Cell Counting Support—Getting Started

The user manuals for the Countess 3 and 3FL may be downloaded from the following page, under the Resources tab:

Countess Automated Cell Counter Resources

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

EVOS light cubes, which enable fluorescent detection in the Countess 3 FL Automated Cell Counter, are compatible with a broad range of fluorescent dyes. Refer to our selection guide for an extensive list of compatible dyes. We also offer the ready-to-use ReadyCount Stains for easy viability staining.

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

The Countess 3/3FL Automated Cell Counter does not require sample-specific settings in order to count, however users may create customized protocols for individual samples or workflows. Please see Chapter 3 of the user guide.

Countess 3 Automated Cell Counter User Guide (Pub. No. MAN0019566 E.0)

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

Please search our Documents and Certificates database for your COA, using the specific serial number for your instrument. If your search is unsuccessful, please go to Contact Us, click on Technical Support, enter your product name, and complete the form to request your COA, or contact technical support at Technicalservices@thermofisher.com. 

For user manuals, instructional videos, and educational content for Countess Automated Cell Counter instruments, please consult the following link:

Countess Automated Cell Counter Resources

Please refer to the following link for many helpful demo videos, found under the Resources tab, covering such topics as "How to save your data" and "How to use on-board calculators."

Countess Automated Cell Counter Resources

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

Instructions for updating the Countess 3/3FL software are below:

1. Go to Countess Software Downloads page.
2. Download the latest version of the Countess 3/3 FL software to a computer.
3. Copy the latest countess software file to a USB drive.
4. Insert the USB drive into the Countess 3/3FL instrument (Ensure the .exe update is not hidden within a folder on the USB, as this will prevent a successful update).
5. Press the Setting icon in the lower right corner of the home screen.

6. Select "Software Update" from the instrument Settings menu.

7. Select the update location (USB or Cloud) and click Next.
8. Select the "Update" button. The update process should only take a minute or two.

9. The instrument will automatically restart, and the screen will show when the update is complete.


Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

Please refer to the following link for many helpful Countess Automated Cell Counter demo videos, found under the Resources tab, covering such topics as "How to Visualize histograms and perform gating.” Our Cell Analysis Resource center contains additional educational resources:

Countess Automated Cell Counter Resources

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

All Countess 3/3 FL Automated Cell Counters come with a standard 1-year warranty. Many customers also choose to purchase a service plan, which extends the standard warranty by two years. Information may be found here under the Services tab.

Countess Automated Cell Counter Services

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

For safety and handing information for your Countess 3/3FL Automated Cell Counter, please refer to “Appendix E Safety” in the User Guide.

Countess 3 Automated Cell Counter User Guide (Pub. No. MAN0019566 E.0)

For information on the regulatory and compliance standards for my Countess 3/3FL Automated cell counter, including 21 CFR Part 11, IQ/OQ, and warranty packages, please see refer to Countess Automated Cell Counter Services on our website.

Users may create customized protocols for individual workflows or sample types. Please refer to Chapter 3 "Protocols" in the User Guide for more information.

Countess 3 Automated Cell Counter User Guide (Pub. No. MAN0019566 E.0)

The Countess offers several ways to save count data. The Report PDF is a convenient summary of count results that includes cell concentration, fluorescence detected (for the properly equipped Countess 3FL only), and images of the counting field. Users may also export data in CSV, FCS, and image formats.

The following is the recommended procedure for decontaminating the external surface of the Countess™ Automated Cell Counter. Please note that internal decontamination is not possible.

• Wipe the instrument case using a soft, lint-free cloth moistened with 70% alcohol. Wipe the instrument dry immediately after cleaning.
• Avoid using bleach, as it may leave residue on the case.
• Ensure that water or other cleaning solutions do not enter the power button, the power inlet, the slide port, or the USB ports.
• Never pour or spray any liquids directly on the instrument to avoid electrical shock when the instrument is plugged in.

The following is the recommended cleaning process for the Countess Reusable Slide (Cat. No. A25750):

• Rinse coverslip and Reusable Slide with deionized water to remove debris. A diluted bleach solution or laboratory soap may also be used.
• Rinse coverslip and Reusable Slide with 70% ethanol to sterilize and reduce drying time.
• Allow coverslip and Reusable Slide to air dry or use lint-free imaging cloths to speed drying.
• Reassemble for next sample.

Countess 3 Automated Cell Counters produce accurate and precise counts across a range of cell types, including human and murine peripheral blood mononuclear cells (PBMCs). Cell types and isolated nuclei smaller than 5 microns in diameter may be counted in FL only mode. Fluorescent staining, compatible EVOS light cubes, and update to the latest software version is required.

For more information on EVOS Light Cubes and compatible dyes, please use the following link:

EVOS Cell Imaging System Accessories

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

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. Bacteria (and particles under 5 microns in diameter) may require fluorescent mode for counting and may not be detected in brightfield mode.

Invitrogen ReadyCount Stains are pre-optimized for viability analysis with Countess 3 FL Automated Cell Counter. Simply mix 10 µL of cell sample with 10 µL of stain, pipet the solution into a Countess chamber or reusable slide and insert the slide into the instrument.

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

Automated features like rapid capture, autosave, and built-in calculators add convenience and time savings over hemocytometers or early-generation automated counters. For more information about Countess Automated Cell Counter Features like fast cell counting capabilities, click on the link below.

