Front view of Countess 3 Automated Cell Counter

Thermo Fisher Scientific offers two high-performance cell counters designed to meet the needs of any lab. The Invitrogen Countess 3 and Countess 3 FL Automated Cell Counters utilize artificial intelligence, applying a deep-learning neural network algorithm to generate highly accurate cell counts even for challenging cell sample types. The machine-learning algorithm was taught by expert cell biologists to ensure accurate and precise cell counting, avoiding user variation associated with manual hemocytometer cell counting.

Designed for convenience and time savings, the Countess 3 Automated Cell Counters come with more automated features like auto-lighting, autofocus, and autosave.

  • Accuracy—a highly accurate machine-learning algorithm is applied to cell counting.
  • Precision—auto-lighting and autofocus minimize user inputs and variability.
  • Speed—Rapid capture and autosave features generate and save results faster.
  • Convenient—built-in pre-dilution and cell splitting calculators, histograms and gating, and a results PDF report.
  • Affordable—both Countess 3 models are compatible with the Countess Reusable Slide.

Machine-learning algorithm generates accurate counts; autofocus and auto-lighting minimize user-to-user variability

The Countess 3 Automated Cell Counters utilize machine-learning algorithms for fast and accurate focus determination as well as cell and viability counts. Countess instruments are compatible with a broad range of cell types and have been verified for use with several commonly used cell lines and primary cell types. Upon insertion of the slide, the Countess instrument will automatically provide optimized illumination and focus on the cells, which helps to minimize user variation associated with manual focusing and lighting adjustments. Cells ranging in size between ~4 µm and 60 µm and in cell suspension density ranging from 1 x 104 to 1 x 107 cells/mL are optimal for counting.

Bar graph of cell counts of different cell types counted by Attune NxT Flow Cytometer, Countess 3 Automated Cell Counter, and manually with a hemocytometer

Figure 1. Machine-learning algorithms result in highly accurate cell counts, comparable with flow cytometer counts. CHO-K1, HeLa, HEK293, Jurkat, and human PBMCs were counted using the Attune NxT Flow Cytometer (red bar), a Countess 3 FL Automated Cell Counter (blue bar), and manual counting using a hemocytometer and microscope (green bar). The Countess 3 FL Automated Cell Counter and hemocytometer bars represent an average of 6 counts. Error bars indicate standard deviation from 6 independent counts.

Scatter dot graph of cell counts of different cell types counted by Countess 3 Automated Cell Counter, and manually with a hemocytometer

Figure 2. Machine-learning algorithms result in highly precise cell counts with lower variability between counts compared to manual counting. CHO-K1, HeLa, HEK293, Jurkat, and human PBMCs were counted using the Countess 3 FL Automated Cell Counter (blue dots) and manual counting using a hemocytometer and microscope (green dots). The lines represent the median count and the dots demonstrate variance from 6 individual counts.

Bar graph of cell counts of human and mouse PBMCs by Countess 3 Automated Cell Counter and manually with a hemocytometer

Figure 3. Machine-learning algorithms result in highly accurate cell counts with challenging cell types and with more precision than manual counting. Human and mouse PBMCs were counted using the Countess 3 FL Automated Cell Counter (blue bar) and the manual counting method using a hemocytometer and microscope (green bar). The Countess 3 FL Automated Cell Counter and hemocytometer bars represent 6 counts. The error bars represent standard deviation.

Cell clumps counted accurately; debris ignored without gating inputs

Countess 3 Automated Cell Counters are able to accurately count cells that clump together. Whether you currently use automated or manual cell counting methods, obtaining accurate cell counts from samples containing clumpy cells can be difficult. Samples that contain debris add further complexity to cell counting. The Countess 3 Automated Cell Counter automatically excludes debris from cell counts. The machine-learning algorithm of the Countess Automated Cell Counter can clearly identify cell boundaries within clumps of cells and ignores debris, resulting in highly accurate cell counts (Figure 4).

Figure 4. Machine-learning algorithms generate accurate counts with clumpy cells and sample debris. The Countess 3 FL Automated Cell Counter was used to count RAW cells, which are both small and have a propensity to clump. The counting algorithm can resolve the cells in the clump and properly segment and count the cells. Debris is properly omitted from counts.

