See the Bigger Picture

Whole-slide images were detected, aligned, and compiled into
a full-resolution 3D volume with BrainMaker.
Blue is Nissl staining, and red, green, and yellow are
AAV-Cre dependent GFP, tdTomato, and FLAG, respectively.

With BrainMaker you can now see labeled cells and structures or view lesions throughout a true 3-dimensional reconstruction of the entire brain (or any organ). At a single glance you can see the location of all neurons expressing a particular gene, visualize axonal projections of specific neurons within the full anatomical context. 

How BrainMaker works

BrainMaker generates high-resolution 3D reconstructions from serial sections imaged with whole slide scanners and research microscopes. Load the images into BrainMaker and then direct your attention to other projects while BrainMaker automatically detects the individual sections on each slide, and then aligns the sections to create the full 3D image reconstruction.

It's fast. And it's smart. If you mount a section upside down, BrainMaker will automatically correct it during the alignment process. BrainMaker uses innovative computational algorithms to align image features found in multiple serial sections. If additional adjustments need to be made to the automatic alignment, researchers can easily edit the 3D reconstruction.

Watch an overview of how BrainMaker works

Quantitative data

BrainMaker allows you to ask bigger, broader questions. Then, dig into the questions by acquiring quantitative data about the structures of interest.  Analyze the size and shape of neurons within the 3D reconstruction using Neurolucida 360. Or analyze the number of neurons or the volume of a lesion with Stereo Investigator.

View, store and share your whole-slide images and 3D reconstructions

Reconstructions created with BrainMaker can be stored, viewed, and shared with Biolucida - our platform for organizing and sharing big image data. Never run out of storage space, or spend hours searching for an image again. And instead of publishing a 2D image of your 3D reconstruction, you can share the actual 3D reconstruction and allow others to dynamically visualize it using our free Biolucida 3D image viewer. 



BrainMaker has been developed with support from the National Institute of Mental Health (NIMH)