Creating a new Protocol

Note: New Protocols can be added if you are own any protocol collection license.

To add a new protocol.

  1. Ensure that Expert Mode is enabled.

    File > Options

  2. From the Count/Size Ribbon, open the Protocol Browser.

  3. Click New.

    The New Protocol dialog opens

  4. Enter a name for the new protocol in the Protocol Name field.

  5. Make a selection from Collection drop down menu. You can choose from any collection for which you are licensed.

  6. Complete the Description field. This will be displayed in the Protocol Browser.

  7. Enter a Version name.

  8. Complete the Version Description field. This will displayed in the Protocol Browser when the version is selected in the Protocol’s drop-down menu of versions.

  9. If you have generated documentation (in the form of a PDF document) to help your colleagues run the protocol, you can embed it into your protocol (optional).

    1. Click the documentation ... button

    2. The Select documentation dialog opens.

    3. Navigate to and select your PDF document.

    4. Click Open.

    Note: Users of your protocol can access embedded documentation by clicking the Help button from the Protocol Panel.

  10. If you want to include a demonstration image that your colleagues can load to practice using the protocol, you can add the path to the image in the Demo Image field (optional).

    1. Click the Demo Image ... button.

    2. The Select demo Image dialog opens.

    3. Navigate to and select your demo image.

    4. Click Open.

    Note: Users of your protocol can open the demo image from the Protocol Panel by selecting the Reset drop down menu and clicking Load Demo with the Open Demo Image check box selected.

  11. Click the Tags button and select from the pre-defined tags, or from your own novel tags (optional).

  12. Define the Number of Child Channels (from 1 to 100) in the protocol.

  13. Make the appropriate selections from the Parent and Seed check boxes.

    A Seed channel contains objects that can be used to separate objects in the Parent channel. Each parent is assigned a single seed. If a Seed channel is set to none, Parents objects seeds are ignored.

    A Child channel contain objects that are expected to be localized within Parents. The relationship of children to parents (such as the number of children per parent, or the mean intensity of children per parent) can be analyzed by the protocol.

  14. Define the Title and Default Dye for every step in the protocol.

    If several steps are going to use the same channel, they can be grouped by selecting table rows and clicking the Create Group button. Grouping steps simplifies the execution of protocols by avoiding the need to set the same channel for multiple steps.

    The Group Name can be set and will be displayed on the protocol’s setup page.

  15. Set the Default Segmentation Method (Threshold, Smart, AI Deep Learning or None) to be automatically selected when the protocol is configured for first time in Interactive Mode. The segmentation method can be changed from the default during setup.

  16. Make the appropriate selection from the Show Calibration and Show ROI check boxes to determine whether these controls will be visible on the protocol’s setup page. When the controls are hidden, the current image calibration will be used, and no ROI is applied to the image set.

  17. Select the controls that will be available to the protocol from the Options group. The visible controls can be customized per step of the protocol using the Options button on each step of the protocol.

  18. Click Ok to create and activate the new protocol in the Protocol dialog.

    Count/Size Protocol Document Setup

 

Learn more about all features in Count/Size