Composite image generated with Mouse Brain Architecture project data. Injections of two fluorescently marked (red and green) adeno-associated viral (AAV) tracers indicate neural pathways, superimposed upon a whole-brain image stained to reveal the protective sheathing around myelinated axons. Axonal paths leaving the injection site are seen, including horizontal ones crossing over to the other side of the brain along the Corpus Callosum.

Neuroscientists at Cold Spring Harbor Laboratory
(CSHL) reached an important milestone today, publicly releasing the
first installment out of 500 TB of data so far collected in their
pathbreaking project to construct the first whole-brain wiring diagram
of a vertebrate brain, that of the mouse.

   

The
data consist of gigapixel images (each close to 1 billion pixels) of
whole-brain sections that can be zoomed to show individual neurons and
their processes, providing a “virtual microscope.” The images are
integrated with other data sources from the web, and are being made
fully accessible to neuroscientists as well as interested members of the
general public (http://mouse.brainarchitecture.org).
The data are being released pre-publication in the spirit of open
science initiatives that have become familiar in digital astronomy
(e.g., Sloan Digital Sky Survey) but are not yet as widespread in
neurobiology.

   

Each
sampled brain is represented in about 500 images, each image showing an
optical section through a 20 micron-thick slice of brain tissue. A
multi-resolution viewer permits users to journey through each brain from
“front” to “back,” and thus enables them to follow the pathways taken
through three-dimensional brain space by tracer-labeled neuronal
pathways. The tracers were picked to follow neuronal inputs and outputs
of given brain regions.

   

“We’re
executing a grid-based “shotgun” strategy for neuronal tract tracing
that we first proposed a few years ago, and which I am pleased to note
has gained acceptance elsewhere within the neuroscience community,” says
Partha P. Mitra, Ph.D., the Crick-Clay Professor of Biomathematics at
CSHL and director of the Mouse Brain Architecture (MBA) Project. After
the initial June 1 release, project data will be made public
continuously on a monthly basis, Mitra says.

   

Project addresses a large gap in knowledge

“Our
project seeks to address a remarkable gap in our knowledge of the
brain,” Mitra explains. “Our knowledge of how the brain is wired remains
piecemeal and partial after a century of intense activity. Francis
Crick and Ted Jones emphasized this in an article published in Nature
nearly 20 years ago. Yet to understand how the brain works (or fails to
work in neurological or neuropsychiatric disease), it is critical that
we understand this wiring diagram more fully. Further, there remain
fundamental questions about brain evolution that cannot be addressed
without obtaining such wiring diagrams for the brains of different
species.”

   

The
MBA Project, which has received critical funding from the Keck
Foundation and from the National Institutes of Health, is distinguished
by the approach advocated by Mitra and colleagues in a position paper
published in 2009. Mitra there proposed mapping vertebrate brains at
what he calls the “mesoscopic” scale, a middle-range amenable to light
microscopy, providing far more detail than, for instance, MRI-based
methods, and yet considerably less detail than is achievable via
electron microscopy (EM). The latter approach, while useful for mapping
synaptic connections between individual neurons, is feasible on a
whole-brain basis only for very small brains (e.g. that of the fruitfly)
or very small portions of the mouse brain.

   

The
pragmatic approach Mitra advocated and which is realized in this first
data release, is to image whole mouse brains in a semi-automated,
quality-controlled process using light microscopy and injected neural
tracers (both viruses and classically used tracer substances). While the
basic methodology has been available for some time, systematically
applying it to a grid of locations spanning the entire brain, and
digitizing and re-assembling the resulting collection of brains, is a
new approach made feasible by the rapidly falling costs of computer
storage. A single mouse brain at light-microscope resolution produces
about a terabyte (1 trillion bytes, or 1000 GB) of data; thus,
generating and storing the data set currently being gathered would have
been prohibitively expensive a decade or so ago.

