microorganisms in a sample. It plays a critical role in various research, clinical, and industrial applications, enabling scientists to understand microbial behavior, ensure product quality, and improve diagnostic capabilities.

Type of Colony Counter

There are two sorts of colony counters, including;

  1. Manual colony counters: The manual colony counter procedure is straightforward: Petri plates are placed inside the colony counter and illuminated and enlarged. A digital display will show the total number of discovered colonies while operators can mark them with a specially designed marker.
  2. Automatic colony counters: A colony counter that is automated reduces counting time from minutes to seconds, eliminates recording mistakes, and standardises counts between users.
Type of Colony Counter
Type of Colony Counter

Manual Colony Counters

Manual colony counters are devices used for counting bacterial or microorganism colonies on agar plates. They rely on the technician’s visual ability to distinguish individual colonies and manually mark them on the plate’s surface using a specific pen or marker. The device keeps track of the marked colonies, allowing for the final count.

While manual colony counters offer a basic method for colony counting, they have certain limitations and drawbacks. Here are some key points to consider:

  1. Time-consuming: Manual colony counting can be a time-consuming process, especially when dealing with plates containing numerous colonies. Technicians need to carefully examine each colony, mark it, and keep track of the count. This process can be tedious and slow, affecting overall laboratory efficiency.
  2. Chaotic: The process of manually marking colonies on the plate’s surface can become chaotic, especially when dealing with plates with densely packed colonies or overlapping growth. It can be challenging to maintain a clear and organized marking pattern, leading to confusion and potential errors in the final count.
  3. Prone to Mistakes: Manual colony counting is susceptible to human errors. Technicians may inadvertently skip or double-count colonies, leading to inaccuracies in the final count. Fatigue, distractions, and subjective interpretation can further contribute to counting errors and discrepancies.
  4. Subjectivity: Manual colony counting is subjective and relies on the technician’s ability to distinguish between colonies accurately. Variations in individual perception and judgment can introduce variability in counting results, impacting data consistency and reliability.

To mitigate these limitations, many laboratories have transitioned to automated or semi-automated colony counting methods. These methods employ image analysis software that automatically detects and counts colonies based on predefined criteria. Automated colony counters offer improved accuracy, speed, and consistency compared to manual counting. They also provide additional features such as data storage, analysis, and report generation, enhancing overall laboratory efficiency.

Working Principle of Manual colony counters

The working principle of a manual colony counter involves the following steps and features:

  1. Placement of Petri Plate: A Petri plate containing bacterial or microorganism colonies is placed on an electronic pressure pad that is part of the manual colony counter. The pressure pad is designed to sense and register the touch or pressure applied to the plate.
  2. Light Illumination: The manual colony counter is equipped with a light source that provides illumination to the Petri plate. This ensures optimal visibility of the colonies for accurate counting.
  3. Marking Colonies: Each colony on the plate is marked by tapping the plate with an auto marker probe pen. When the pen touches a colony, the pressure applied is sensed by the pressure pad.
  4. Count Registration: The count is registered in the digital display of the manual colony counter based on the pressure detected by the pressure pad. The count is updated in real-time, allowing the user to track the progress of counting.
  5. Adjustable Pressure: The pressure applied by the auto marker probe pen can be adjusted based on the specific situation. This feature helps prevent errors such as overlooking colonies or counting colonies multiple times. Adjusting the pressure ensures accurate and reliable colony counting results.

Additional Features: Manual colony counters may include additional features to enhance the counting process. These features can include a graticule for Wolfheugel, which aids in measuring colony sizes, a segmentation disc for dividing the plate into sectors for counting, and centering adapters for plates of different sizes (e.g., 50-90mm). Other added features may include a darkening background to enhance the visibility of transparent colonies, glare-free illumination for optimal peripheral colony viewing, and an integrated averaging tool for counting multiple plates and calculating average colony counts.

Overall, the working principle of a manual colony counter involves marking colonies on a Petri plate using an auto marker probe pen, with the pressure detected and registered by the pressure pad. The count is displayed digitally, and additional features may be included to improve accuracy, ease of use, and data management during the colony counting process.

