2016 Summer Project Week/Brain atlas combining histology and MRI

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Home < 2016 Summer Project Week < Histological Brain Atlas

  • Manually segmented structures of a human brainstem superimposed on a histological slice, a block-face volume and a 11.7 MRI.

  • 3D visualization of the manually traced contours that have been used to interpolate the masks of the structures.

Key Investigators

Project Description

Multimodal 3D visualization is important during the construction of a 3D histology / MRI atlas. Also, the interface must be very intuitive so that the user can easily trace the many contours needed for a precise 3D reconstruction.

We have chosen 3D Slicer as our development platform because of its flexibility and its huge potential for multimodal 3D visualization. Our goal is to develop an integrated, intuitive extension for manual tracing of contours on stained histological slices that have been coregistered to a high resolution MRI.

Objective Approach and Plan Progress and Next Steps
  • A Slicer Extension to aid in the creation of a 3D MRI/histological atlas. Different modules in the extension are used for:
    • Contours tracing
    • Count neurons
    • Visualize the results
  • Study the available tools in modules such as "Editor", "Segment Editor" and "Segmentations" so that they can be used in our extension.
  • Create a small preview of the current histological slice (as in this image), so that the user knows where they are in the slice while zooming.
  • A prototype of the "Show unzoomed slice" widget has been developed (YouTube video). With the help of the Slicer community, it will be improved in order to be more generic and, at some point, be integrated into Slicer's Data Probe module.
  • A lot of feedback has been given to the developers of the "Segmentations" and "Segment Editor" modules. This will lead to improvements of these modules and will help us using their features.
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