Small cells accurately counted

Rodent PBMCs are small cells around 5-7 microns and can be challenging to count whether manually on a hemocytometer or on an automated cell counter. The Countess 3 Automated Cell Counter’s machine-learning algorithm is robust and accurately counts these cells in both brightfield and fluorescence modes (Figure 5).

Figure 5. Rodent PBMCs accurately counted with machine-learning algorithm. The Countess 3 FL Automated Cell Counter was used to count small rodent PBMCs. Counts were performed with brightfield lighting (A) and with fluorescence lighting (B).

Streamlined process

There is always an abundance of work awaiting scientists in the lab. The Countess 3 Automated Cell Counter streamlines the process of cell counting. There are several tedious steps it takes to work through the manual cell counting process. The Countess 3 Automated Cell Counter eliminates many of those steps and the hands-on time to perform those steps (Figure 6). This additional time can be applied to other activities in the lab, resulting in a significant advantage when switching from manual to automated cell counting.

Comparison of cell counting processes

Rapid capture

Using the brightfield mode, once the slide is inserted, there is nothing further to do. The Countess 3 counter will automatically illuminate, auto-focus, and auto-count. This saves time with additional menu selections, getting you quickly to the results.

Home screen with Rapid capture enabled

Autosave

By selecting the autosave feature, cell counts and data are automatically saved. Couple this with the Rapid capture mode and the cell counting and data retention process becomes fully automated.

Save Options Screen shows various files that can be saved, data destinations, and editable field for sample name along with field for enabling autosave

Countess Cell Counting Chamber Slides

The disposable slides are convenient for quickly processing cell samples when there are many to process. There is no need to clean the reusable slide and wait for it to dry between cell samples.

Pipet is loading sample into chamber slide

Built-in pre-dilution and cell splitting calculators make any necessary calculations seamless and integrated into the cell counting process. Viewing histograms and any additional desired gating of cell counts are easy to do on the Countess 3 cell counter, and a printable PDF report of your results can be saved and printed.

Pre-dilution calculator

If the cell sample is concentrated and a dilution is required prior to cell counting, the Countess 3 cell counter can quickly and easily calculate the sample concentration. The Countess 3 cell counters can easily calculate or remove calculation of a 1:1 dilution with trypan blue.

Fields to input sample volume, buffer volume and a field to select if concentration should account for 1 to 1 trypan blue dilution

Cell splitting calculator

Easily determine the amount of cell sample and buffer needed for your experiment with the built-in cell splitting calculator. The cell count results are automatically used in the calculation; simply input the desired concentration and the volume needed.

Fields to choose Live or Total cells, desired concentration, and volume needed. At the bottom third of the screen, the Countess 3 instrument informs how much cell solution should be mixed with how much buffer

Easily gate cells and view histograms

Cells can be gated based on cell size, brightness, and circularity to fine-tune what is included or excluded for specific applications. View the histogram by selecting the graph icon and watch the changes in real time as you use the gating features. Using brightfield, the average cell size is aligned on the x-axis. Using fluorescence, the relative fluorescence units (RFU) is aligned on the x-axis.

Histogram of cells detected by GFP fluorescence and the low intensity cells are gated out

Printable report with cell counting results

Using a USB drive or Wi-Fi to establish cloud connectivity on the Countess 3 and 3 FL Automated Cell Counters, you can save your cell count results and images and then transfer them to your own computer. Image files can be saved as TIFF, PNG, or JPEG files, and the results are saved as a CSV file. A printable PDF report with results, images, and settings used can also be saved.

Report file includes summary of cell count concentration results in the different fluorescent channels, the intensity, histograms, and captured cell images

Responsive touchscreen and intuitive interface

The Countess 3 Automated Cell Counter’s screen selections are intuitive and easy to navigate. The LCD screen is a responsive touchscreen, not requiring an external computer. Its 1280 x 800 resolution provides high-quality cell images. The cell images can be supplemented with aids for identifying live/dead counts and, in the Countess 3 FL Automated Cell Counter, the ability to visualize fluorescence. The display is flush across the instrument, making it easy to keep clean. While the touchscreen is increasingly popular, the Countess 3 cell counter can accommodate use with a mouse connected with the USB port in the back of the instrument.