Countess Automated Cell Counter Features

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

Relative to the Countess II, the Countess 3/3FL Automated Cell Counter offers the following core improvements:

• Increased accuracy and precision
• Artificial intelligence deep-learning algorithm
• Rapid capture & autosave

Fewer touch points; time-savings

Compared to manual hemocytometer counts with Countess 3/3FL Automated Cell Counter instruments can reduce data errors and variability from many causes, including operator subjectivity and fatigue, counting area, and challenging samples. Countess 3 cell counters achieve both the accuracy of manual cell counts and the precision of flow cytometer counts, without the expense or training required by flow cytometry.

Find more information about the accuracy and precision of cell counting with Countess 3 instruments using the links below:

Countess Automated Cell Counter Features

Cell counting accuracy and precision: Why it matters and how to achieve it (White Paper)

The Countess is compatible with easy-to-use ReadyCount reagents for viability counting. We offer both disposable chamber slides and a reusable chamber slide for a greener and more cost-effective option. Additionally, Countess instruments are compatible with the entire line of EVOS light cubes. For more information about these accessories and consumables, use the links below.

ReadyCount Stains (Cat. No. A49903, A49904, A49905)

Countess Cell Counting Chamber Slides and Holder, disposable (Cat. Nos. C10228, C10312, C10313, C10314, C10215, T10282, AMEP4745, C10283)

Countess Reusable Slide and Holder (Cat. Nos. A25750, A48208)

EVOS Light Cubes (Cat. No. AMEP4950, AMEP4951, AMEP4932, AMEP4955, AMEP4956, AMEP4667)

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

Storage and handling recommendations may be found in the product manuals for each individual reagent.

For more information about Countess 3 consumables, use the links below.
ReadyCount Stains (Cat. No. A49903, A49904, A49905)

Countess Cell Counting Chamber Slides and Holder, disposable (Cat. Nos. C10228, C10312, C10313, C10314, C10215, T10282, AMEP4745, C10283)

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

Please refer to the following link for helpful demo videos for EVOS light cube installation, reusable slide usage, and more.

Countess Automated Cell Counter Resources

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.

Countess II and II FL Automated Cell Counter FAQs can be found in our Product FAQ DB. 

You can find the service retirement letter for Countess II and II FL Automated Cell Counters below:

Service Retirement Letter: Important end-of-life Communication for Countess II and IIFL Products

We recommend adding 0.1 mL of trypan blue stock solution to 1 mL of cells (final concentration 0.04% w/v). Final concentrations may range from 0.0.04% to 0.2% (w/v) dependent upon the sample and instrumentation. 

Yes, you can find the protocol at the following link.

Trypan blue will stain cells that have a compromised membrane. It cannot differentiate between compromised membranes caused by apoptosis or necrosis.

It depends on the type of fluorescent stain used on the cells. Trypan blue is a cell-impermeant chromophore that can quench fluorescence. It may quench fluorescent staining on the surface of live cells or internal fluorescent staining in dead cells.

Trypan blue will bind to serum proteins as well as cellular proteins, which may result a high level of background staining. If the background is too dark, cells should be pelleted and resuspended in protein-free medium, buffer, or normal saline prior to counting.

Trypan blue is a cell impermeant stain used to estimate the number of dead cells in a viable population. Its utility is based on the fact that it is a charged dye and does not enter cells unless the membrane is compromised. Live (viable) cells exclude the dye but dead (non-viable) cells or cells with a compromised membrane are stained an intense blue.

The formulation/identity of components in the solution of ReadyCount Blue Nuclear Stain (Cat. No. A49904) is proprietary.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

The concentration of Hoechst 33342 in ReadyCount Blue Nuclear Stain (Cat. No. A49904) is proprietary. If you need to use a defined concentration of Hoechst 33342, we do offer this as a standalone product (Cat. Nos. 62249, H1399, and H21492).

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

If an expiration date or warranty period is not posted on any public-facing document, the ReadyCount reagents have the standard warranty period of 1 year from the date of shipment.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

If an expiration date or warranty period is not posted on any public-facing document, the ReadyCount reagents have the standard warranty period of 1 year from the date of shipment.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

The concentration of Propidium iodide in ReadyCount Red Dead Cell Stain (Cat. No. A49903) is proprietary. If you need to use a defined concentration of Propidium iodide we do offer this as a standalone product (Cat. Nos. P3566, P1304MP, P21493).

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

The formulation/identity of components in the solution ReadyCount Red Dead Cell Stain (Cat. No. A49903) is proprietary.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

The formulation/identity of components in the solution of ReadyCount Green/Red Viability Stain (Cat. No. A49905) is proprietary.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

The concentrations of Acridine Orange and Propidium iodide in ReadyCount Green/Red Viability Stain (Cat. No. A49905) are proprietary. If you need to use a defined concentration of Acridine Orange, we do offer this as a standalone product (Cat. Nos. A1301 and A3568). If you need to use a defined concentration of Propidium iodide, we do offer this as a standalone product (Cat. Nos. P3566, P1304MP, and P21493).

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

If an expiration date or warranty period is not posted on any public-facing document, the ReadyCount reagents have the standard warranty period of 1 year from the date of shipment.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

Yes. While the excitation of the ReadyCount Red Dead Cell Stain (Cat. No. A49903) is not ideal under the EVOS Light Cube,Texas Red 2.0 (Cat. No. AMEP4955) compared to the recommended EVOS Light Cube, RFP 2.0 (Cat. No. AMEP4952), the EVOS Light Cube,Texas Red 2.0, may be used.

Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.

Invitrogen ReadyCount Stains are pre-optimized for viability analysis with Countess 3 FL Automated Cell Counter. Simply mix 10 µL of cell sample with 10 µL of stain, pipet the solution into a Countess chamber or reusable slide and insert the slide into the instrument.

Find additional tips, troubleshooting help, and resources within our Cell Counting Support Center.