Parts of manual colony counters

Manual colony counters typically consist of several key parts that aid in the counting process. Here are some common parts found in manual colony counters:

  1. Auto Marker Probe Pen: The counter pen is a crucial component of a manual colony counter. It is designed to register a count when pressure is applied to a colony on the agar plate. The pen is equipped with a mechanism that triggers an audible beep and advances the count on a connected computer screen or display. The auto marker probe pen simplifies the counting process by automatically recording the count with each marked colony.
  2. Digital Display: The manual colony counter is equipped with a digital display that reflects the total count made by the counter pen. The display provides a numerical representation of the colony count, allowing the user to track and monitor the progress of counting.
  3. Lens: A magnifying lens is often included in manual colony counters to aid in the visual inspection of colonies. The lens provides enhanced magnification, enabling technicians to observe and differentiate individual colonies more accurately. This helps in distinguishing closely spaced or overlapping colonies during the counting process.
  4. Light Source: A backlight or light source is an essential part of a manual colony counter. It is used for illumination purposes, providing uniform and optimal lighting conditions to enhance visibility of the colonies on the agar plate. The light source helps illuminate the colonies, making them more distinct and easier to identify during counting.

These parts work together to facilitate the manual colony counting process. The auto marker probe pen allows for efficient marking of colonies, the digital display provides real-time count updates, the lens assists in magnifying the colonies for better visualization, and the light source ensures proper illumination for accurate colony identification.

Parts of manual colony counters
Parts of manual colony counters

Operating Procedure for Manual Colony Counter

Here is an operating procedure for a manual colony counter, based on the provided information:

  1. Turn On the Instrument: Press the On/Off switch to turn on the manual colony counter. This will power up the device and prepare it for operation.
  2. Place the Petri Plate: Put the Petri plate containing bacterial or microorganism colonies on top of the glass grid or surface provided on the colony counter. Ensure that the plate is positioned securely and in a way that allows clear visibility of the colonies.
  3. Prepare the Pen: Remove the cap from the pen or marker used for marking the colonies. Ensure that the pen is ready for use and held straight.
  4. Marking Colonies: Press the pen firmly and directly onto the Petri dish surface where a bacterial colony is located. Apply enough pressure to mark the colony with a dot of ink. As each colony is marked, the manual colony counter will automatically record a count, emit a beep sound, and mark the Petri dish.
  5. Counting Process: Continue marking each colony on the Petri dish using the pen until all colonies have been counted. The manual colony counter will record the counts, and the ink markings will ensure that no colony is missed or counted twice.
  6. Note the Count: Once all colonies have been counted, take note of the count displayed on the manual colony counter. This count reflects the total number of colonies counted on the Petri plate.
  7. Additional Counting Tasks: The manual colony counter may have additional features or buttons, such as a COUNT push button switch. This can be used for counting plates with few colonies or for other counting tasks. The switch may have different modes, including an increment mode for increasing the count and a decrement mode for decreasing the count by one.

It’s important to note that the specific operating procedures may vary slightly depending on the model and manufacturer of the manual colony counter. Always refer to the manufacturer’s instructions and guidelines for the specific device being used to ensure proper operation and accurate colony counting.

Limitations of Manual colony counter 

Manual colony counters have several limitations that can impact their efficiency and accuracy. Here are some common limitations associated with manual colony counters:

  • Labor Intensive: Manual colony counting is a labor-intensive process as it requires technicians to visually identify and mark individual colonies on Petri plates. The process can be physically demanding, especially when dealing with a large number of plates or densely packed colonies.
  • Time-Consuming: Manual colony counting is a time-consuming task, particularly when multiple plates need to be counted. Technicians must carefully examine each plate, mark the colonies, and record the counts manually. This can significantly slow down the overall workflow in a laboratory.
  • Low Throughput: Manual colony counters typically have a relatively low throughput compared to automated or semi-automated counting methods. The time and effort required to count colonies manually limit the number of plates that can be processed within a given timeframe.
  • High Risk of Human Error: Manual colony counting is prone to human error, which can lead to inaccuracies in the final count. Fatigue, distractions, and subjective judgment can result in mistakes such as overlooking colonies, double-counting, or misinterpreting colony boundaries. These errors can impact the reliability of the data obtained.
  • Dependence on Sight: Manual colony counting heavily relies on visual observation by technicians. The accuracy of the count is subject to the technician’s ability to distinguish individual colonies accurately. Factors like colony size, shape, color, and density can introduce variability and subjectivity into the counting process.
  • Limited Data Management: Manual colony counters do not typically have built-in features for plate tracking or image capture. The plates and their corresponding counts need to be manually recorded and entered into a Laboratory Information Management System (LIMS). This manual data entry can be time-consuming and increases the risk of transcription errors.
  • Lack of Tracking and Reporting: Manual colony counters may lack advanced tracking capabilities. Tracking colony counts over time or across different experiments may be challenging without automated data management systems. Generating comprehensive reports or analyzing trends may require additional manual efforts.
  • Technician Variability: Different technicians may have variations in counting techniques, interpretations, and judgment. This can result in discrepancies in the colony counts obtained by different individuals, affecting data consistency and comparability.

