Automated Cell Counting vs. Manual Cell Counting: What’s the Difference?

Cell counting is an important as well as a routine part of most cell culture workflows in the laboratory. It often involves counting of cells in small volumes so as to estimate the number of cells in a large volume. This process is important in setting an assay, assessing viability/health of cells in the culture, diagnostic/clinical applications, and culture maintenance. But the question is – what’s the difference between automated and manual cell counting? Let’s find out.

Automated Cell Counting

This method involves using automated cell counters to count the number of cells. Compared to manual cell counting, this approach is faster and is capable of counting a large volume of cells, increasing accuracy of making statistics. But this doesn’t justify the costs of viability analysis and cell counting because of high costs of consumables and disposable plastic slides. This is why some companies develop proprietary techniques for viability testing and ultra-precise counting of cells without depending on those disposable plastic slides. Their innovation combines low costs of counting cells manually with high accuracy and high speed of automated cell counts. You can conduct automated cell counting using different systems. Some of these systems include the following:

  • Coulter counters – These system measure changes in the electrical resistance. With this, you can determine the size, volume, and number of cells in a sample.
  • Flow cytometers – These systems show report on different values, including percentage of cells in a particular sample, which has specific properties. You must determine the sample’s volume so as to calculate the total number of cells. To achieve this, you will have to spike your sample with some fluorescent beads.
  • Image-based counters – These systems use fluorescent or brightfield microscopy to capture cells’ images. Some of them work using flow imaging approach. In this approach, cells are drawn into the capillary and cells are counted as well as imaged as they go through a detector. You may calculate cell viability using Trypan Blue. This dye analyzes the image depending on very specific parameters, including cell diameter, circularity, and brightness. With this, you can determine the cells number and viability of cells.

Manual Cell Counting

This conventional approach of counting cells is often done manually at benchtop microscopes using special slides with a grid called hemocytometer. The slides have a chamber with etched grids below the surface. Originally, this device was created to analyze blood samples, but today, it is used to count cells and conduct viability analysis of mammalian cells. You can manually count cells with or without a stain. For analysis of viability, you can use an exclusion dye, like Trypan Blue. In this, you will have to mix cells with Trypan Blue and incubate the mixture before you pipette it into a measurement chamber. Once your sample fills in the chamber, you can directly observe cells using microscopes and count cells in a specific sector on the grid.

In conclusion, manual cell counting is vulnerable to errors. For example, improper cleaning of this approach poses a biological danger. This is why researchers prefer counting cells automatically because it’s more accurate and quicker than manual cell counting.


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