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NeuroScience Associates

 3D Reconstructions

While volume calculation can provide a quantitative endpoint to researchers, having a 3-dimensional volume or surface map rendering of the same tissue that accompanies this data can offer visualization that otherwise might be difficult to picture.  This is especially helpful for viewing and comparing smaller portions of tissue in relation to the whole specimen (entire brain or hemisphere), such as tumor or lesion volume reconstructions or renderings of structures within the brain.

Block-face images (shown as an abbreviated series below) are taken during the sectioning process.  These images are combined to create a 3D volume rendering of the tissue that can be digitally sliced in any plane (coronal, sagittal, and horizontal shown below).

Block-Face Stack

Block-Face Stack



Myelin Stain

Myelin Stain

In addition to reconstructing tissue from block-face images, stained tissue can also be used to create volume renderings.  Stained tissue reconstructions require a higher than normal frequency of staining in order to render a volume with enough resolution for identifying regions of interest.

In the example shown to the right, coronal, sagittal, and horizontal planes for block-face images as well as Weil-Myelin stained tissue of the same grizzly bear brain are shown.  The images at the bottom of each column represent volume renderings of the respective column of images.

By using the block-face images as a template, the Weil-Myelin stained tissue can be matched to corresponding block-face images  using linear and non-linear transformations.  This transformed stack of images can then be rendered as its own volume.

3D Reconstruction Services

Below, we show examples of a surface map and a modeling video.


Demo: Pig brain surface map



Demo: Grizzly bear 3D modeling video

The video below shows a volume rendering of a grizzly bear brain. After sectioning of the brain in the coronal plane and completion of the reconstruction, all three planes (coronal, sagittal, and horizontal) can be viewed.

Reconstructions performed by Tate York, NSA Image Analyst


Common Questions:

How are they made?

Images of the block face are photographed during the sectioning process at a high frequency. These images are compiled into an image stack, aligned, and rendered into a 3D volume as well as a 3D surface map.


What are the benefits?

3D rendered volumes can be cut at any axis (coronal, sagittal, horizontal, or oblique) so multiple views of the tissue can be seen. Specific structures can be segmented from the entire brain and viewed as its own rendered volume or surface map.

Viewing surface maps will allow the viewer to see the brain as a shell with secondary segmented structures visible inside. These secondary segmentations can include anatomical structures, lesions, or certain neuronal populations. Adjustments to the image stacks can be made using a variety of filters, such as thresholding, which can reveal even more information about the tissue in these interactive 3D renderings.

How much does it cost?

Pricing starts at just $2000 per MultiBrain® or MultiCord® block, which includes up to 40 mouse brain hemispheres, 25 mouse brains, 16 rat brains, 1 monkey brain, and a variety of spinal cord and brain configurations.