Considering these limitations, laboratories may opt for automated or semi-automated colony counting methods to overcome these challenges and improve efficiency, accuracy, and data management capabilities.

Video Guide of Manual Colony Counter

Automatic Colony Counters

Automatic colony counters are advanced devices that utilize image processing techniques to efficiently and accurately count colonies on agar plates. These devices automate the colony counting process, reducing manual labor and improving efficiency. Here is some information about automatic colony counters:

  1. Image Processing Methods: Automatic colony counters rely on image processing algorithms to analyze and interpret images of agar plates. These methods include gray scaling, which converts the colored image into a grayscale representation, thresholding, which segments the image to differentiate colonies from the background, and filtering techniques to enhance colony visibility and reduce noise.
  2. Efficient Colony Detection: Automatic colony counters use sophisticated algorithms to detect and identify individual colonies based on their size, shape, and other distinguishing features. These algorithms can handle variations in colony appearance, such as differences in color, shape, and overlapping colonies.
  3. High-Speed Processing: With the help of advanced image processing techniques, automatic colony counters can quickly analyze large numbers of colonies in a relatively short amount of time. This high-speed processing enables higher throughput and faster data acquisition compared to manual counting methods.
  4. Accuracy and Consistency: Automatic colony counters offer improved accuracy and consistency in colony counting compared to manual methods, as they minimize the risk of human error and subjectivity. By utilizing standardized image processing algorithms, these devices provide more reliable and reproducible results.
  5. Data Management and Analysis: Automatic colony counters often have built-in data management systems or software that can store and organize colony count data. This allows for easy retrieval, tracking, and analysis of colony counts over time or across different experiments. It enables researchers to generate comprehensive reports, perform statistical analyses, and monitor trends.
  6. User-Friendly Interface: Automatic colony counters typically have user-friendly interfaces that facilitate ease of use. They may feature intuitive software with graphical interfaces, allowing users to interact with the device, adjust settings, and visualize the colony counting results.

Automatic colony counters are particularly beneficial in research laboratories, clinical settings, and industries where large-scale colony counting is required. By automating the counting process and utilizing advanced image processing techniques, these devices offer improved efficiency, accuracy, and data management capabilities, thereby enhancing productivity and facilitating scientific analysis.

Working Principle of Automatic colony counters

The principle of automatic colony counters involves the utilization of computer-based systems and image processing techniques. Here is an explanation of the principle:

  1. Image Collection: Automatic colony counters utilize digital image-capturing devices such as document scanners, CCD cameras, digital cameras, webcams, or video equipment to capture images of agar plates containing colonies. Each plate is photographed to obtain a digital image for analysis.
  2. Digital Image Processing: The recorded photos are converted into digital files and transferred to a computer. Programmable image-processing software is then used to analyze these digital images. The software provides tools and algorithms specifically designed for colony counting.
  3. Colony Enumeration: Single or multi-threshold segmentation techniques are applied to the digital images to separate and identify the colonies present on the agar plate. These techniques involve setting thresholds to distinguish between the colonies and the background. The software detects and marks the individual colonies based on their size, shape, and other characteristics.
  4. Illumination Techniques: In automated systems, the visibility and accuracy of colony detection can be improved by choosing one of three illumination techniques:
  • Transmission Technique: This technique is applied to objects with common, high-contrast characteristics and largely clear backgrounds. It utilizes transmitted light to enhance the visibility of colonies.
  • Reflection Technique: The reflection technique is used for objects with high contrast and opaque backgrounds. It relies on reflected light to highlight the colonies and differentiate them from the background.
  • Darkfield Technique: The darkfield technique is employed for low-contrast, largely transparent objects. It uses specialized lighting to create a dark background, making the colonies stand out more clearly.

