Creating a Novel Museum-Based Resource for Neuroscience: Mass whole-slide imaging of the R. Glenn Northcutt Collection of Comparative Vertebrate Neuroanatomy and Embryology

This project will enable online access to a unique, irreplaceable resource for comparative studies of the evolution and development of the vertebrate brain. The R. Glenn Northcutt Collection of Comparative Vertebrate Neuroanatomy and Embryology, housed in Harvard’s Museum of Comparative Zoology (MCZ), is the world’s largest and most taxonomically diverse collection of histological preparations of developing and adult vertebrate brains mounted on glass microscope slides.

It is of particular interest and relevance to the current generation of neuroscientists who use molecular and genetic approaches to elucidate mechanisms underlying evolutionary innovations, but the slides are fragile and access to them is difficult and time consuming. By utilizing a whole-slide-imaging workflow developed through a novel collaboration with Harvard’s Center for Brain Science, the project will allow professional scientists, educators and students to easily and routinely access the slides’ content via high-resolution digital images.

Such access will facilitate use of the slides in research and education and complement novel technologies for studying brain structure, development and function. It will facilitate collaborations between the neuroscience and biodiversity communities and, together with other projects that seek mass digitization and sharing of biological collections, it will enhance the ability of natural history institutions to more fully serve both science and society beyond their traditional constituencies.

Indeed, the project’s imaging workflow and associated training components offer an exemplar method for rapid and cost-effective digitization that can be used by other institutions, whose slide holdings number in the millions, most of which remain dark data.

The project will use a high-throughput, semi-automated slide scanner to make high-resolution digital images of the approximately 33,000 glass microscope slides in the Northcutt Collection. When completed, the project will provide online access to approximately 500,000 serial sections and whole-mount preparations of adult brains and embryos of more than 240 genera and 270 species of living vertebrates.

A cost-effective whole-slide imaging workflow will be utilized to process as many as 360 slides/week while yielding excellent image resolution (0.2 and 0.4 μm/pixel at 40X and 20X magnification, respectively). A digital image of each slide will be served to potential users via two online portals: MCZbase, the Museum of Comparative Zoology’s permanent specimen database; and MorphoSource, an NSF-supported online repository for specimen digital imagery.

Both portals will be configured with Girder and SlideAtlas, two open-source software tools for whole-slide image viewing, downloading and analysis. In addition, for as many as 20 species widely used to teach comparative vertebrate anatomy, digital images of a subset of histological sections labelled to point out principal brain regions will be uploaded to BrainMaps, an online resource for vertebrate neuroanatomy.

Finally, the project will produce several resources for training both students and professionals in methods for mass digitization and computer-assisted visualization of slide collections regardless of subject matter. These resources include four “how-to” videos, two online tutorials, undergraduate and graduate student internships and a graduate-level course in museum studies.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.