Create Data Structure with ImageJ/Fiji macros

Follow this steps to create the required data structure from the raw microscopy files using the provided Fiji macros:

  1. If you don’t have it, install ImageJ/Fiji from here Fiji Downloads.

  2. Download the Fiji macros from here Cell-ACDC Fiji macros.

  3. Open the macro with Fiji:

    If you have one or more microscopy files one for each position use the macro called multiple_files.ijm, while if you have multiple positions within a single file use the single_file.ijm macro.

  4. Modify the list of channels:

    In the first lines of the macro you will find the variable channels defined as follows:

    channels = newArray("phase_contr", "mCitrine");

    Modify that list with the correct order of channels as they are found in your microscopy file(s).

  5. Run the macro with the Run --> Run menu

  6. If you are using single_file.ijm select the microscopy file, if not select the folder containing the microscopy file(s).

If successful, at the end of the process you should have all the Position folders correctly generated and ready to be opened in Cell-ACDC.

If you are having issues, feel free to open an issue on our GitHub page.

Until next time!