By employing these illumination techniques, the automatic colony counter can adapt to different types of colonies and backgrounds, ensuring accurate detection and enumeration.

Overall, the principle of automatic colony counters involves capturing digital images of agar plates, analyzing the images using image-processing software, applying segmentation techniques to identify colonies, and utilizing appropriate illumination techniques to enhance visibility. This computer-based approach enables efficient and precise colony counting, minimizing the need for manual labor and reducing the potential for human error.

Parts of Automated Colony Counter 

The automated colony counter consists of several essential parts that contribute to its functionality and efficiency. Here are the key parts of an automated colony counter:

  1. Culture Dish: The automated colony counter is compatible with various types of culture dishes, including traditional plate inoculation and spiral inoculation methods. It can accommodate standard sizes of culture dishes, typically 90mm and 55mm in diameter, allowing flexibility in the types of experiments and plates used.
  2. Light Source: An automated colony counter incorporates a durable LED light source for illumination purposes. The device offers four different light source and background color combinations to cater to different media colors and types. Some advanced models even feature an intelligent remote control multi-color light source background, enhancing the accuracy of colony counting for media with diverse colors and characteristics.
  3. Imaging: Unlike traditional manual colony counters that rely on magnifying glasses, automated colony counters utilize advanced imaging technology. They are equipped with cameras, with CCD specifications continually improving. For example, modern models may feature high-resolution cameras with 5 million pixels, allowing for clear and detailed colony images. The higher resolution and camera capabilities enable accurate colony identification and analysis.
  4. Image Processing: Automated colony counters excel in image processing capabilities. Their associated software provides robust features such as background processing, color marking, interference correction, colony enlargement, and area calculation. These advanced image processing tools enhance the accuracy and efficiency of colony counting. Such features are not typically found in traditional colony counting methods, making automated colony counters highly valuable in research and analysis.
  5. Database: Automated colony counters offer significant advantages in terms of data management and processing compared to traditional methods. They have built-in database functionality that allows for efficient data storage, intelligent query capabilities, and data export. Some models even provide options to configure operator permissions and data modification permissions, ensuring the security and integrity of measured data. Additionally, the ability to print and edit reports online simultaneously simplifies the reporting process.

Overall, the parts of an automated colony counter work together to provide accurate and efficient colony counting capabilities. From the culture dish compatibility and LED light source for illumination to advanced imaging technology and powerful image processing software, these features enhance the accuracy, speed, and data management capabilities of automated colony counters.

Operating Procedure of Automated Colony Counter

The operating procedure of an automated colony counter involves the following steps:

  1. Prepare the instrument: Ensure that the automated colony counter is turned on and allowed to warm up. It should be placed in a stable environment, free from vibrations and drafts, to maintain accuracy during counting.
  2. Load the petri dish: Place the petri dish containing the colonies onto the stage or platform of the automated colony counter. Ensure that the dish is properly positioned for optimal imaging.
  3. Select the magnification: Choose the appropriate magnification level on the colony counter based on the size of the colonies present on the petri dish. This will ensure clear and accurate counting.
  4. Start the count: Press the designated start button or initiate the counting process through the control panel of the colony counter. This action will activate the imaging and analysis functions of the instrument.
  5. Count the colonies: The automated colony counter will analyze the digital image of the petri dish and automatically detect and count the colonies present. The counted colonies will be displayed on the screen or monitor of the colony counter.
  6. Repeat steps 4-5 for each petri dish: If there are multiple petri dishes to be counted, repeat the counting process for each dish individually. Ensure that the petri dish is properly positioned and the instrument is ready for counting before initiating each count.
  7. Save the results: Once the colonies are counted for all the petri dishes, the results can be saved electronically to a file or printed out for record-keeping and further analysis. Follow the instructions provided by the colony counter for saving or exporting the results.

