Go to step 1 Go to step 2 Go to step 3 Go to step 4 Go to step 5 Go to step 6

Serial Section Assembler overview

(formerly the BrainMaker workflow)

Purpose

The Serial Section Assembler (formerly the BrainMaker workflow) generates high-resolution 3D volume reconstructions from serial sections imaged with whole slide scanners and research microscopes. The workflow employs innovative computational algorithms to automatically detect the individual sections on each slide and align them to create the full 3D brain reconstruction.

  • To open the workflow, go to Registration > Serial Section Assembler.
  • The workflow window displays a list of the steps in the workflow, with settings and information specific to the step selected.
  • To return to a previous step, click the Previous step / Next Step buttons or the name of the step.
  • Save your work at any time as a Case file. To continue at a later time, open your case file and keep working.

Before You Start

Image-file requirements

  • The Serial Section Assembler is compatible with single-plane image files. Image stacks cannot be used.

  • Do not use the Serial Section Assembler over a LAN, bring the slide image files onto the hard drive of the computer that you use to run NeuroInfo software before you start the workflow.

  • The workflow is compatible with many file types. We recommend, however, that you convert your image files to jpeg 2000 (.jp2) format using our free MicroFile+ tool.

    If you have any trouble loading your images into the workflow or see unexpected results while using the workflow, your first troubleshooting step should be to convert your images to jpeg 2000 (.jp2) format using MicroFile+.

Adjust images to emphasize structure and orientation information

Use the histogram controls in the Image Adjustment panel to maximize visibility of the color channel(s) that display(s) architectural and/or orientation-related information about the tissue; this will facilitate assembly of the images into a 3D reconstruction. If there are color channels in the images that are not relevant for assembly, minimize display of those color channels.

  • Click the Adjust button on the Image or Workspace ribbon to open the Image Adjustment panel.

  • In the color channels with information that is useful rag the white point in the histogram Use the

Workflow overview

Click on any step in the workflow-overview diagram below to jump to the page that describes the step.

Commands available in every step of the workflow:

Previous step / Next Step: Click to advance in the workflow or revisit a previous step. Alternatively, you can click a step in the list at the top of the workflow to jump to that step.
Click the help link to view information in the User Guide on completing the current step in the workflow.

Save your work as a case file

You can save your work in the Serial Section Assembler and resume later by saving your Case File before closing NeuroInfo software and opening the case file to resume work later.

  • To save your work: Go to File > Save As and choose Case file.

    In the Save Case file name as? window that opens, navigate to your desired location on the local computer and type in a file name, then click Save.

  • To continue working: Go to File > Open and choose Case file.

    In the Case file name to open? window, navigate to and select the file, then click Open.