photo of a Countess II FL Automated Cell Counter

Automated cell counter with the option for a reusable hemocytometer and fluorescence capabilities

With the option for a reusable slide and fluorescence capabilities—brightfield and two user-changeable fluorescence channels—the Invitrogen Countess II FL Automated Cell Counter can count cells, monitor fluorescent protein expression, and measure cell viability.

  • Affordable—option for reusable slide to significantly reduce consumables cost
  • Accuracy—eliminate the subjectivity of manual cell counting and minimize user-to-user variability
  • Speed—count live and dead cells and measure viability and average cell size in as little as 10 seconds

Now affordable–option for reusable or disposable slides

The mounting costs of disposable slides and tips have deterred many labs from giving up tedious manual cell counting. In response to this, the Countess II FL instrument was designed to work with a reusable glass slide , which significantly reduces the long-term consumable costs of automated counting. Convenient disposable slides are also available.

Advanced autofocusing and counting algorithms

The Countess automated cell counters contain advanced autofocusing and counting algorithms to allow you to quickly and accurately identify and count cells within a population (Figure 1). Countess instruments are compatible with a broad range of cell types and cell lines, and we have validated their use on a number of commonly used cell lines. Upon insertion of the slide the Countess instrument will automatically focus on cells, which helps to minimize user variation associated with manual focusing.

Figure 1. User variability counting with a hemocytometer compared to using a Countess II instrument. Identical samples of A549, COS-7, HeLa, and U2OS cells were counted by three different operators using a Countess II Cell Counter and then manually with a hemocytomer and microscope. The user-to-user variability for the hemocytometer is much higher than for the Countess II instrument.

Easily gate cells and view histograms

Cells can be easily gated based on cell size, brightness, and circularity to fine-tune precisely 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. The average cell size is also displayed on the histogram (Figure 2).

Figure 2. Histogram is updated to reflect gating changes. Multiple gating options can be selected separately for live cells and dead cells, allowing easy inclusion or exclusion of debris or specific populations.

Dilution calculator

Easily determine the amount of cell sample and buffer needed for your experiment with the built-in dilution calculator. The cell count results are automatically used in the calculation; simply input the desired concentration and the volume needed (Figure 3).

Figure 3. A dilution calculator quickly determines the amount of cell sample and buffer needed.

Streamline your workflow with custom profiles

Custom profiles can be saved and easily accessed from the capture and results screens (Figure 4). Settings for cell size, brightness, and circularity as well as fluorescence thresholds can be customized and saved for easy retrieval.

Figure 4. Easily access custom assay profiles.

Printable report with cell counting results

Using the USB port on the Countess II FL Automated Cell Counter, you can save your cell count results and images, and then transfer them to your own computer. Image files can be saved as TIF, PNG, or JPG files, and the results are saved as a CSV file. A printable PDF report with results, images, and settings used can also be saved (Figure 5).

Figure 5. PDF report with results and images.

Time savings

The additional time it takes to manually count cells using a hemocytometer (up to 5 minutes) compared to counting with the Countess II automated cell counters (10 seconds) is often overlooked as an added cost. An individual counting five slides per day (two samples per slide) can save ~10 hours per month by switching to an automated counter with a reusable slide. The time savings increases to ~15 hours per month when using disposable slides (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.

Figure 6. Estimated hours saved per month when switching from counting cells with a hemocytometer to using an automated cell counter.

Full spectrum of fluorescence detection–not limited to GFP and RFP

The Countess II FL instrument has two optional fluorescence channels. The fluorescent colors collected are determined by the insertion of individual light cubes. With 20 light cubes to choose from, the Countess II FL instrument is not limited to detection of GFP- and RFP-expressing cells. Looking to measure the transfection efficiency of cells transduced with an RFP-expression construct with a blue nuclear counterstain? No problem. Simply add the RFP and DAPI light cubes, and you can effectively count the number of cells expressing the RFP fusion within the total population and accurately determine the transfection efficiency.

Gating based on fluorescence intensity

The ability to use up to two customizable fluorescence colors with the Countess II FL Automated Cell Counter allows for more accurate counts when dealing with complex samples that contain significant amounts of platelets, RBCs, or debris. In addition, the ability to gate based on fluorescence intensity to determine how many cells are dim vs. bright, or are expressing a fluorescent protein, can save time and effort prior to downstream analysis with techniques such as flow cytometry or high-content analysis (Figure 7).