Additional tips for using an automated colony counter:

  • Use clean and sterile petri dishes to prevent contamination and interference with accurate counting.
  • Handle the petri dishes with care to avoid any damage that may affect the clarity of colony images.
  • Do not overload the colony counter with too many petri dishes at once, as it may compromise the accuracy and performance of the instrument.
  • Regularly calibrate the automated colony counter according to the manufacturer’s guidelines to maintain its accuracy and reliability. Calibration should be performed at least once a year or as recommended by the manufacturer.

Advantages of Automated Colony Counter

Automated colony counters offer several advantages over manual counting methods:

  1. Time-saving: Automated colony counters significantly reduce the time required for counting colonies. The advanced image processing algorithms and efficient detection capabilities allow for rapid and efficient colony counting.
  2. Increased throughput: Automated colony counters can process a larger number of samples per hour compared to manual counting methods. This increased throughput is particularly beneficial for high-volume laboratories or situations where time is critical.
  3. Improved accuracy: The use of advanced image processing techniques ensures accurate and consistent colony counting. It eliminates human error, such as overlooking or double-counting colonies, resulting in more reliable and precise results.
  4. Standardized results: Automated colony counters provide standardized results by applying consistent counting criteria and algorithms. This helps in achieving uniformity in counting across different users or laboratories.
  5. Enhanced sensitivity: Automated colony counters have a higher sensitivity to detect smaller colonies that may be missed or difficult to detect using manual methods. This enables better detection and enumeration of microorganisms present in low concentrations.
  6. Automatic data transfer: Automated colony counters have the capability to transfer counting data directly to a database or Laboratory Information Management System (LIMS). This streamlines data management, reduces transcription errors, and improves data traceability.
  7. Image and data storage: The automated colony counters store images and counting data, allowing for future reference, analysis, and traceability. The stored data can be used for quality control, audits, or further research purposes.
  8. Complete audit trail and report production: Automated colony counters generate comprehensive audit trails and reports in formats like PDF and Excel. These reports provide a detailed record of the counting process, facilitating traceability and compliance with regulatory requirements.
  9. Integration with barcode readers: Automated colony counters can be linked to barcode readers, minimizing data input errors and improving efficiency in sample identification and tracking.
  10. Ability to handle diverse sample types: Automated colony counters are capable of accurately counting colonies even in challenging sample types with low contrast or overlapping colonies. They can handle colonies of various sizes, shapes, and forms.
  11. Reduction in manual effort: The use of software in automated colony counters reduces manual effort involved in counting, resulting in improved workflow efficiency and reduced strain on laboratory staff.

In summary, automated colony counters offer significant advantages in terms of time savings, increased throughput, improved accuracy, standardized results, data management capabilities, and the ability to handle diverse samples. These benefits make them valuable tools in microbiology laboratories for colony counting and analysis.

Disadvantages of Automated Colony Counter

Automated colony counters, despite their many advantages, also come with a few disadvantages. Here are some of the drawbacks associated with automated colony counters:

  1. Cost: Automated colony counters can be expensive, especially for small laboratories with limited budgets. The initial investment required to purchase the equipment may be prohibitive for some institutions.
  2. Maintenance: Automated colony counters require regular maintenance, including cleaning and calibration. This can be time-consuming and may require additional resources. Failure to properly maintain the equipment can lead to inaccurate results.
  3. Complexity: Operating automated colony counters can be complex, especially for users with limited experience or technical expertise. Understanding the software, adjusting settings, and troubleshooting any issues may pose challenges for some users.
  4. Accuracy limitations: Automated colony counters can be accurate when properly calibrated and maintained. However, if calibration is not performed correctly or if the equipment is not regularly maintained, it can lead to inaccurate results. Some automated colony counters may struggle to accurately count very small or closely spaced colonies.
  5. Limited applications: Automated colony counters may not be suitable for all applications. For instance, they may not be effective in counting colonies that are extremely small, close together, or not evenly spaced. In such cases, manual counting methods or alternative techniques may be more appropriate.
  6. Delicate nature: Automated colony counters can be delicate and require careful handling. The precision components used in their construction can be easily damaged if mishandled, leading to malfunctions and the need for repairs.
  7. Calibration challenges: Calibrating an automated colony counter can be a complex and time-consuming process. Achieving accurate calibration may require specialized knowledge or assistance from technical experts.
  8. Speed limitations: While automated colony counters can count colonies relatively quickly, they may be slower when large numbers of colonies need to be counted. The counting rate may not meet the demands of applications that require rapid processing of a high volume of samples.
  9. Limitations in detecting obscured or contaminated colonies: Automated colony counters rely on light sources or cameras to detect colonies. If colonies are obscured by other objects or contaminated with other microorganisms, the automated system may struggle to accurately identify and count them.

