Image-Pro "protocols" allow you to generate relational measurement data from multiple channels of images sets, or from different classes on the same image. It can be used to analyze relationships such as the number of objects contained within a parent object (for example organelles within cells), while also analyzing each of these objects. Protocols are designed to work with 2 types of data sets: 1) Multi-channel image sets and image sequences, and 2) individual images which have been grouped into image sets or sequences using Open Set from Files, Group related files or the Open as Sequence options.
The Protocols tool is located on the Count/Size tab. It can be expanded to display the selection of the pre-defined protocols.
Click on an icon to load the associated protocol. Protocols developed on other systems or saved to non-default locations can be loaded as PCH files using the Import protocol button. Advanced users can also create new protocols using the Add Protocol button. Note, that the Add Protocol button is only visible when Expert Mode is active.
When a protocol is loaded, the first panel of the Protocols wizard opens. The bottom of the panel shows how many setup steps the protocol has.
Some steps are common to one or more protocols:
- Setting Up the Document (Image, Image Set, Etc.)
- Performing Segmentation
- Configuring Results Options
Click on the topics above to learn more about each step. To learn more about the steps of a specific protocol, reference the help topic for that protocol in the navigation bar.
Running protocols in automatic mode on current location
When a protocol is complete, it can be quickly executed on the active location of the active document by deselecting the Interactive Mode option and clicking the Run on Current Location button in the dropdown:
In this mode the protocol is executed without user interaction, but all intermediate steps are shown. The protocol will stop on the Results step where you can modify, data collector types and other results options.
The dropdown also contains the Open Folder as Set of Sites button. This button can be used to open all of the images in a folder as a single image set. Each Site (frame) of the set has the name of the source image, which is displayed in the results table. This is the recommended method of processing folders of images, and is superior to opening files As Sequence, in which the file names are lost.
When the protocol has been tuned to your dataset, you can execute it in fully automatic mode. This is fast and does not require any user interaction. Click the Run Selected button to execute a protocol automatically.
The protocol is executed in parallel background threads, the number of threads in use is displayed in a balloon tooltip over the active document.
The execution progress is shown at the bottom of Protocols dialog.
On completion of protocol execution, data will be displayed in the Data Collector table and the selected protocol data windows.
Expert mode can be used by advanced users to create new and modify existing protocols.
The Expert Mode can be activated in the Application Options dialog (File – Options) on the Advanced page.