Figure 7. Gating based on fluorescence intensity. (A) The dim cells (around 50 RFU) have been excluded from the GFP-positive count. (B) Two fluorescence colors are present, each of which can be gated by size, brightness, circularity, and fluorescence intensity.

Up to two optional user-changeable light cubes

Central to the fluorescence detection technology inside the Countess II FL instrument are the proprietary Invitrogen EVOS LED light cubes. Light cubes are user-changeable and auto-configured by the Countess system with plug-and-play capability.

photo of 3 EVOS light cubes

Convince your lab to purchase a Countess II FL Automated Cell Counter

  1. Download and circulate petition
  2. Download and customize prewritten letter
  3. Download application note comparing automated and manual counting
  4. Submit request to PI or lab manager
  5. Ditch your clicker and celebrate


Countess II FL Automated Cell Counter information

Technical specifications
  • Processing time: <10 seconds
  • Sample concentration range: 1 x 104–1 x 107 cells/mL
  • Particle diameter range: ~4–60 µm
  • Cell diameter range: ~7–60 µm
  • Required sample volume: 10 μL
  • USB drive: 4 gigabyte, FAT file system
  • Optics: 5 megapixels, 2.5X optical magnification, 3 channels (bright-field plus 2 slots for EVOS LED light cubes)
Physical characteristics
  • Instrument dimensions: 
    9" (W) x 5½" (D) x 9" (H); 228.6 mm (W) X 139.7 mm (D) x 228.6 mm (H)
  • Weight: 8 lbs
Counting area
  • Area: 2.15 mm x 1.62 mm (3.48 mm2)
    graphic showing larger counting area of Countess II FL compared to hemocytometers
Included in the box
  • Countess USB drive for storing and transferring data to your computer
  • Disposable slide holder
  • Reusable slide holder
  • Light cube removal tool
  • Power cord and 4 plug adaptors to accommodate most countries
  • Quick reference card (QRC)

Sold separately:

Researchers use Invitrogen Countess II and Countess II FL Cell Imaging Systems in their labs every day. Here's what some of our users have to say:

"Fast count and nice instruments, easy to use!! I love the small counter!"Dr. Xin Xu, Baylor College of Medicine

"It's very easy to use and it also allows me to quickly update my lab notebook so that each experiment uses the same number of cells. Quick and efficient."Lakeisha Tillery, Meharry Medical College

"It outperformed all other competitor's models that we tried."Michael DaCosta, The Jackson Laboratory

"It's very consistent!"Kim Sylvia, Sanford Burnham Medical Research Institute

"It is very effective at counting cells. It works very well."Mairead Bretney, Sanford Burnham Medical Research Institute

"The Countess II makes it very easy to count cells accurately and quickly - the fact that it tells you the dead cell and live cell count is icing on the cake."Faryal Mir, MIT

"We compared to a hemocytometer and the Countess II always obtained very close results. The fluorescent measurements are a great tool for us to quantify the % transfection and transduction efficiency in our experiments. The light cubes used to detect fluorescence are very easy to switch out when more than two fluorescence sources are needing to be detected. The automatic focusing is very effective and accurate with the option to manually focus."David Waynar, Santa Cruz Biotechnology

"This equipment is very useful for the purposes it is used in our lab. We love it!"Kristin Harwood, BioMarker Strategies, LLC

"Great for a quick check of transfection/transduction efficiency. Easy to use and seems pretty sensitive."Alex Peister, Morehouse College

"Great device. Broad range of cell densities that it can handle. Good at distinguishing clumps and counting cells within clumps."Joanna Rzepka, Veterinary Medical Research & Development

"Low maintenance, fast easy accurate cell counts. Easy for students to use and comprehend."Robert Dean, D'Youville College

"A very accurate cell counter and you can use it to count fluorescent cells as well. Excellent product. I'm very happy with it. I highly recommend it."Massimo Ammirante, University of California, San Diego

The result, image, and data files can be easily exported to a USB drive. The result and image files can be saved as .bmp, .jpg, .tiff, or .png files. The data file is saved as a .csv file that can be easily imported into your current analysis software or viewed in Excel™ software.