It’s important for users to be aware of these disadvantages and consider their specific needs and limitations before opting for an automated colony counter. Proper training, maintenance, and adherence to best practices can help mitigate these drawbacks and ensure optimal performance of the equipment.


When using an automated colony counter, it is important to take certain precautions to ensure accurate and reliable results. Here are some precautions to consider:

  1. Avoid contaminating the petri dish with pen ink: To prevent contamination, you can use alternative methods for marking the colonies. For carefully plated Petri plates with a thin layer, you can invert the plate and mark on the bottom surface. Another option is to place the glass cover over the plate and use it for marking. However, in this case, counting should be done in a single sitting without adjusting the viewing angle or moving/tilting the plate or its cover. Keep the probe’s cap on when it is not in use to prevent accidental marking.
  2. Counting on standard plates: For plates with a standard number of colonies (e.g., 25 or 250), count all colony forming units (CFUs) on the specified plate, including pinpoint-sized colonies. Note the dilution(s) used and the total number of colonies enumerated.
  3. Plates with around 250 colonies: When the number of CFUs exceeds 250 per plate for all dilutions, record the counts as “too numerous to count” (TNTC) for all plates except the one closest to 250. In that plate, count the CFUs in representative areas. Mark the plate as APC (aerobic plate count) with EAPC (estimated aerobic plate count) to indicate that it was estimated from counts outside the range of 25/250 per plate.
  4. Spreaders: Differentiate between colonies and spreaders. There are typically three types of spreading colonies: chains of colonies, colonies in a film of water between the agar and the bottom of the dish, and colonies in a film of water at the edge or on the surface of the agar. Report plates as spreaders if the area covered by spreaders, including the repressed growth, exceeds 50% of the plate area or if the area of repressed growth exceeds 25% of the plate area. Count each type of spreader separately, treating them as a single source or colony depending on their characteristics.
  5. Plates without CFUs: If all dilutions on the plates lack colonies, report the APC as less than one times the lowest dilution used. Indicate with an asterisk if the APC was estimated from counts outside the 25/250 per plate range.

These precautions help ensure accuracy and consistency in the counting process and provide reliable results. Always follow the guidelines specific to your automated colony counter and the standard protocols for colony counting in your laboratory.

Importance of Colony counting

Colony counting holds significant importance in various industries, including the food and beverage sector, as well as in healthcare settings. Here are some key reasons highlighting its importance:

  1. Quality Control in Food and Beverage Industries: Colony counting is crucial for ensuring the safety and quality of food and beverage products. By determining colony counts, manufacturers can assess the level of microbial contamination in their products. Excessive colony counts may indicate poor hygiene practices or inadequate processing, which can pose health risks to consumers. Regular monitoring of colony counts helps in maintaining product safety and complying with regulatory standards.
  2. Microbial Detection and Diagnosis: In healthcare settings, colony counting plays a vital role in detecting and diagnosing microbial infections. By quantifying the concentration of microorganisms in clinical samples, healthcare professionals can identify the presence of pathogens and determine appropriate treatment strategies. Colony counting provides valuable information about the progression of contagious diseases and allows for monitoring the efficacy of an individual’s immune system.
  3. Antibiotic Efficacy Assessment: Colony counting is essential in assessing the effectiveness of antibiotics and antimicrobial agents. By counting colonies before and after treatment, researchers can determine the ability of antimicrobial agents to inhibit or kill microorganisms. This information aids in evaluating the efficacy of different treatment regimens and contributes to the development of appropriate antibiotic prescribing practices.
  4. Research and Development: Colony counting is fundamental in various research and development activities. It allows scientists to study the growth characteristics and behavior of microorganisms under different conditions. By accurately quantifying colony counts, researchers can analyze microbial responses to environmental factors, evaluate the effectiveness of new antimicrobial agents, and understand the dynamics of microbial populations in various settings.
  5. Environmental Monitoring: Colony counting is utilized in environmental monitoring programs to assess the quality of water, air, and other environmental samples. By quantifying the colony counts, researchers can identify potential sources of contamination and evaluate the impact of environmental factors on microbial populations. This information is crucial for maintaining environmental health and ensuring the safety of ecosystems.

