Count/Size Protocol Document Setup

In the document setup step of Count/Size protocols, you use the controls on the initial panel of the Protocols wizard to define the image/image set, channel(s), and desired data collector options to be used for the multi-channel analysis. Some protocols also allow you to specify regions of interest and calibration options. The panel’s controls are described below:

Data Collector: From this pull-down list box, select the desired data collector option. Select "Show Table" to show the Data Collector table. Select "Heat Map" to show the Data Collector heat map. Select the Export to Excel to export the data using the Data Collector to Excel export option. The "Delete All" option and the "Delete Last" option delete the last measurements.

Reset: Resets the protocol to its default parameters. This can be use before starting a new protocol or to reset a protocol that is partially configured.

Clear: Clears temporary images and sets. The button can be used to clean up data in the middle of a protocol on one of the interactive steps, before the results are generated. Note, the data is also reset when a protocol is executed, and when the Finish button is clicked on the last step.

  1. Active Document: This group shows the name of the document to analyze along with the number and configuration of the locations or frames that will be processed. Note, the active range to process can be defined using the image set navigation toolbar, the plate view or the sequence toolbar.

  2. Edit names and choose channels: This group is used to assign channels to classes of objects. Click the Sync button to read channel names from the active document and populate the combo-boxes. Note that in case of single channel color images you can select color channels (Red, Green or Blue) or select Composite to process the whole color image. You can select None to exclude a class of objects from the analysis. The Edit and Delete buttons are only visible in Expert Mode (see the Expert Mode chapter for details). They can be used to edit or delete the active protocol.
    When the Interactive Mode check box is selected the step names can be edited.

  3. Calibrate: This group can be used to define a spatial calibration for the active dataset. If the dataset is calibrated, then this should be set to "Current."

  4. ROI: This group defines a Region of Interest that we be applied to the protocol. Anything outside an ROI is ignored by the protocol. An ROI can be used to exclude the info pane of SEM images (at the bottom of the image) from the analysis. A new ROI can be defined and added by clicking the Add button and cleared by clicking the Delete button.

Note: Calibration and ROI groups are optional and can be hidden if they are not required.

When all the parameters in groups 2 to 4 are set the analysis can be executed in the interactive mode (to setup the protocol), or automatically for batch processing.

Interactive Mode: Interactive Mode can be used to create new protocols or modify the parameters of existing protocols.
When channels are defined and Interactive Mode is selected, you can start to configure your protocol on the active document by clicking the Next Step button.