Protocols - josalggui/MaRGE GitHub Wiki

Step-by-Step Guide to Creating a Protocol in MaRGE

MaRGE allows you to run predefined protocols, which are collections of sequences with preset parameters. Protocols help streamline and standardize your experimental workflows. Follow these steps to create and manage them:

Creating a New Protocol

  1. Click the New Protocol button
    This opens a dialog where you can enter a name for the new protocol.

  2. Save in the protocols folder

    • All protocols must be stored in the protocols directory.
    • After saving, the protocol will appear in the list under the Protocols tab.

Adding Sequences to the Protocol

  1. Select a sequence
    Navigate to the Custom tab and choose a sequence from the list.

  2. Customize sequence parameters
    Adjust the parameters to match the requirements of your protocol.

  3. Switch to the Protocol tab
    Select the protocol you want to edit.

  4. Add the sequence
    Click the Add Sequence button.

  5. Name the sequence
    Enter the name as you want it displayed in the Protocol tab.

Executing Sequences from the Protocol

  • Double-click a sequence to add it to the waiting list and execute it.

Removing Sequences from a Protocol

  • Right-click → Delete
    Right-click the sequence in the protocol and select Delete.

  • Or use the Delete Sequence button Select the sequence you want to remove.

Deleting a Protocol

  • Click the Delete Protocol button
  • In the dialog, choose the protocol you wish to delete.

Notes

  • In the current version of MaRGE, protocols use the FOV defined in the session window.
  • To run a sequence from a protocol with a custom FOV:
    1. Right-click the sequence and load its parameters.
    2. Go to the Custom tab and modify the FOV as needed.