Whole Brain Analysis

Fields Of Study
MBF Bioscience > Whole Brain Analysis


Whole brain analysis consists of analytical and graphical methods to study the anatomy and function of the brain and spinal cord in combination with the use of imaging, immunohistochemistry, molecular & optogenetics, stem cell and cellular biology, engineering, neurophysiology and nanotechnology. Whole brain analysis techniques are constantly evolving, and rely on the development and refinement of microscopic and tomographic image acquisition, representation, analysis, visualization and interpretation techniques. 


MBF Bioscience has been a pioneer and leader in the field of whole brain analysis and neuroimaging since the invention by MBF Bioscience co-founder, Dr. Edmund Glaser, of the image combining computer microscope. MBF Bioscience continues the tradition of innovation by working collaboratively with scientists in research institutions around the world, including the National Institutes of Mental Health (NIMH), RIKEN, and the Allen Institute for Brain Research to develop and refine new whole brain analysis and neuroimaging techniques.


The locations and distribution of cell types in the brain, can be analyzed with NeurolucidaNeuroInfo, and BrainMaker. Researchers can map the distributions of a particular cell type, like those producing parvalbumin for example, and obtain analyses such as the nearest neighbor analysis to determine the distance from one cell to another or the distance from the cells to an anatomical boundary. 

Neuronal Mapping

Mapping a neuron’s arborizations and its projections can be accomplished with Neurolucida and Neurolucida 360. Trace a neuron through multiple serial sections to its projection field, and then analyze its path through various brain regions. 

Whole-Brain Reconstruction, Annotation, and Registration

Recent advances in molecular neuroanatomical tools have expanded the ability to map connections of specific neuron subtypes in the context of behaviorally driven patterns of neuronal activity. Analysis of such data across the whole mouse brain, registered to a reference atlas, aids in understanding the functional organization of brain circuits related to behavior. NeuroInfo works on mouse brain sections labeled with standard histochemical techniques, reconstructs those images into a whole brain image volume and registers those images to the Allen Mouse Brain Atlas. Image detection of cells and quantification of axon density labeling are then combined with the structures in the annotated reference atlas. Examples of these analyses include mapping the axonal projections of layer‐specific cortical neurons using Cre‐dependent AAV vectors and for mapping inputs to such neurons using retrograde transsynaptic tracing with modified rabies viral vectors.

Serial Section Reconstruction

BrainMaker and NeuroInfo can generate 3D image reconstructions of an entire brain from whole slide images of serial sections so that you can easily view cells, structures and lesions. With just a glance, you can see the location of all neurons expressing a particular gene, visualize the axonal projections of specific neurons with full anatomical context, or automatically detect cells throughout the brain. Neurolucida and Stereo Investigator with the Serial Section Reconstruction module can be used to produce 3D solid modeling graphics representations from serial sections.

Topographic Organization

The neurons comprising many brain areas are known to be arranged topographically such that nearby neurons have receptive fields at nearby locations in the brain. The anatomical overlap of terminal arborizations often corresponds to shared targeting of functional synaptic output to specific single neurons. NeuroInfo uses a methodology to quantitatively compare projections from different injections sites.


Vascular Mapping

Morphological profiling of the brain’s vasculature can be performed with the Vesselucida 360 software. Image data may be obtained from cleared tissue techniques imaged with light sheet microscopes, immunohistochemistry labeled slides imaged with brightfield or confocal microscopy, or micro-CT scans. Automatic reconstruction of the vasculature may be performed using identical settings for all experimental animals Also, manual editing may be performed.

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