Whole Slide Imaging & Analysis

The locations and distribution of cell types in the whole slide images, can be analyzed with sophisticated automatic detection and image processing techniques in Neurolucida 360, NeuroInfo, TissueMaker, Tissue Mapper and BrainMaker. Each of these products provide cutting-edge solutions for specific classes of analyses. For example, researchers can map the distributions of a particular cell type, like those producing parvalbumin, 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.

BrainMaker, TissueMaker and NeuroInfo can generate 3D image reconstructions from whole slide images of serial sections so that you can easily view cells, structures and lesions. With the integrated 3D visualization, you can see the reconstruction of the entire organ. For example, 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.

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 with whole slide images of 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.

Design-based stereology is a rigorous set of data analysis methods to ensure integrity in the quantitative analysis of the size, shape, and number of objects (usually cells) in a tissue sample. Stereology is considered to be the gold standard in quantification. It is essential to validating and rejecting experimental hypotheses and produces results that are unbiased, efficient, and more reliable than non-stereological quantitative analyses. Non-stereological cell and object detection methods are highly susceptible to sampling bias and often fail to account for differences in object size and distribution within a region of interest.

Many medical educators now use whole slide images, also known as virtual slides, instead of microscopes to teach histology and histopathology. Virtual slides allow instructors to present the very best specimens ranging from traditional H & E staining to immuno-labeled confocal slides. Biolucida is in use worldwide in leading universities and medical schools and works with virtual slides in 2D or focusable 3D formats. To date, over 300,000 students have learned histology and histopathology using Biolucida.