A comma-separated values (CSV) file stores tabular data (numbers and text) in plaintext form. Plain text means that the file is a sequence of characters, with no data that has to be interpreted as binary numbers. A CSV file can be opened with any third party software or spreadsheet program. The table below describes the categories of the Countess II data saved as a CSV file and opened with a spreadsheet program.

Category Column Name Description
General A Number Sequential sample run number
B File Name Name of file
C Date & Time Date and time of sample run
D Mode BF-Brightfield or FL-Fluorescence
Trypan Blue/
Brightfield
E Total concentration Concentration of the entire sample
F Total cells counted Total number of cells counted in the sample
G Live concentration Concentration of just the “live” portion of the sample
H Live cells counted Total number of “live” cells counted
I Dead concentration Concentration of just the “dead” portion of the sample
J Dead cells counted Total number of “dead” cells counted
K Viability (%) Percent viability of the sample based on trypan blue staining
L Average size (μm) Average cell size in microns
Fluorescence M Cube 1 name EVOS light cube name in the first (top) position
N Cube 1 concentration Concentration of cells showing fluorescence in the first cube position
O Cube 1 (%) Percentage of the total cells in brightfield that show fluorescence in the first cube position
P Cube 1 cells counted Total number of cells counted in the first cube position
Q Cube 2 name EVOS light cube name in the second (bottom) position
R Cube 2 concentration Concentration of cells showing fluorescence in the second cube position
S Cube 2 (%) Percentage of the total cells in brightfield that show fluorescence in the second cube position
T Cube 2 cells counted Total number of cells counted in the second cube position
U Cube 1+2 concentration Concentration of cells showing fluorescence in the first and second cube positions combined
V Cube 1+2 (%) Percentage of the total cells in brightfield that show fluorescence in the first and second cube position combined
W Cube 1+2 cells counted Total number of cells counted in the first and second cube position combined
General Details X Focus value Focal position number
Y BF Light intensity Brightfield light intensity value from 0-100%
Trypan Blue/
Brightfield Count Parameters
Z Live Size min Minimum size of “live” cells in microns
AA Live Size max Maximum size of “live” cells in microns
AB Live Brightness min “Live” adjustment slider value for minimum brightness
AC Live Brightness max “Live” adjustment slider value for maximum brightness
AD Live Circularity “Live” adjustment slider value for circularity
AE Dead Size min Minimum size of “dead” cells in microns
AF Dead Size max Maximum size of “dead” cells in microns
AG Dead Bright min “Dead” adjustment slider value for minimum brightness
AH Dead Bright max “Dead” adjustment slider value for maximum brightness
AI Dead Circ “Dead” adjustment slider value for circularity
Fluorescence Count Parameters AJ Cube 1 Light intensity First (top) light cube light intensity value from 0-100%
AK Cube 2 Light intensity Second (bottom) light cube light intensity value from 0-100%
AL BF Size min Minimum size of “Brightfield” cells in microns
AM BF Size max Maximum size of “Brightfield” cells in microns
AN BF Brightness min “Brightfield” adjustment slider value for minimum brightness
AO BF Brightness max “Brightfield” adjustment slider value for maximum brightness
AP BF Circularity “Brightfield” adjustment slider value for circularity
AQ Cube 1 Brightness min First (top) light cube adjustment slider value for minimum brightness
AR Cube 1 Brightness max First (top) light cube adjustment slider value for maximum brightness
AS Cube 2 Brightness min Second (bottom) light cube adjustment slider value for minimum brightness
AT Cube 2 Brightness max Second (bottom) light cube adjustment slider value for maximum brightness

Counting has been successfully performed on the following cell lines using the Countess II FL Automated Cell Counter:

