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NeuroScience Associates

NSA MultiBrain Minute Newsletters > 2017 Fall Newsletter

Digitization/Image Analysis: 3D Reconstruction

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 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).

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 below, 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.

Learn more about NSA’s 3D reconstruction and digital imaging services


NSA MultiBrain Minute Newsletters > 2017 Fall Newsletter

COVID-19 IMPACT: Our labs are currently OPEN for business. We are fully operational with uninterrupted delivery services ready to receive your tissue.


For clients with projects in process: NSA will communicate with you prior to shipping materials to ensure you are able to accept deliveries. If you are unable to receive deliveries due to the current global situation, NSA will hold shipments at our facility until your delivery system returns to normal. If you have not added digital imaging to your order but need it to expedite or continue your research, contact us right away so we can work together to meet your needs.

For clients with tissues, sections and/or slides located at our facility: Please allow us to help you continue your research, particularly if you are working remotely. We are able to perform additional stains, digitize slides for secure remote viewing, and perform additional analysis. Contact us today via email at or using our contact form.

For new clients: We are ready to assist you with all of your neurohistology needs. We are open and fully operational with uninterrupted delivery services ready to receive your tissue.. This is a dynamic situation and we will update this message as things change.

NSA strives to minimize the impact of this global situation on your research and the neuroscience community as a whole. We wish you and yours the best as we maneuver through uncharted waters. Please contact us if we can assist you in any way.