Keep your Countess instrument functioning with the latest improvements and features by downloading the latest software.
Select from these available software downloads appropriate for your instrument.
Software updates
Since the original release of Countess 3 and Countess 3 FL instruments, continual innovations have been made to the instrument software. Below are the updates since release that keep your instrument functioning at peak performance.
- Accuracy—highly accurate machine-learning algorithm applied to cell counting in brightfield and fluorescence modes, enabling single cell workflows and nuclei counting
- Precision—autolighting and autofocus minimize user inputs and variability
- Manages cell clumping and debris—automatically exclude debris from cell counts and advanced algorithms can clearly identify cell boundaries within cell clumps, resulting in highly accurate cell counts
- Reports cluster analysis—identify singlets within cell clumps and detect these cell clusters to further measure the total percent aggregation within a sample
- Increased counting speed—optimization of image analysis algorithm increases count speed
- LAN saving capabilities—in addition to cloud and USB drive saving capabilities
- Scatter plot visualization—visualize post-count populations using scatter plots and histograms
- Self-service IQ/OQ—qualify your instrument operation when it is convenient for you
- Improved cell identification—increased contrast of contours outlining counted cells
- FCS file—updates to the FCS file enable greater usability of post-count analysis via third party software
- Optimized lighting settings—improved brightfield and fluorescence counting performance with the use of the updated EVOS 2.0 light cubes in the Countess 3 FL instrument
- Expanded profile function—Allows customer to include preferred dilution settings to a customized profile
- 21 CFR part 11—software enabling compliance support (purchase of license required to activate Countess SAE Software Solution for 21 CFR Part 11 Compliance Support)
Countess 3/3 FL software download instructions
Review the installation instructions before updating the software.
Download instructions:
- Download the latest version of the Countess 3/3 FL software to a computer.
- Copy the "SetupCountess3_1.4.1625.619" file to a USB drive.
- 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).
- Press the Setting icon in the lower right corner of the home screen. (Figure 1)
- Select "Software Update" from the instrument Settings menu. (Figure 2)
- Select the update location (USB or Cloud) and click Next.
- Select the "Update" button. (Figure 3) The update process should only take a minute or two.
- The instrument will automatically restart and the screen will show when the update is complete. (Figure 4)
Figure 1. Home screen with the Settings link in the bottom right corner.
Figure 2. Settings menu with Software update link.
Figure 3. Software update available screen.
Figure 4. Updating screen prior to the restart and update complete screen.
Register your Countess Automated Cell Counter
Registering your Countess instrument ensures that you will receive important notifications, including those for new software upgrades.
Software component files and general instructions
To implement the Countess SAE Software Solution to support the technical 21 CFR Part 11 compliance portion on the Countess 3 and Countess 3 FL Automated Cell Counters, the following components need to be installed, activated, and communicating with each other.
The Countess SAE Software Solution for 21 CFR Part 11 Compliance Support consists of:
- SAE Software—used to configure the Security, Audit and Electronic-signature settings for Countess Automated Cell Counter. SAE software consists of:
- the SAE Administrator Console (installed on a server with a static IP address)
- the Countess SAE Application Profile.
- SAE License—Used to activate the SAE settings for the Countess Automated Cell Counter
- SAE Mode—Countess Automated Cell Counter software that is remotely connected with the SAE Administrator Console and activated using the SAE License Key File
For more details on these components, please refer to our Countess SAE Software Solution for 21 CFR Part 11 Support
SAE software
To download the SAE Administrator Console Software and the Countess Application profile, please click the relevant download buttons below. Release notes are also available for the SAE Administrator Console Software
IMPORTANT: The SAE Administrator Console Software only needs to be downloaded by the personnel who manages the security, audit, and e-signature procedures within the institution. The Countess Application Profile should also be downloaded only by the personnel who will utilize the SAE Administrator Console software.
SAE license
A Countess SAE License MUST be purchased to obtain a license key file that will enable the SAE Mode on the Countess 3/3 FL instrument. Visit the product page or contact your Thermo Fisher Scientific sales representative for more information.
License for Countess SAE Software Solution for 21 CFR Part 11 Compliance Support
Instructions to download License Key Files
- Go to apps.thermofisher.com
- Sign in
- Open the Countess Image Analysis App from the My Apps section on the homepage
Figure 1. Countess Image Analysis App displayed on My Apps homepage.
Note: If the Countess app has not been opened before and it is not displayed on the Home page, click View All Apps and locate the Countess app from the list of apps
Figure 2. Countess Image Analysis App displayed on the View All Apps page.
- Click on the SAE Activation link in the top-right corner of the page
Figure 3. Location of the SAE Activation link in the Countess Image Analysis app.
- Enter the Order ID and Countess 3 Serial Number into the appropriate fields Select Get activation file.
