For working with the CAT module you need to set up an experiment in the ZEN software first. As this is already described in the ZEN Online Help, we will focus here on the most important settings which are essential for the CAT workflow:

  • In the menu Tools > Options > Acquisition > Acquisition tab the checkbox Enable Advanced Imaging Setup must be activated.
  • In the Imaging Setup tool Show All must be activated.
  • In the Imaging Setup tool Advanced Imaging Setup must be selected.
  • In the Imaging Setup tool in the light path display the following settings have to be adjusted:
    • The Microscope Manager must be excluded from all settings. To exclude a setting, click on the icon of the component/setting. You will see a menu where you can activate/deactivate the checkbox Include in this Setting. If the checkbox is not activated, the component/setting is excluded from the selected setting. Note that you have to select each Before/After setting and check if the components are excluded or included and adjust it accordingly.
    • The TL/RL Switch must be excluded from all settings.
    • All TL/RL Shutters in the light path must be included in all settings. Note that icons of included settings are highlighted in blue color.
    • All light sources (TL/RL) within the light path must be included in all settings.
    • The light intensity of the light sources for all settings must be the same (e.g. 2V).
  • In general for the Before Experiment and After Experiment settings adjust the following:
    • All Shutters must be closed.
  • Example for Phase Contrast settings:
    • For the Before TL Phase settings adjust the following:
    • - The TL Shutter must be opened.
    • - The RL Shutter must be closed.
    • For the After TL Phase adjust the following:
    • - The TL Shutter must be closed.
    • - The RL Shutter must be closed.
  • Example for one Fluorescence Channel (here DAPI) settings:
    • For the Before DAPI settings adjust the following:
    • - The TL Shutter must be closed.
    • - The RL Shutter must be opened.
    • For the After DAPI adjust the following:
    • - The TL Shutter must be closed.
    • - The RL Shutter must be closed.