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Serial Section Manager

Use the Serial Section Manager to define the key parameters (i.e., initial section thickness, current average mounted thickness, Z position, etc.) for each section before you sample from them.

The Serial Section Manager stores information about all of the sampled sections, even when performing stereological probes through volumes of interest that extend over numerous sections (e.g., Optical Fractionator for estimating cell populations).

Closed Adding new sections
  1. Click Trace >Sections>Serial Section Manager.
  2. In the Serial Section Manager window, click New section ; if no section has been defined, the program displays the Serial Section Setup window.
    1. Under Section Information, modify the values as needed, optional: Mounted Thickness (post-processing thickness).
    2. Enter the starting section number OR click Pick Random to have the program select a random section as the start.
    3. Select Added or Subtracted then click OK.

      When you focus down through a section, the depth value increases in the negative direction. For example, if sections are 10µm-thick, and the top of the section is at a depth of 0, the bottom of the section is at a depth of -10µm.

Once the first section (or series of sections) has been defined, New section automatically adds a new section to the end of the section list using the parameters previously specified in Serial Section Setup.

To add a section to the existing list of sections at a specific Z, use Insert Section.

ClosedCreating sections from contours

This is useful when you have multiple sections in one image. After outlining each section, you have the option to create serial sections based on the contours of the sections (see instructions for using Outline objects to automatically create contours).

  1. In the the Serial Section Manager window, click New section.
  2. In the Serial Section Setup window,
    1. Fill out Section Information, including section thickness.
    2. Check Place contours into serial sections.

The first serial section contains the top left section (i.e., contour) in the image. Contours are used from left to right, from top row to bottom row.

ClosedSerial Section Manager settings

Section Z

Displays the depth value associated with each section. This is usually the Z coordinate for the top of the section.

Data contained within a section is not restricted to the Z range of that particular section.

Data points placed in a section can have any Z value, but generally the data makes more sense if you restrict the Z values to those contained within the section.

Section Name

Displays the name assigned to each section; either the default name, or the name you assign.

Toolbar

New section

Adds a new section.
Insert section

Inserts a section between existing sections.

Edit section

Lets you edit the properties of the selected section.
Select by section

Selects all objects in the current section.
Show current section

Displays the currently selected section only.
Gray other sections

Displays objects not in the current section as gray

  1. Click Show current section to enable this command.
  2. Click Gray other sections.
Display flanking sections

Displays the sections immediately above and below the current section (e.g., if section 9 is active, sections 8, 9 and 10 are displayed).

  1. Click Show current section to enable this command.
  2. Click Display flanking sections.

 
Delete section

Deletes the currently selected section. The locations of the other sections are not changed with the deletion of a section.
Delete all other sections

Deletes all sections except the currently selected section.There is no Undo function for this operation.