Countess™ 3 21 CFR Part 11 Software Module - FAQs

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

Important end-of-life communication for Countess II and II FL products

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

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Troubleshooting information for Countess 3 and 3FL can be found on the Cell Counting Support Center.

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Our guarantee period for disposable Countess Cell Counting Chamber Slides is 5 years.

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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.

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For safety and handling 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)

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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

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

Countess Automated Cell Counter Resources

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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.

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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)

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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

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Please consult the following link for basic troubleshooting tips: Cell Counting Information for more information. If the above fails to correct the problem, please contact technical support at Technicalservices@thermofisher.com.

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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.

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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.

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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)

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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.

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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)

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To reinstall the software on your Countess 3/3FL Automated Cell Counter, take the following steps:

•      Check the exact SW version numbers and make sure that a higher version number is being installed. The Countess instrument will not install a version that has a lower number.
•      Insert a USB drive containing the update file into the Countess with the unit powered on. There is a USB port on the front and back of the instrument and either may be used. The device may take a few seconds to recognize the USB drive. Click on Settings > Software Update > USB > Next > Update. The instrument will update to the software version. Please note this may take many minutes, during which the screen may go black.
•      The USB drive must be FAT32 formatted; verify this before proceeding.
•      The update file must sit on the top level of the USB drive, not within a folder or subfolder.
•      The update file cannot be renamed in any way.
•      The update file cannot be zipped or compressed during distribution.

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To resolve connectivity issues between your Countess 3/3FL Automated Cell Counter and your computer, take the following steps:

Step 1: Network compatibility
Ensure that the Wi-Fi dongle can support 5 GHz network as they will help get a stronger signal. This can be verified by matching the back of the Wi-Fi dongle with the image below:


Step 2: Strength of the network
Ensure that there are enough bars in the Wi-Fi strength icon. Weaker Wi-Fi signal can cause connectivity issues.


Check if other instruments with Wi-Fi connectivity are also experiencing similar issues.

Test the Wi-Fi connectivity of the Countess instrument with a mobile hotspot. If mobile hot spot is working, then it would indicate issues with the Wi-Fi signal in the lab.

Step 3: USB port malfunction
The Countess has a front and a rear USB port. Try plugging the USB dongle to the other port and see if that resolves the issue. The USB ports are highlighted as #2 and #7 in the image.


Step 4: Thermo Fisher Cloud set up
Please ensure that the instrument is linked to a Thermo Fisher Connect account. The files will not save without a Thermo Fisher Cloud destination. Please set up an account and then try again to connect.

Step 5: Instrument country
Please make sure that the instrument is set to the correct country 'USA & Others' to save the files correctly. To check the country, go to Settings > Instrument Settings > Cloud region

Step 6: File format
Our R&D team found that when naming the files, if there is an extra space after the file name, the instrument would not be able to save the file, and an error screen will appear. Please ensure that there are no extra spaces after the file name.

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If the screen to your Countess 3/3FL Automated Cell Counter does not turn on, there could be 2 reasons for this mode of failure:

1) Power Supply malfunction: If the power supply is malfunctioning then the instrument will not receive power indicated by the blue light not turning on.

Here are some troubleshooting suggestions:
- Please ensure that there is no damage (cuts, breaks or bends) to the cord and the pins on both ends.
- Test if the power outlet is working with other functional devices.
- Purchase a new Countess™ 3 & 3 FL Power Supply (Cat. No. A48207) and see if the new power supply resolves the issue.

2) Countess hardware issue: Once the power supply being the issue is eliminated then it is likely a Countess hardware failure. In this case, the instrument will have to be sent in for repairs or replaced depending on the service contract. Please contact technical support at Technicalservices@thermofisher.com for further assistance.

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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.


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Tips for troubleshooting a failed Countess 3/3FL software update:

•     Check the exact software version numbers and make sure that a higher version number is being installed. The Countess instrument will not install a version that has a lower number.
•     Insert a USB drive containing the update file into the Countess with the unit powered on. There is a USB port on the front and back of the instrument, and either may be used. The device may take a few seconds to recognize the USB drive. Click on Settings > Software Update > USB > Next > Update. The instrument will update to the software version. Please note this may take many minutes, during which the screen may go black.
•      The USB drive must be FAT32 formatted; verify this before proceeding.
•      The update file must sit within the top level of the USB drive, not within a folder or subfolder.
•      The update file cannot be renamed in any way.
•      The update file cannot be zipped or compressed during distribution.
•      If the update fails, try resetting the instrument. Click Settings > instrument settings > reset instrument.
•      If the update fails, try power-cycling the instrument. Remove the power cable and flip the On/Off switch several times. Allow the instrument to remain powered off for 5 minutes to fully discharge the capacitors. After 5 minutes, plug the instrument back in and reboot.
•      If the above fails to correct the problem, please contact technical support at Technicalservices@thermofisher.com.

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To reset your Countess 3 Automated Cell Counter to factory settings, use the following steps:

Step 1: Open the settings menu



Step 2: Go to 'Instrument settings'



Step 3: Press 'Reset instrument' button



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If the dongle is not recognized, please restart the instrument with the dongle plugged in. This can help the instrument properly detect the dongle.

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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

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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

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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

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Yes, you can order the disposable slides without trypan blue here:

Countess Cell Counting Chamber Slide, without Trypan Blue Stain (Cat. No. C10283)

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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

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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)

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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)

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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

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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.

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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.

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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

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If your Countess 3 Automated Cell Counter freezes during operation, try power-cycling the instrument. Remove the power cable or flip the On/Off switch several times. This will discharge the capacitors fully. Allow the instrument to remain powered off for 5 minutes. After 5 minutes, plug the instrument back in and reboot. If the above fails to correct the problem, please contact technical support at Technicalservices@thermofisher.com.

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Yes. Each Countess 3 21 CFR Part 11 Software Module (Cat. No. A51025) purchase covers only one Countess instrument.

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The activation key is a file that can be downloaded from the Countess Software Downloads web page upon entering the Order ID and the instrument serial number on the prompt screen.

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With your purchase of the Countess 3 21 CFR Part 11 Software Module (Cat. No. A51025) you will receive an envelope with instructions on how to create a license key via Thermo Fisher Cloud and how to install this on your Countess 3 or 3 FL Automated Cell Counter.

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