In summary, colony counting holds significant importance in industries such as food and beverage, healthcare, and research. It enables quality control, aids in microbial detection and diagnosis, assesses antibiotic efficacy, supports research and development activities, and facilitates environmental monitoring. By accurately quantifying colony counts, professionals can make informed decisions, ensure product safety, and protect public health.

Issues with colony counting

Counting bacterial colonies in a sample or on a filter can present several challenges and issues that need to be addressed to obtain an accurate count. Some of the common concerns include:

  1. Overlapping Colonies: When colonies grow in close proximity, they can overlap, making it difficult to distinguish and count individual colonies accurately. Overlapping colonies can lead to an underestimation of the true colony count.
  2. Colonies in Contact with Edges: Colonies that touch the edges of the agar plate or filter can be challenging to count accurately. The colonies at the edges may be partially cut off or obscured, affecting the final count.
  3. Noise and Background Contamination: Noise refers to any non-colony structures or artifacts present on the plate or filter that can interfere with accurate counting. These may include debris, air bubbles, or growth patterns that resemble colonies but are not actual viable cells. Noise can lead to an overestimation of the colony count if not properly accounted for.
  4. Varied Sizes, Shapes, and Colors: Bacterial colonies can exhibit variations in size, shape, and color, making it challenging to standardize the counting criteria. Differentiating between small or irregularly shaped colonies and colonies with distinct colors adds complexity to the counting process.

Addressing these issues requires careful consideration and appropriate techniques:

  • a) Dilution Techniques: Dilution techniques involve diluting the sample to obtain plates with a suitable number of colonies for counting. This helps to reduce overcrowding and overlapping colonies, allowing for more accurate counting.
  • b) Plate Rotations and Multiple Counting: Rotating plates or filters and performing multiple counts can help ensure that all colonies, including those at the edges, are accounted for. This approach helps mitigate the problem of colonies in contact with the edges.
  • c) Threshold and Image Analysis: Setting a threshold for colony detection and employing image analysis software can aid in distinguishing true colonies from noise or background contamination. This approach improves accuracy and reduces errors associated with noise and artifacts.
  • d) Standardized Criteria: Establishing clear criteria for counting, such as defining colony size and color parameters, can help reduce subjectivity and improve consistency in counting across different samples and operators.

In summary, counting bacterial colonies can be challenging due to issues such as overlapping colonies, colonies in contact with edges, noise, and variations in colony sizes, shapes, and colors. Dilution techniques, plate rotations, threshold setting, and standardized criteria are some of the strategies employed to address these issues and obtain accurate colony counts. By considering and mitigating these concerns, researchers can minimize errors and obtain reliable results in microbiological studies and analyses.

Why switch to an automated colony counter?

In an effort to standardise count results and enhance traceability, a growing number of laboratories are adopting automated and semi-automatic colony counters. These methods not only accelerate the testing process, but also generate a consistent pattern of data that removes human error and variation. In recent years, there has also been a push for ‘lean laboratory’ efforts, which aim to enhance throughput and efficiency by focusing on value-added activities and minimising inefficient lab operations. Colony counting is one of the easiest processes to automate, as automated colony counters can analyse up to 75 plates in 5 minutes. This can free up a substantial amount of time for laboratory analysts to devote to “value-added” duties and initiatives.