   

Assembling the circuit diagram at a mesoscopic scale using ‘shotgun approach’

A
key point is that at the mesoscopic scale, the team expects to assemble
a picture of connections that are stereotypical—that is, essentially
the same in different individuals, and probably genetically determined
in a species-specific manner. By dividing the volume of a hemisphere of
the mouse brain into 250 equidistant, predefined grid-points, and
administering four different kinds of tracer injections at each grid
point—in different animals of the same sex and age—the eight-member team
at CSHL assisted by collaborating scientists at Boston University, MIT
and the University of California, San Diego seeks to assemble a complete
wiring diagram that will be stitched together from the full dataset.

   

The
project in this sense is analogous to the Human Genome Project’s
“shotgun” approach, in that its final product—a comprehensive wiring
diagram—will be the product of many individually obtained data
components, woven together thanks to the power of advanced computing and
informatics. Indeed, Mitra says one of the genome project’s early
advocates, Dr. James D. Watson (now CSHL chairman emeritus), provided
him with motivation and encouragement to pursue the project.

   

“We
will never understand how the brain works until we have the wiring
diagram,” Dr. Watson comments today. “Mitra is on the right track and
I’m impressed he’s gone from conception to putting out data in a couple
of years on a quite modest budget. His approach deserves strong funding
support.”

   

The
MBA Project was also inspired by early efforts of the Allen Institute,
funded by Microsoft co-founder and philanthropist Paul Allen, which
resulted in assembly of a comprehensive map of gene expression across
the mouse brain. That effort was the product of standard molecular
biology procedures iterated in a quasi-industrialized process. The
resulting whole-brain gene-expression map, while a triumph, was not
designed to shed light on connections in the brain, which became a point
of departure for Mitra.

   

Since
the 2009 publication of Mitra and colleagues’ proposal for meso-scale
circuit-mapping projects for whole vertebrate brains, the approach has
not only spawned Mitra’s CSHL project, but also other meso-scale
circuit-mapping projects for the mouse at the Allen Institute and at
UCLA. Each differs in aim and technical detail.

   

A
number of features distinguish the “meso-scale” circuit project at
CSHL. The 20-micrometer spacing between brain “slices” gives the CSHL
results a particularly rich sense of 3D depth and detail. The team’s use
of four tracers including both classical tracer substances as well as
neurotropic viruses (attenuated or disabled viruses that infect nerve
cells), provides redundancy and helps control for differing efficacies
of the different tracer substances. The images one sees on the MBA
Project website begininng today provide hard data on actual neuronal
processes—the “ground truth” of neuroanatomy, in Mitra’s words—and do
not rely on inferential methodologies such as functional MRI scans and
diffusion tensor imaging to suggest areas in which connections occur.
Finally, it is noteworthy that the slides generated by the project are
being physically stored, to permit re-examination at a later date, using
more refined imaging methods if necessary or as new methods become
available.

   

“Our
project is what I’d call a necessary first step in a much larger
enterprise, that of understanding both structure and dynamics of the
vertebrate, and ultimately, the human brain,” says Mitra. “While facile
comparisons with Genome projects should be avoided, the data sets
generated by the MBA and similar projects will provide a useful
framework—not unlike a reference genome—on which we can ‘hang’ all kinds
of neuroscience knowledge, the body of which has always been notably
fragmentary.”

   

Data from the Mouse Brain Architecture Project

   

A technical whitepaper on the project

   

2009 position paper proposing the project

   

The
planning stage of the project, including meetings at the Banbury
conference center at CSHL as well as initial informatics work, was made
possible by an award from the Keck Foundation. Major funding for the
Mouse Brain Architecture project comes from a Challenge Grant from the
National Institutes of Health (RC1MH088659) and a Transformative Award
from the Office of the NIH Director (R01MH087988). Additional sources of
funding include internal funding at Cold Spring Harbor Laboratory and
the Crick-Clay Professorship.

Source: Cold Spring Harbor Laboratory