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Assemble Serial Sections Workflow overview

Purpose and image-file requirements

The Assemble Serial Sections 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 > Assemble Serial Sections.
  • 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.

Image-file requirements

  • The Assemble Serial Sections workflow is compatible with single-plane image files. Image stacks cannot be used.

  • The workflow is compatible with many file types. If, however, your image files will not load into the workflow, use our free tool MicroFile+ to convert your images to a format such as jpeg 2000 (.jp2) that is compatible.

  • Do not perform this operation over a LAN, bring the slide image files onto the hard drive of the computer that you use to run NeuroInfo software.

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 Assemble Serial Sections workflow 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.