How to import compensation matrix from Kaluza to Flowjo?

To import a compensation matrix created in Kaluza into FlowJo, you don't need to manually type the matrix values. FlowJo provides a straightforward way to import compensation matrices generated in other software. You can follow these steps:

Export the compensation matrix from Kaluza: In Kaluza, look for an option to export the compensation matrix. It's usually available under the compensation settings or analysis settings. Save the matrix as a file, such as a CSV or TXT file.

Open FlowJo: Launch FlowJo on your computer.

Open the sample(s) in FlowJo: Import your flow cytometry sample(s) into FlowJo, either by dragging and dropping the FCS files onto the workspace or using the File > Import menu.

Access compensation settings: In FlowJo, select the sample(s) for which you want to import the compensation matrix. Then, navigate to the Compensation tab, usually located at the top of the workspace.

Import the compensation matrix: In the Compensation tab, click on the Import button or look for an option to import a compensation matrix. This action will open a file browser.

Locate and select the compensation matrix file: Use the file browser to locate the compensation matrix file that you exported from Kaluza. Select the file and click Open or Import, depending on the specific FlowJo version.

Verify and apply the compensation matrix: After importing the matrix, FlowJo will display the matrix values for verification. Ensure that the matrix is correct and accurately represents the compensation you performed in Kaluza. If everything looks accurate, click Apply or OK to apply the compensation matrix to the selected sample(s).

FlowJo will then use the imported compensation matrix to properly compensate the fluorescence channels during analysis.

S.M.Ali Dadfar

From ChatGPT:

While FlowJo and Kaluza are both popular flow cytometry data analysis software, they have different file formats and functionalities. If you have already performed compensation in Kaluza and want to import the compensation matrix into FlowJo, there are a few options available to you. Here are a couple of alternatives that can potentially save you from manually typing the compensation matrix:

Export and Import FCS Files: Both Kaluza and FlowJo support the FCS (Flow Cytometry Standard) file format. You can export your compensated data as FCS files from Kaluza and then import them into FlowJo. This way, you won't need to manually input the compensation matrix but rather analyze the already compensated data in FlowJo directly.

Use Transformation Keywords: FlowJo allows you to use transformation keywords to apply compensation. Instead of importing a compensation matrix, you can specify the compensation directly using these keywords. The exact syntax may vary depending on the version of FlowJo you are using, so it's best to consult the FlowJo documentation or support resources for the correct syntax.

Contact FlowJo Support: FlowJo has a dedicated support team that can assist you with various technical issues, including data import. You can reach out to them and explain your situation, providing details about the compensation matrix format and ask if there are any additional methods or tools available to simplify the import process. They might have specific solutions or recommendations tailored to your situation.

Remember to keep backups of your original data and ensure compatibility between the versions of Kaluza and FlowJo you are using to minimize potential compatibility issues during data transfer.

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