Cell Animal Organ
A431 Human Skin
A549 Human Lung
Adipocytes Human Adipose-derived stem cells
Aortic smooth muscle Human Smooth muscle
CHO-M1WT2 Chinese hamster Ovary
CHSE Chinook salmon Embryo
COLO-205 Human Colon
COS-7 African monkey Kidney
HeLa Human Cervix
HepG2 Human Liver
HL-60 Human Blood
J774A.1 Mouse Blood
Jurkat Human Blood
K562 Human Bone marrow
MCF7 Human Breast
MCPIP1 Mouse Bone
MRC-5 Human Lung
NIH/3T3 Mouse Embryo
PBMC Human Blood
PC-12 Rat Adrenal gland
Pulmonary artery endothelial Human Blood vessel
Pulmonary artery smooth muscle Human Smooth muscle
Raji Human Lymphocyte
SF-21 Insect Ovary
U266 Human Blood
U2OS Human Bone
Umbilical vein endothelial Human Blood vessel
Whole lysed blood Human Blood
Technical specifications
  • Processing time: <10 seconds
  • Sample concentration range: 1 x 104–1 x 107 cells/mL
  • Particle diameter range: ~4–60 µm
  • Cell diameter range: ~7–60 µm
  • Required sample volume: 10 μL
  • USB drive: 4 gigabyte, FAT file system
  • Optics: 5 megapixels, 2.5X optical magnification, 3 channels (bright-field plus 2 slots for EVOS LED light cubes)
Physical characteristics
  • Instrument dimensions: 
    9" (W) x 5½" (D) x 9" (H); 228.6 mm (W) X 139.7 mm (D) x 228.6 mm (H)
  • Weight: 8 lbs
Counting area
  • Area: 2.15 mm x 1.62 mm (3.48 mm2)
    graphic showing larger counting area of Countess II FL compared to hemocytometers
Included in the box
  • Countess USB drive for storing and transferring data to your computer
  • Disposable slide holder
  • Reusable slide holder
  • Light cube removal tool
  • Power cord and 4 plug adaptors to accommodate most countries
  • Quick reference card (QRC)

Sold separately:

Researchers use Invitrogen Countess II and Countess II FL Cell Imaging Systems in their labs every day. Here's what some of our users have to say:

"Fast count and nice instruments, easy to use!! I love the small counter!"Dr. Xin Xu, Baylor College of Medicine

"It's very easy to use and it also allows me to quickly update my lab notebook so that each experiment uses the same number of cells. Quick and efficient."Lakeisha Tillery, Meharry Medical College

"It outperformed all other competitor's models that we tried."Michael DaCosta, The Jackson Laboratory

"It's very consistent!"Kim Sylvia, Sanford Burnham Medical Research Institute

"It is very effective at counting cells. It works very well."Mairead Bretney, Sanford Burnham Medical Research Institute

"The Countess II makes it very easy to count cells accurately and quickly - the fact that it tells you the dead cell and live cell count is icing on the cake."Faryal Mir, MIT

"We compared to a hemocytometer and the Countess II always obtained very close results. The fluorescent measurements are a great tool for us to quantify the % transfection and transduction efficiency in our experiments. The light cubes used to detect fluorescence are very easy to switch out when more than two fluorescence sources are needing to be detected. The automatic focusing is very effective and accurate with the option to manually focus."David Waynar, Santa Cruz Biotechnology

"This equipment is very useful for the purposes it is used in our lab. We love it!"Kristin Harwood, BioMarker Strategies, LLC

"Great for a quick check of transfection/transduction efficiency. Easy to use and seems pretty sensitive."Alex Peister, Morehouse College

"Great device. Broad range of cell densities that it can handle. Good at distinguishing clumps and counting cells within clumps."Joanna Rzepka, Veterinary Medical Research & Development

"Low maintenance, fast easy accurate cell counts. Easy for students to use and comprehend."Robert Dean, D'Youville College

"A very accurate cell counter and you can use it to count fluorescent cells as well. Excellent product. I'm very happy with it. I highly recommend it."Massimo Ammirante, University of California, San Diego

The result, image, and data files can be easily exported to a USB drive. The result and image files can be saved as .bmp, .jpg, .tiff, or .png files. The data file is saved as a .csv file that can be easily imported into your current analysis software or viewed in Excel™ software.

A comma-separated values (CSV) file stores tabular data (numbers and text) in plaintext form. Plain text means that the file is a sequence of characters, with no data that has to be interpreted as binary numbers. A CSV file can be opened with any third party software or spreadsheet program. The table below describes the categories of the Countess II data saved as a CSV file and opened with a spreadsheet program.

