Creating a new Protocol

New Count/Size "protocols" can be created by clicking the Add Protocol button on the Count/Size ribbon. When you click on the Add Protocol button, the New Protocol dialog opens:

You can Name of the protocol, specify the Version and add a Description. Click on the Icon button if you wish to select an image file to use as the protocol’s icon (the preferred size is 64x64 pixels, 32-bit RGBA format). You can select a PDF Documentation file; this can be selected by users of the protocol from the protocol’s tooltip.

You must define the Number of Child channels (from 1 to 100) in the protocol, and whether the protocol requires Parent and Seed channels.

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

Child channels 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.  

You must define 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. If 2 channels are going to be used with Colocalization, the Colocalization group checkbox must be checked.

The Default Segmentation Method (Threshold, Smart or None) will 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.

The Show Calibration and Show ROI options determine whether the corresponding 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.

Selections made in the Options group determine which controls will be shown on the segmentation steps of the protocol (see Count/Size Protocol Segmentation for more details). The visible controls can be customized per every step independently using the Options button on each step in Expert Mode.

Clicking the Ok button will create and activate the new protocol in the Protocol dialog, at which point it can be setup with your data (see Count/Size Protocol Document Setup).