You will see a "Request Submitted" message when the order information has been validated
- Once the file is ready, you will see a "Download is Ready" notification in the top-right corner. Click on the notification and select Download.zip to begin the license key file download to your computer.
- Proceed with the activation process as detailed in the SAE Admin Console User Guide.
SAE mode
The SAE Admin Console software allows 21 CFR Part 11 support through enablement of the SAE Mode setting on the Countess instrument.
Refer to the Countess SAE Software Solution for 21 CFR Part 11 Compliance Support User Guide for further instructions to enable SAE mode on the Countess 3/3 FL cell counter.
Register your Countess Automated Cell Counter
Registering your Countess instrument ensures that you will receive important notifications, including those for new software upgrades.
Software update benefits
Your updated Countess II or Countess II FL instrument will have these added benefits:
- Dilution calculator—new built-in dilution calculator displays volume of cell sample and buffer needed (Figure 1)
- Report—save a printer-friendly PDF report of the results, graph(s), and image (Figure 2)
- Simplified workflow—easily save protocols from the adjustments screen
- Modified profile indicator—see when the gating settings for the displayed profile have been modified
- Expanded profile options—pre-dilution correction factor of 1:1 dilution ratio of cell sample to stain for fluorescence counting
Figure 1. Convenient built-in dilution calculator to prepare cells for next steps in experimentation or for splitting.
Figure 2. PDF report with data, histograms, and images.
Countess II/II FL software download and instructions
Review the installation instructions before updating your software.
Download instructions
- Download the latest Countess II/II FL software version to your desktop.
- Copy the "countess_update_1_0_251.lft" file to a USB drive, then insert the USB drive into the Countess II/II FL instrument. (Ensure the .lft update is not hidden within a folder on the USB, as this will prevent a successful update).
- Press the Settings icon in the upper right corner of the home screen. (Figure 3)
- Select "Software Update" from the Instrument Settings menu. (Figure 4)
- Select the "Update Now" icon. (Figure 5)
- Once the update has completed, restart the instrument. (Figure 6)
Figure 3. The settings icon is located on home screen.
Figure 4. Software Update is located on the Instrument Settings menu.
Figure 5. When ready to update the software, select Update Now.
Figure 6. Restart the instrument to complete the update.
Register your Countess Automated Cell Counter
Registering your Countess instrument ensures that you will receive important notifications, including those for new software upgrades.
Original Countess software download
Software updates
Since the original release of Countess 3 and Countess 3 FL instruments, continual innovations have been made to the instrument software. Below are the updates since release that keep your instrument functioning at peak performance.
- Accuracy—highly accurate machine-learning algorithm applied to cell counting in brightfield and fluorescence modes, enabling single cell workflows and nuclei counting
- Precision—autolighting and autofocus minimize user inputs and variability
- Manages cell clumping and debris—automatically exclude debris from cell counts and advanced algorithms can clearly identify cell boundaries within cell clumps, resulting in highly accurate cell counts
- Reports cluster analysis—identify singlets within cell clumps and detect these cell clusters to further measure the total percent aggregation within a sample
- Increased counting speed—optimization of image analysis algorithm increases count speed
- LAN saving capabilities—in addition to cloud and USB drive saving capabilities
- Scatter plot visualization—visualize post-count populations using scatter plots and histograms
- Self-service IQ/OQ—qualify your instrument operation when it is convenient for you
- Improved cell identification—increased contrast of contours outlining counted cells
- FCS file—updates to the FCS file enable greater usability of post-count analysis via third party software
- Optimized lighting settings—improved brightfield and fluorescence counting performance with the use of the updated EVOS 2.0 light cubes in the Countess 3 FL instrument
- Expanded profile function—Allows customer to include preferred dilution settings to a customized profile
- 21 CFR part 11—software enabling compliance support (purchase of license required to activate Countess SAE Software Solution for 21 CFR Part 11 Compliance Support)
Countess 3/3 FL software download instructions
Review the installation instructions before updating the software.
Download instructions:
- Download the latest version of the Countess 3/3 FL software to a computer.
- Copy the "SetupCountess3_1.4.1625.619" file to a USB drive.
- 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).
- Press the Setting icon in the lower right corner of the home screen. (Figure 1)
- Select "Software Update" from the instrument Settings menu. (Figure 2)
- Select the update location (USB or Cloud) and click Next.
- Select the "Update" button. (Figure 3) The update process should only take a minute or two.
- The instrument will automatically restart and the screen will show when the update is complete. (Figure 4)
Figure 1. Home screen with the Settings link in the bottom right corner.
Figure 2. Settings menu with Software update link.
Figure 3. Software update available screen.
Figure 4. Updating screen prior to the restart and update complete screen.
