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Tired of manual cell counting?

Classic vs. Automated Cell Counting:

Which Method Should You Choose?


If you work with cells, you probably spend hours in the lab counting them.

As much as researchers love bench work, it can be handy to automate certain processes, especially when it comes to larger laboratories with high demands.

To solve this problem Cellix has recently released the Inish Analyser. It is a simple, automated and easy to use instrument for cell counting and viability.

This article discusses the main differences between classic cell counting with the famous hemocytometer and automated alternatives. You will learn the benefits of automatization and when to choose one method or another depending on your lab needs.

Cell Counting

Cell counting is a fundamental process in R&D and quality control of cell-based products. It allows:

  • Maintaining cell cultures

  • Preparing cells for transfection experiments

  • Preparing cells for downstream experiments like qPCR

You can either count cells manually using a hemocytometer or by using an automated cell counter.


Manual cell counting with a hemocytometer

The hemocytometer is a thick glass microscope slide with a grid in the middle. The area covered by this grid makes it possible to determine the number of cells in a volume of solution.

In short, counting cells with the hemocytometer involves:

  • Preparing the hemocytometer and the cell suspension

  • Loading the hemocytometer and placing it on the microscope

  • Counting the cells

  • Calculating cell concentration

The hemocytometer's grid contains nine squares of 1 mm2. The central counting area has 25 large squares, each of them with 16 smaller squares.

With the help of a clicker, you can count the cells in each square, remembering that you must only count the cells set within a square or on the right-hand or bottom line.

To differentiate dead from viable cells, you usually add a stain such as Trypan blue that penetrates dead cells membrane coloring them blue.

The whole process is manual, so it has its limitations.

Flow cytometry

Flow Cytometry Illustration

This method involves running cells labeled with fluorescent dyes through a flow cytometer. When cells pass through the light source of the cytometer, detectors measure scattered light and fluorescence.

Flow cytometry involves complex and costly equipment that is overkill for simple cell counting applications.

Image-based cytometry is a less expensive option but requires handling large amounts of image data, which can be limiting.

Automated Cell Counting

As the name says, automated cell counters like the Inish Analyser are devices that can count cells automatically. It is a pretty straightforward process - you load your sample into the cell counter, which aspirates or pumps your cell sample through a small tube. These devices typically use optical or electrical impedance sensors or image-based analysis to count how many cells go through the tube.

The main features and benefits of the Inish Analyser include:

  • Label-free: No fluorescent stains or dyes.

  • Single-cell Analysis: Every cell is counted!

  • High-throughput: Analyse thousands of cells per second.

  • Compatible with a wide variety of cell samples: cell lines (e.g. Jurkats, CHO cells etc.), primary cells (e.g. PBMCs), stem cells, yeast cells, sperm cells.

  • Fast Set-up & Analysis: 90 seconds including sample preparation.

  • Easy-to-use Benchtop Instrument: fits inside standard biosafety cabinet and operated by simple touchscreen workflow.

  • Compatible with FCS & CSV file format: easily exportable.

This method offers reliable cell counting with high precision and throughput.

Cellix's Inish Analyser uses impedance spectroscopy, a method based on differences in the electrical impedance between the cell and a buffer. It has a distinct advantage over other aforementioned methods – it’s label free! What does that mean? It means no fluorescent dyes or labels to stain or tag the cells for detection.

How does it work?

Cells flow through a microfluidic channel with embedded electrodes which form a current path. As the cells flow past the electrodes, they disturb the electric field resulting in a change in impedance. In this method, impedance measurements are made at wide frequency ranges, providing information on cell size, membrane capacitance, and cytoplasm conductivity, along with cell concentration.

Things to Consider When Choosing a Cell Counting Method


The Inish Analyser gives you an automatic cell count in minutes. You put your sample in a tube, put the tube in the device, and follow the instructions on the touchscreen. And just like that, the results are available to you automatically.

Unlike laborious manual cell counting with hemocytometers, image-based analysis, or flow cytometry, the Inish Analyser requires no cell staining, reducing the steps in your workflow.


We all know that making mistakes is human, and yes, scientists make mistakes too. Manual cell counting with the hemocytometer is subject to errors since it depends on human judgment in differentiating between cells and debris. Plus, even the best-trained eyes have a bad day now and then.

Automated cell counters like the Inish Analyser are a great option if you want to make sure your results are accurate. It also helps to avoid user-to-user variability for higher reproducibility of the results.


The hemocytometer ends up being the choice of many researchers due to its low cost.

But when we take a closer look, we realize that other factors make the final price of the assay more expensive. As it involves several steps, it uses more disposable plastics and the need for fluorescent dyes.

Other methods like flow cytometry and image-based analysis also require staining, adding several steps to the workflow. Additionally, flow cytometers are complex instruments and demand costs that may be too high for a simple task like counting cells.

The Inish Analyser is a cost-effective option for your lab by reducing the sample volume and power consumption.

When choosing your cell counter, consider your lab's needs. Is it a large laboratory with future expansion plans?

If this is the case, investing in an automatic cell counter can be highly beneficial.

But suppose your lab is on a tighter budget. In that case, it's important to consider whether the upfront cost is worth significant savings in the future.

If you'd like to learn more about Cellix's Inish Analyser, contact Cellix to book an online demo or request a quote.

In Summary

There is a lot to consider when choosing solutions for our research. In the case of the cell counting method, you must consider some fundamental aspects such as budget, time and resources, laboratory size and needs, accuracy, and data reproducibility.

Weighing the pros and cons of each method will help you make the decision that best suits your needs.


Click here to learn more about Cellix’s Inish Analyser. If you have any questions, would like an online demo or if you’d like a quote, contact us now.



1. Cell Counting with a Hemocytometer: Easy as 1, 2, 3. Bite-Size Bio, 2014. Available: Access: 06/18/2021.

2. Introduction to flow cytometry. Abcam. Available: Access: 06/18/2021.


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