Photo taken from above the Countess 3 cell counter with a good view of the touchscreen

Wi-Fi enabled cloud connection

The Countess 3 Automated Cell Counter can save files directly to the Thermo Fisher Connect cloud-based platform service. By connecting to a local Wi-Fi network with the Wi-Fi dongle, files can be saved to the cloud. Access these files now or later, inside the lab or out – data that is available when and where you need it.

Access your Countess 3 data from anywhere with Wi-Fi cloud connectivity

Machine-learning algorithm generates accurate counts; autofocus and auto-lighting minimize user-to-user variability

The Countess 3 Automated Cell Counters utilize machine-learning algorithms for fast and accurate focus determination as well as cell and viability counts. Countess instruments are compatible with a broad range of cell types and have been verified for use with several commonly used cell lines and primary cell types. Upon insertion of the slide, the Countess instrument will automatically provide optimized illumination and focus on the cells, which helps to minimize user variation associated with manual focusing and lighting adjustments. Cells ranging in size between ~4 µm and 60 µm and in cell suspension density ranging from 1 x 104 to 1 x 107 cells/mL are optimal for counting.

Bar graph of cell counts of different cell types counted by Attune NxT Flow Cytometer, Countess 3 Automated Cell Counter, and manually with a hemocytometer

Figure 1. Machine-learning algorithms result in highly accurate cell counts, comparable with flow cytometer counts. CHO-K1, HeLa, HEK293, Jurkat, and human PBMCs were counted using the Attune NxT Flow Cytometer (red bar), a Countess 3 FL Automated Cell Counter (blue bar), and manual counting using a hemocytometer and microscope (green bar). The Countess 3 FL Automated Cell Counter and hemocytometer bars represent an average of 6 counts. Error bars indicate standard deviation from 6 independent counts.

Scatter dot graph of cell counts of different cell types counted by Countess 3 Automated Cell Counter, and manually with a hemocytometer

Figure 2. Machine-learning algorithms result in highly precise cell counts with lower variability between counts compared to manual counting. CHO-K1, HeLa, HEK293, Jurkat, and human PBMCs were counted using the Countess 3 FL Automated Cell Counter (blue dots) and manual counting using a hemocytometer and microscope (green dots). The lines represent the median count and the dots demonstrate variance from 6 individual counts.

Bar graph of cell counts of human and mouse PBMCs by Countess 3 Automated Cell Counter and manually with a hemocytometer

Figure 3. Machine-learning algorithms result in highly accurate cell counts with challenging cell types and with more precision than manual counting. Human and mouse PBMCs were counted using the Countess 3 FL Automated Cell Counter (blue bar) and the manual counting method using a hemocytometer and microscope (green bar). The Countess 3 FL Automated Cell Counter and hemocytometer bars represent 6 counts. The error bars represent standard deviation.

Cell clumps counted accurately; debris ignored without gating inputs

Countess 3 Automated Cell Counters are able to accurately count cells that clump together. Whether you currently use automated or manual cell counting methods, obtaining accurate cell counts from samples containing clumpy cells can be difficult. Samples that contain debris add further complexity to cell counting. The Countess 3 Automated Cell Counter automatically excludes debris from cell counts. The machine-learning algorithm of the Countess Automated Cell Counter can clearly identify cell boundaries within clumps of cells and ignores debris, resulting in highly accurate cell counts (Figure 4).

Figure 4. Machine-learning algorithms generate accurate counts with clumpy cells and sample debris. The Countess 3 FL Automated Cell Counter was used to count RAW cells, which are both small and have a propensity to clump. The counting algorithm can resolve the cells in the clump and properly segment and count the cells. Debris is properly omitted from counts.

Small cells accurately counted

Rodent PBMCs are small cells around 5-7 microns and can be challenging to count whether manually on a hemocytometer or on an automated cell counter. The Countess 3 Automated Cell Counter’s machine-learning algorithm is robust and accurately counts these cells in both brightfield and fluorescence modes (Figure 5).

Figure 5. Rodent PBMCs accurately counted with machine-learning algorithm. The Countess 3 FL Automated Cell Counter was used to count small rodent PBMCs. Counts were performed with brightfield lighting (A) and with fluorescence lighting (B).