Register your Countess Automated Cell Counter
Registering your Countess instrument ensures that you will receive important notifications, including those for new software upgrades.
Software component files and general instructions
To implement the Countess SAE Software Solution to support the technical 21 CFR Part 11 compliance portion on the Countess 3 and Countess 3 FL Automated Cell Counters, the following components need to be installed, activated, and communicating with each other.
The Countess SAE Software Solution for 21 CFR Part 11 Compliance Support consists of:
- SAE Software—used to configure the Security, Audit and Electronic-signature settings for Countess Automated Cell Counter. SAE software consists of:
- the SAE Administrator Console (installed on a server with a static IP address)
- the Countess SAE Application Profile.
- SAE License—Used to activate the SAE settings for the Countess Automated Cell Counter
- SAE Mode—Countess Automated Cell Counter software that is remotely connected with the SAE Administrator Console and activated using the SAE License Key File
For more details on these components, please refer to our Countess SAE Software Solution for 21 CFR Part 11 Support
SAE software
To download the SAE Administrator Console Software and the Countess Application profile, please click the relevant download buttons below. Release notes are also available for the SAE Administrator Console Software
IMPORTANT: The SAE Administrator Console Software only needs to be downloaded by the personnel who manages the security, audit, and e-signature procedures within the institution. The Countess Application Profile should also be downloaded only by the personnel who will utilize the SAE Administrator Console software.
SAE license
A Countess SAE License MUST be purchased to obtain a license key file that will enable the SAE Mode on the Countess 3/3 FL instrument. Visit the product page or contact your Thermo Fisher Scientific sales representative for more information.
License for Countess SAE Software Solution for 21 CFR Part 11 Compliance Support
Instructions to download License Key Files
- Go to apps.thermofisher.com
- Sign in
- Open the Countess Image Analysis App from the My Apps section on the homepage
Figure 1. Countess Image Analysis App displayed on My Apps homepage.
Note: If the Countess app has not been opened before and it is not displayed on the Home page, click View All Apps and locate the Countess app from the list of apps
Figure 2. Countess Image Analysis App displayed on the View All Apps page.
- Click on the SAE Activation link in the top-right corner of the page
Figure 3. Location of the SAE Activation link in the Countess Image Analysis app.
- Enter the Order ID and Countess 3 Serial Number into the appropriate fields Select Get activation file.
You will see a "Request Submitted" message when the order information has been validated
- Once the file is ready, you will see a "Download is Ready" notification in the top-right corner. Click on the notification and select Download.zip to begin the license key file download to your computer.
- Proceed with the activation process as detailed in the SAE Admin Console User Guide.
SAE mode
The SAE Admin Console software allows 21 CFR Part 11 support through enablement of the SAE Mode setting on the Countess instrument.
Refer to the Countess SAE Software Solution for 21 CFR Part 11 Compliance Support User Guide for further instructions to enable SAE mode on the Countess 3/3 FL cell counter.
Register your Countess Automated Cell Counter
Registering your Countess instrument ensures that you will receive important notifications, including those for new software upgrades.
Software update benefits
Your updated Countess II or Countess II FL instrument will have these added benefits:
- Dilution calculator—new built-in dilution calculator displays volume of cell sample and buffer needed (Figure 1)
- Report—save a printer-friendly PDF report of the results, graph(s), and image (Figure 2)
- Simplified workflow—easily save protocols from the adjustments screen
- Modified profile indicator—see when the gating settings for the displayed profile have been modified
- Expanded profile options—pre-dilution correction factor of 1:1 dilution ratio of cell sample to stain for fluorescence counting
Figure 1. Convenient built-in dilution calculator to prepare cells for next steps in experimentation or for splitting.
Figure 2. PDF report with data, histograms, and images.
Countess II/II FL software download and instructions
Review the installation instructions before updating your software.
Download instructions
- Download the latest Countess II/II FL software version to your desktop.
- Copy the "countess_update_1_0_251.lft" file to a USB drive, then insert the USB drive into the Countess II/II FL instrument. (Ensure the .lft update is not hidden within a folder on the USB, as this will prevent a successful update).
- Press the Settings icon in the upper right corner of the home screen. (Figure 3)
- Select "Software Update" from the Instrument Settings menu. (Figure 4)
- Select the "Update Now" icon. (Figure 5)
- Once the update has completed, restart the instrument. (Figure 6)
Figure 3. The settings icon is located on home screen.
Figure 4. Software Update is located on the Instrument Settings menu.
Figure 5. When ready to update the software, select Update Now.
Figure 6. Restart the instrument to complete the update.
Register your Countess Automated Cell Counter
Registering your Countess instrument ensures that you will receive important notifications, including those for new software upgrades.
Original Countess software download
For Research Use Only. Not for use in diagnostic procedures.