Application of colony counters

Colony counters have various applications in microbiology and other fields. Here are some common applications of colony counters:

  1. Filter and membrane capacity assessment: Colony counting is used to evaluate the capacity of filters or membranes to retain bacteria. By counting the colonies that grow on the filter or membrane, researchers can assess its efficiency in capturing microorganisms.
  2. Disinfectant efficacy testing: Colony counting plays a crucial role in determining the effectiveness of disinfectants. It is used to evaluate the ability of disinfectants to kill or inhibit the growth of bacteria. This application is important for testing the safety of food and drugs, as well as ensuring proper sanitation in medical facilities and the pharmaceutical industry.
  3. Microbial density measurement: Colony counting is commonly used to measure the density of microorganisms in liquid cultures. By counting the colonies on agar plates, slide mini gels, or petri dishes, researchers can estimate the number of viable microorganisms present in the sample. This information is valuable for various microbiological studies and experiments.
  4. AMES testing: The AMES test is a widely used bacterial mutation assay that helps evaluate the mutagenic potential of various chemicals and substances. Colony counting is an essential step in this testing method, as it involves assessing the number of revertant colonies formed by bacteria exposed to the test substance. This information helps determine the mutagenic properties of the tested substances.

Colony counters provide a reliable and efficient way to quantify bacterial colonies in these applications, enabling researchers to obtain accurate data and make informed decisions in their studies and experiments.


What is a colony counter?

A colony counter is a laboratory instrument used to count and analyze bacterial or fungal colonies on agar plates. It provides an efficient and accurate way to determine colony numbers and sizes.

How does a colony counter work?

A colony counter typically uses image processing techniques to analyze images of agar plates. It distinguishes individual colonies based on contrast and automatically counts them. Some colony counters may also offer additional features such as size measurement and data analysis.

Why is colony counting important?

Colony counting is important in microbiology research and testing. It helps assess the effectiveness of antimicrobial agents, evaluate the growth of microorganisms, determine bacterial concentrations, and perform quality control in various industries such as pharmaceuticals, food, and environmental monitoring.

What are the advantages of using a colony counter?

Using a colony counter saves time, improves accuracy, standardizes results, eliminates human error, enhances sensitivity to smaller colonies, and enables automatic data transfer to databases or Laboratory Information Management Systems (LIMS). It also provides features like image storage, traceability, and report generation.

Can a colony counter count colonies of different shapes and sizes?

Yes, most colony counters are designed to count colonies of various shapes and sizes. They typically have adjustable parameters to accommodate different colony morphologies and can differentiate between true colonies and debris or artifacts.

Are colony counters compatible with different types of culture media?

Yes, colony counters are generally compatible with different types of culture media, including agar plates with specific additives or selective media. However, it’s important to ensure that the colony counter you choose is suitable for the specific media you will be using.

How accurate are colony counters?

Colony counters provide a high level of accuracy, especially when properly calibrated and maintained. However, accuracy may vary depending on the specific instrument, image processing algorithms, and user techniques. Regular calibration and adherence to operating procedures are essential for obtaining accurate results.

Can a colony counter handle high-throughput analysis?

Yes, many modern colony counters are designed to handle high-throughput analysis. They offer features such as automatic plate loading, rapid counting algorithms, and data management capabilities to accommodate large sample sizes and increase efficiency.

Are colony counters user-friendly?

Most colony counters are designed with user-friendly interfaces and intuitive controls. They often come with software that provides easy navigation, customizable settings, and on-screen prompts. However, familiarity with the instrument and proper training are still important to ensure accurate and efficient operation.

What are the maintenance requirements for a colony counter?

Maintenance requirements may vary depending on the specific model. Generally, regular cleaning of the instrument’s components, such as the stage and lens, is necessary to prevent contamination and maintain accurate counting. Some colony counters may also require periodic calibration or servicing by trained professionals to ensure optimal performance.


  • Gupta, Surbhi & Kamboj, Priyanka & Kaushik, Sumit. (2012). Methodology for Automatic Bacterial Colony Counter. 10.1007/978-3-642-30157-5_56. 
  • Colony Counter, Automated. (2019). Compendium of Biomedical Instrumentation, 491–494. doi:10.1002/9781119288190.ch95
  • file:///C:/Users/Soura/Desktop/Blog%20Img/colony-counter-automated-2019.pdf

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Why do Laboratory incubators need CO2? What is Karyotyping? What are the scope of Microbiology? What is DNA Library? What is Simple Staining? What is Negative Staining? What is Western Blot? What are Transgenic Plants? Breakthrough Discovery: Crystal Cells in Fruit Flies Key to Oxygen Transport What is Northern Blotting?
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