Category Column Name Description
General A Number Sequential sample run number
B File Name Name of file
C Date & Time Date and time of sample run
D Mode BF-Brightfield or FL-Fluorescence
Trypan Blue/
Brightfield
E Total concentration Concentration of the entire sample
F Total cells counted Total number of cells counted in the sample
G Live concentration Concentration of just the “live” portion of the sample
H Live cells counted Total number of “live” cells counted
I Dead concentration Concentration of just the “dead” portion of the sample
J Dead cells counted Total number of “dead” cells counted
K Viability (%) Percent viability of the sample based on trypan blue staining
L Average size (μm) Average cell size in microns
Fluorescence M Cube 1 name EVOS light cube name in the first (top) position
N Cube 1 concentration Concentration of cells showing fluorescence in the first cube position
O Cube 1 (%) Percentage of the total cells in brightfield that show fluorescence in the first cube position
P Cube 1 cells counted Total number of cells counted in the first cube position
Q Cube 2 name EVOS light cube name in the second (bottom) position
R Cube 2 concentration Concentration of cells showing fluorescence in the second cube position
S Cube 2 (%) Percentage of the total cells in brightfield that show fluorescence in the second cube position
T Cube 2 cells counted Total number of cells counted in the second cube position
U Cube 1+2 concentration Concentration of cells showing fluorescence in the first and second cube positions combined
V Cube 1+2 (%) Percentage of the total cells in brightfield that show fluorescence in the first and second cube position combined
W Cube 1+2 cells counted Total number of cells counted in the first and second cube position combined
General Details X Focus value Focal position number
Y BF Light intensity Brightfield light intensity value from 0-100%
Trypan Blue/
Brightfield Count Parameters
Z Live Size min Minimum size of “live” cells in microns
AA Live Size max Maximum size of “live” cells in microns
AB Live Brightness min “Live” adjustment slider value for minimum brightness
AC Live Brightness max “Live” adjustment slider value for maximum brightness
AD Live Circularity “Live” adjustment slider value for circularity
AE Dead Size min Minimum size of “dead” cells in microns
AF Dead Size max Maximum size of “dead” cells in microns
AG Dead Bright min “Dead” adjustment slider value for minimum brightness
AH Dead Bright max “Dead” adjustment slider value for maximum brightness
AI Dead Circ “Dead” adjustment slider value for circularity
Fluorescence Count Parameters AJ Cube 1 Light intensity First (top) light cube light intensity value from 0-100%
AK Cube 2 Light intensity Second (bottom) light cube light intensity value from 0-100%
AL BF Size min Minimum size of “Brightfield” cells in microns
AM BF Size max Maximum size of “Brightfield” cells in microns
AN BF Brightness min “Brightfield” adjustment slider value for minimum brightness
AO BF Brightness max “Brightfield” adjustment slider value for maximum brightness
AP BF Circularity “Brightfield” adjustment slider value for circularity
AQ Cube 1 Brightness min First (top) light cube adjustment slider value for minimum brightness
AR Cube 1 Brightness max First (top) light cube adjustment slider value for maximum brightness
AS Cube 2 Brightness min Second (bottom) light cube adjustment slider value for minimum brightness
AT Cube 2 Brightness max Second (bottom) light cube adjustment slider value for maximum brightness

Counting has been successfully performed on the following cell lines using the Countess II FL Automated Cell Counter:

Cell Animal Organ
A431 Human Skin
A549 Human Lung
Adipocytes Human Adipose-derived stem cells
Aortic smooth muscle Human Smooth muscle
CHO-M1WT2 Chinese hamster Ovary
CHSE Chinook salmon Embryo
COLO-205 Human Colon
COS-7 African monkey Kidney
HeLa Human Cervix
HepG2 Human Liver
HL-60 Human Blood
J774A.1 Mouse Blood
Jurkat Human Blood
K562 Human Bone marrow
MCF7 Human Breast
MCPIP1 Mouse Bone
MRC-5 Human Lung
NIH/3T3 Mouse Embryo
PBMC Human Blood
PC-12 Rat Adrenal gland
Pulmonary artery endothelial Human Blood vessel
Pulmonary artery smooth muscle Human Smooth muscle
Raji Human Lymphocyte
SF-21 Insect Ovary
U266 Human Blood
U2OS Human Bone
Umbilical vein endothelial Human Blood vessel
Whole lysed blood Human Blood

Ordering information

NOTE: The reusable slide (Cat. No. A25750) is only compatible with the Countess II FL instrument.