To determine the positions of regions of interest (ROIs) within the sections, you have to define the sections. The section lines generate the reference system for the ROI positions. The sections are marked and outlined with a frame.

Note that you must mark one section on each ribbon. Meaning when your sample has three ribbons, three sections have to be marked overall.

We recommend using phase contrast images for the section specification. The algorithm used for the automatic section specification is most reliable when using phase contrast images. When bright field images are used, the algorithm might be suboptimal. In that case you have the opportunity to add and to move the section contours manually.

On the Section Definition tab you will find tools and options for creating sections in the image.

Parameter

Description

Reference Section

-

Select

Activates the selection mode (default).

-

Contour

By selecting this mode, you can mark a contour line of a section.

-

Keep

Keeps the selected tool active. You can then use the tool several times without interruption.

-

Step Backward

Undo the last step

-

Step Forward

Repeats the last step.

-

Delete

Deletes a selected graphical element.

Section Index

Here you can determine the starting number of the ribbons. This is important when the ribbons of a sample are deposited on more than one sample carrier.

Selected Channel

Shows the selected channel which is used for the detection.

Detection Sensitivity

Here you can adjust the detection sensitivity from Low to High by using the slider.

This will be done by modifying the contrast thresholds for the section detection algorithm.

When setting a low sensitivity, sections will be recognized even if the contrast between the section and the substrate is low; disadvantage: sections will be recognized, even in areas where no serial sections are deposited.

When setting a high sensitivity, the algorithm only recognizes sections, if there is a high contrast between section and substrate. If not, all sections were recognized, you have the possibility to copy section contours or to stamp section contours.

Section Detection

-

Apply

Starts the section detection on the sample. The software tries to detect each section within the ribbon.

Contrast Method

-

Auto

Auto is used by default. The system recognizes the contrast method of the image automatically.

-

Ph. Contrast

Applies the phase contrast method. Even if you are using a brightfield image, phase contrast will be applied as contrast method.

-

Brigthfield

Applies the brightfield contrast method. Even if you are using a phase contrast image, brightfield will be applied as contrast method.

Use Internal Structure

Activate this checkbox only when sample structures are clearly visible within the sections.

If activated, sample structures are used for section detection, additional to contrast differences between sections and substrate.

In case that sections are not detected properly, you have the possibility either to stamp section contours or to copy section contours.

Post Definitions

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Stamp tool

By selecting this tool, you can stamp in undetected sections after the section detection is finished.

Therefore simply select the tool and move the mouse cursor in the area nearby the last detected section. The cursor will change to a stamp icon and you will be able to stamp in the missing section contours.

-

Accept Ref. Section

If you click on this button, reference contours will transform into section contours.

When the section detection is finished, you have different options for sorting the sections according to your needs, if necessary. Therefore right-click on the detected sections. You will see a context menu with the following sorting options:

Parameter

Description

Sort
  • Sort all sections in reverse order
    Sorts all sections which have a section contour. The initial section with number 1 becomes the last section, the last section becomes the first section with the number 1
  • Sort selected Ribbon elements in reverse order
    Sorts the selected sections on a ribbon. The initial section with number 1 becomes the last section, the last section becomes the first section with the number 1

Copy selected sections from here

Copies the selected sections.

Copy selected Ribbon sections from here

Copies all section contours on the selected ribbon.

Paste Section(s) to here

Pastes the section contours (selection of certain section contours or all sections of a ribbon) to the selected position.

Exchange numbering of selected Ribbon sections

Exchanges the numbering of selected sections on different ribbons.

Highlight Related Ribbon Sections

Highlights selected sections on a ribbon.

Merge two Ribbon Sections

Merges sections on two different ribbons to one.