CAT Tool

Using this tool you can calibrate and manage the sample holders and start the wizards which are used for acquiring images from serial sections, generating Z-stack images out of the single images and correlate two Z-Stack images from the light microscope (LM) and the scanning electron microscope (SEM).

Parameter	Description
Sample Name	Displays the name of the sample.
Select/Specify...	Opens the Select Sample Dialog. There you can select a sample data sheet from the list or specify a new sample with user specific information. The specified sample information will be used for image processing (i.e. Z-Stack alignment) or for data management.
Sample Holder	Displays the name of the selected sample holder.
Select...	Opens the Select Template dialog. There you select the preferred sample holder or define new holder templates, see Selecting the sample holder.
Calibrate...	Opens the Sample Holder Calibration Wizard. There you can calibrate the selected sample holder.
Apply to Image	Only visible if the Show All mode is activated. Use this button only when you forgot to calibrate the holder before you acquire the image. Applies a calibration to an acquired image. Do not remove the sample from the correlative holder between image acquisition and calibration. Exception: correlative markers are on the sample holder.
Start Acquisition Wizard	Starts the Acquisition Wizard. For more information see Acquisition Wizard.
Start Z-Stack Alignment Wizard	Starts the Z-Stack Alignment Wizard. For more information, see Z-Stack Alignment Wizard.
Start Correlation Wizard	Starts the Correlation Wizard. For more information, see Correlation Wizard.

Select Sample Dialog

Here you can select or create a sample data sheet.

Parameter	Description
Folder	Shows the location, where the files are saved. If you click on the button, you can change the storage location. The default path and folder is C:\Users\user\Pictures\CAT Samples. Within this folder, each sample is saved in a sub-folder. Images taken during image acquisition within the CAT Acquisition Wizard will be saved within the sub-folder automatically. For a better clarity sub-folders with the name „[Date][Time]“ will be generated when another CAT run is started within the CAT acquisition wizard. In case the file name will exceed a certain number of characters the name will be shortened using the sign „°“.
List of specified samples	Shows the samples which are already specified within the software. If you select a sample in the list and click OK, the sample will be used in your experiment. If you click on the button, the New Sample dialog opens. There you can create a new sample definition which will be added to the list, see Creating a New Sample. If you click on the Options button, you will see further options for managing samples like Show/Edit or Refresh Sample List.
Information	Shows the specified sample information, e.g. name, description, number of sample carriers, sample carrier, and section thickness.

Parameter

Description

Folder

Shows the location, where the files are saved.

If you click on the Dark rounded square button with three white horizontal dots button, you can change the storage location. The default path and folder is
C:\Users\user\Pictures\CAT Samples.

Within this folder, each sample is saved in a sub-folder. Images taken during image acquisition within the CAT Acquisition Wizard will be saved within the sub-folder automatically.

For a better clarity sub-folders with the name „[Date][Time]“ will be generated when another CAT run is started within the CAT acquisition wizard. In case the file name will exceed a certain number of characters the name will be shortened using the sign „°“.

List of specified samples

Shows the samples which are already specified within the software.

If you select a sample in the list and click OK, the sample will be used in your experiment.

If you click on the White plus sign centered on dark blue rounded-square icon button, the New Sample dialog opens. There you can create a new sample definition which will be added to the list, see Creating a New Sample.

If you click on the Options button, you will see further options for managing samples like Show/Edit or Refresh Sample List.

Information

Shows the specified sample information, e.g. name, description, number of sample carriers, sample carrier, and section thickness.

CAT Tool

Select Sample Dialog

See also

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