Streamlined process

There is always an abundance of work awaiting scientists in the lab. The Countess 3 Automated Cell Counter streamlines the process of cell counting. There are several tedious steps it takes to work through the manual cell counting process. The Countess 3 Automated Cell Counter eliminates many of those steps and the hands-on time to perform those steps (Figure 6). This additional time can be applied to other activities in the lab, resulting in a significant advantage when switching from manual to automated cell counting.

Comparison of cell counting processes

Rapid capture

Using the brightfield mode, once the slide is inserted, there is nothing further to do. The Countess 3 counter will automatically illuminate, auto-focus, and auto-count. This saves time with additional menu selections, getting you quickly to the results.

Home screen with Rapid capture enabled

Autosave

By selecting the autosave feature, cell counts and data are automatically saved. Couple this with the Rapid capture mode and the cell counting and data retention process becomes fully automated.

Save Options Screen shows various files that can be saved, data destinations, and editable field for sample name along with field for enabling autosave

Countess Cell Counting Chamber Slides

The disposable slides are convenient for quickly processing cell samples when there are many to process. There is no need to clean the reusable slide and wait for it to dry between cell samples.

Pipet is loading sample into chamber slide

Built-in pre-dilution and cell splitting calculators make any necessary calculations seamless and integrated into the cell counting process. Viewing histograms and any additional desired gating of cell counts are easy to do on the Countess 3 cell counter, and a printable PDF report of your results can be saved and printed.

Pre-dilution calculator

If the cell sample is concentrated and a dilution is required prior to cell counting, the Countess 3 cell counter can quickly and easily calculate the sample concentration. The Countess 3 cell counters can easily calculate or remove calculation of a 1:1 dilution with trypan blue.

Fields to input sample volume, buffer volume and a field to select if concentration should account for 1 to 1 trypan blue dilution

Cell splitting calculator

Easily determine the amount of cell sample and buffer needed for your experiment with the built-in cell splitting calculator. The cell count results are automatically used in the calculation; simply input the desired concentration and the volume needed.

Fields to choose Live or Total cells, desired concentration, and volume needed. At the bottom third of the screen, the Countess 3 instrument informs how much cell solution should be mixed with how much buffer

Easily gate cells and view histograms

Cells can be gated based on cell size, brightness, and circularity to fine-tune what is included or excluded for specific applications. View the histogram by selecting the graph icon and watch the changes in real time as you use the gating features. Using brightfield, the average cell size is aligned on the x-axis. Using fluorescence, the relative fluorescence units (RFU) is aligned on the x-axis.

Histogram of cells detected by GFP fluorescence and the low intensity cells are gated out

Printable report with cell counting results

Using a USB drive or Wi-Fi to establish cloud connectivity on the Countess 3 and 3 FL Automated Cell Counters, you can save your cell count results and images and then transfer them to your own computer. Image files can be saved as TIFF, PNG, or JPEG files, and the results are saved as a CSV file. A printable PDF report with results, images, and settings used can also be saved.

Report file includes summary of cell count concentration results in the different fluorescent channels, the intensity, histograms, and captured cell images

Responsive touchscreen and intuitive interface

The Countess 3 Automated Cell Counter’s screen selections are intuitive and easy to navigate. The LCD screen is a responsive touchscreen, not requiring an external computer. Its 1280 x 800 resolution provides high-quality cell images. The cell images can be supplemented with aids for identifying live/dead counts and, in the Countess 3 FL Automated Cell Counter, the ability to visualize fluorescence. The display is flush across the instrument, making it easy to keep clean. While the touchscreen is increasingly popular, the Countess 3 cell counter can accommodate use with a mouse connected with the USB port in the back of the instrument.

Photo taken from above the Countess 3 cell counter with a good view of the touchscreen

Wi-Fi enabled cloud connection

The Countess 3 Automated Cell Counter can save files directly to the Thermo Fisher Connect cloud-based platform service. By connecting to a local Wi-Fi network with the Wi-Fi dongle, files can be saved to the cloud. Access these files now or later, inside the lab or out – data that is available when and where you need it.

Access your Countess 3 data from anywhere with Wi-Fi cloud connectivity


Countess 3 Automated Cell Counter videos

How to use the reusable slide and accelerate your cell counting with Rapid capture

The reusable slide is a cost effective way to perform automated cell counting and Rapid capture will minimize steps when using the Countess 3 Automated Cell Counter in brightfield mode.

