Open data files into serial sections

Purpose

Combine multiple data files into one file that includes serial sections.

Context

  • To perform serial section reconstruction, our recommendation is to create one data file per specimen, containing multiple sections. If, instead, you have separate data files for each section in a specimen (i.e., multiple data files per specimen, each containing one section), use this command to combine the files into a single file with serial sections.

  • The command can be used to create serial sections from other types of data files, but the resulting files require further manipulation in the :

    • Multiple data files from a single specimen, each containing some, but not all of the sections for the specimen.

    • Multiple data files for a specimen, each containing sections from different specimens.

Procedure

  1. Go to File > Open and click Data files into Serial Sections.

  2. In the Open File window, use the SHIFT and CTRL keys to select all files to be opened into sections and click OK.

  3. The Step 1: File Import Order dialog opens. The selected files are listed in the order that will be used for serial sections.

    • Arrange the files in the list if needed by selecting a file and clicking Move Up or Move Down.

    • Click OK to continue to the next step.

  4. The Step 2: Section Mapping dialog opens.

    1. Enter the information shown in Section Information.

    2. Indicate whether The section cut thickness should be Added or Subtracted to the Z-position of subsequent sections.

    3. Flatten All: Click to set the Z-position of all tracings in each file to the same Z-position. Alternatively, you can flatten tracings in the individual files you're opening by using the Z Level Change drop-down menu in the mapping table.

    4. Mapping table controls: The bottom half of the window contains a mapping table, with a line corresponding to each file you selected to open.

      • File Name: The original filename

      • Section Name (file): For files without defined sections, Stereo Investigator Cleared Tissue Edition generates a section called None. You can double-click the word None and type a name if desired.

      • In New Section: To assign multiple objects containing data to a single section; select a section number from the drop-down list.

      • Z Level Change: The default, Relative (default) preserve the Z location of tracings within a section.

        Use the drop-down menu to select Flatten objects to set the Z-position of all tracings in the file to the same Z-position. This may be useful if you need to generate a map for visualization purposes; all objects within the section are mapped at the same Z depth.

Stereo Investigator Cleared Tissue Edition merges previously existing sections with the same Z value into a single section. But newly generated sections are not merged with other sections, even if they have the same Z value.