Connectivity assay workflow

Purpose

The connectivity assay is a second order probe used to makes estimates about the total number of connections or trabeculae. More information on connectivity in stereology is available at stereology.info.

Starting the connectivity assay workflow

1. Click the Connectivity assay workflow button on the Probes ribbon.

   If you haven't used the workflow recently, find the Connectivity assay workflow button in the Second order drop-down menu in the All Probes section of the Probes ribbon.

2. In the dialog box that opens, the following choices may be available, depending on what files, if any are currently open. Choose what you would like to do:

   • Start a new subject: Count objects on a live-camera feed from your microscope or in an image file, containing the entire region to be counted that you have already opened.
   • Load subject data from existing file: Continue working in a stored data file that is not currently open.

Workflow overview

The workflow is dynamic; your choices determine which steps are included, and what information is requested and displayed. Because of this, the step numbers you see onscreen in Stereo Investigator Cleared Tissue Edition may be different than those in the complete workflow described here.

Click any of the underlined steps to jump to the instructions:

	New workflow: Click the new workflow button to start over; the settings will revert to the defaults or those specified in the previous completed workflow.
	Previous step / Next Step: Click to advance in the workflow or revisit a previous step. Alternatively, you can click the steps listed at the top of the workflow to jump to that step.
	Click the help link to view information in the User Guide on completing the current step in the workflow.