How to save your data

Following cell counts, data can be saved in the cloud or to a USB drive. Select from five file types and select Autosave to automatically save the files of your choice.

How to use onboard calculators

Use the pre-dilution calculator to correct for dilutions prior to counting including a quick trypan blue 1:1 dilution correction selection. Use the cell splitting calculator to set up cell culture vessels with the optimal cell densities.


Countess 3 instruments angled toward one another and the Countess 3 FL has 2 EVOS light cubes in the front right side

Comparison between Countess 3 Automated Cell Counter and Countess 3 FL Automated Cell Counter

Features Countess 3
Automated Cell Counter
Countess 3 FL
Automated Cell Counter
Machine-learning algorithm   *   *
1280 x 800 LCD screen   *   *
Wi-Fi enabled cloud connectivity   *   *
Brightfield image & count    
Brightfield auto-lighting    
Brightfield Rapid capture   *   *
Fluorescence images & counts n/a Two user-changeable fluorescence channels (optional)
Fluorescence auto-lighting n/a   *
Saturated pixel indicator n/a   *
Autofocus    
Autosave   *   *
Countess Chamber Counting Slides    
Countess Reusable Slide   *  
Pre-dilution calculator   *   *
Cell splitting calculator    
Single-cell data   *   *
* New features in the Countess 3 Automated Cell Counters.
n/a = not applicable.


Ordering information

Countess 3 Automated Cell Counter

Cat. No. Description Includes
AMQAX2000 Countess 3 Automated Cell Counter
  • Countess 3 Automated Cell Counter
  • Countess Cell Counting Chamber Slides (50 slides/box)
  • Countess Disposable Slide Holder
  • USB drive
  • Power Cord with 4 adapters
  • Countess 3 Automated Cell Counter Quick Reference Card
  • One-year standard warranty


Countess 3 Automated Cell Counter—Starter Kit

Cat. No. Description Includes
A49865 Countess 3 Automated Cell Counter Starter Kit
  • Countess 3 Automated Cell Counter (AMQAX2000)
  • Countess Reusable Slide
  • Countess Cell Counting Chamber Slides (500 slides)


Countess 3 Automated Cell Counter—Productivity Package

Cat. No. Description Will provide a custom quote with the selection from the following items:

Request a quote

Countess 3 Automated Cell Counter Productivity Package
  • Countess 3 Automated Cell Counter
  • Invitrogen Trypan Blue Stain (0.4%)
  • Countess Cell Counting Chamber Slides
  • 3 years Rapid Exchange Extended Warranty

Countess 3 FL Automated Cell Counter

Cat. No. Description Includes
AMQAF2000 Countess 3 FL Automated Cell Counter
  • Countess 3 FL Automated Cell Counter
  • Countess Cell Counting Chamber Slides (50 slides/box)
  • Countess Disposable Slide Holder
  • Countess Reusable Slide Holder
  • USB drive
  • WiFi Dongle
  • Countess Light Cube Removal Tool
  • Power Cord with 4 adapters
  • Countess 3 Automated Cell Counter Quick Reference Card
  • One-year standard warranty


Countess 3 FL Automated Cell Counter—Starter Kit

Cat. No. Description Includes
A49866 Countess 3 FL Automated Cell Counter Starter Kit
  • Countess 3 FL Automated Counter (AMQAF2000)
  • Countess Reusable Slide
  • Countess Cell Counting Chamber Slides (500 slides)
  • Two EVOS Light Cubes (RFP and GFP)


Countess 3 FL Automated Cell Counter—Productivity Package

Cat. No. Description Will provide a custom quote with the selection from the following items:
Request a quote Countess 3 FL Automated Cell Counter Productivity Package
  • Countess 3 FL Automated Counter
  • Countess Reusable Slide
  • Countess Cell Counting Chamber Slides
  • Invitrogen Trypan Blue Stain (0.4%)
  • EVOS Light Cube, GFP
  • EVOS Light Cube, RFP
  • EVOS Light Cube, DAPI
  • Live/Dead Viability/Cytotoxicity Kit (Green/Red)
  • 3 years Rapid Exchange Extended Warranty

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