Working with missing sections

See BrainMaker Workflow overview

You noticed that some of the tissue sections were unusable/missing from the slides. So you re-imaged the slides with missing sections to create replacement sections. To integrate the replacement sections into the reconstruction, follow this procedure (instructions below are for one missing/unusable section):

1. In step 1, select the original files and the files with the re-imaged data. The files with the re-imaged data must be placed at the end of the list.
2. In step 2 under Slides for missing sections, enter the number of slides containing replacement sections.

The number of slides to be used for the reconstruction is automatically updated.

3. In step 3, review the slides.
   1. When you reach the slide with an unusable section, click it to select its outline and press Delete to remove the outline.
   2. Click the Add button and select Placeholder for a missing section.
   3. Click once over the unusable section to place the placeholder.
   4. Click the Start Ordering button.
   5. Continue reviewing the slides until you reach the slide with the replacement section.
   6. Delete the outlines that are not needed for the reconstruction; keep the replacement section outlined.
   7. Click Start Ordering.
   8. Finish reviewing the slides and go to the next step.

   For more than one missing/unusable section, keep track of the location of the missing sections and of their corresponding replacement sections for step 4.

4. In step 4, click Modify Final Section Order.
   1. Select the replacement section in the list (labeled Substitute) and drag it over the section to be replaced (labeled Missing).
   2. Highlight the Missing section you are replacing and click the Delete button.