New Staining Method Could Help Map Entire Brain

Staining method brings the reconstruction of all nerve cells and their connections within reach.

Learning, it is widely believed, is based on changes in the connections between nerve cells. Knowing which nerve cells are connected to which other nerve cells would considerably help us to understand how the brain works. Scientists have therefore long dreamed of mapping and then decoding the connectome, the circuit diagram of the brain. With the development of a special staining method, Shawn Mikula and Winfried Denk and of the Max Planck Institute of Neurobiology in Martinsried have now closed one of the last methodological gaps: how to stain an entire brain. The mapping of a whole mouse brain now seems within reach, but even if the equipment works as designed, the collection of the data alone will take several years and the analysis of the approx. 40 petabytes of data may take decades.

A lot has happened since scientists in the late 19th century first started examining nerve cells under the microscope. Anatomy, chemistry, physiology and cell biology in healthy as well as in sick brains has since been extensively explored. How thoughts and feelings arise from the activity of individual cells and what happens when cells disconnect from the network through degenerative diseases, for example, is still unclear. It is, therefore, clearly important to know the network’s connections. Finding all of those connections is the aim of connectomics.

The human brain contains around 100 billion neurons and close to a quadrillion (1015) cell-to-cell connections. While mapping a human brain’s connectome is currently science fiction, the development of the serial block-face scanning electron microscope and other imaging and analysis methods has brought the connectome of the mouse brain, which is 3000 times smaller than the human one, within reach. “A crucial step, which was still missing, was the preparation of a whole-brain sample”, says Shawn Mikula. For the last six years he has been working on staining of a complete mouse brain so that the contrast is uniform across the brain and the ultrastructural information needed for tracing the brain’s wires and detecting its synapse doesn’t get destroyed. Previous staining methods could only reliably stain relatively small tissue samples. But once the brain is divided into small pieces, neural wires can no longer be pursued between the pieces, preventing the subsequent generation of a brain-wide map. Methods that aim to stain the whole-brain either stained the brain too weakly or unevenly, or they destroyed brain ultrastructure. As a result, the reconstruction of all nerve cell connections remained impossible.

This image shows a mouse brain.
A new staining method closes one of the last methodological gaps: Now it’s possible to map every nerve cell and its synapses in a mouse brain. Image credit: MPI of Neurobiology/ S. Mikula.

Shawn Mikula and Winfried Denk have now presented their BROPA method for the staining of a whole brain. The abbreviation, BROPA, stands for a complex sequence of staining and rinsing steps, including osmium and pyrogallol solutions. The whole staining process takes around four weeks. “My patience was sorely tested because it is not until the end of this period that one knows whether a change in the staining process was good or bad”, explains Shawn Mikula. But after a lot of waiting and refining, the two scientists are now satisfied with their new method: “Our results show that single axons can be followed reliably and synapses recognized with the serial block-face scanning electron microscope in a BROPA-stained mouse brain”, says Mikula. An important success for the team, as Winfried Denk invented the serial block-face scanning electron microscope more than 10 years ago with this goal in mind.

“We are now an important step closer to our goal of recording a complete mouse brain with all its cells and connections under the electron microscope”, explains Winfried Denk, Director at the Max Planck Institute of Neurobiology. As soon as the latest generation of instruments is delivered and tested, which is planned to take over a year, the scientists intend to start the project. “I estimate that just collecting the data will take around two-and-a-half years”, says Denk. In this time, around 40 petabytes of data will be generated. “We will manage the storage somehow, it’s the analysis we’re still worried about”, adds Mikula. The results so far show that automated computer programs can recognize BROPA-stained synapses and cell bodies quite reliably. But even rare breaks will leave the nerve fibers unacceptably fragmented. “I am confident that we, as a field, will be able to solve that as well”, says Winfried Denk. Against the background of the deciphering of the human genome, this actually does not sound unlikely: When the first DNA sections were decoded in the mid-1970s, the sequencing of an entire human genome initially seemed as impossible as now does the connectomic mapping of an entire human brain.

About this brain mapping research

University of Missouri researchers Micah Mazurek, Joseph Hilgard, Jeffrey Rouder and Bruce Bartholow of the Department of Health Psychology, Department of Psychological Sciences and the Thompson Center for Autism and Neurodevelopmental Disorders also contributed to the study.

Source: Dr. Stefanie Merker – Max Planck Institute
Image Source: The image is credited to MPI of Neurobiology/ S. Mikula
Original Research: Abstract for “High-resolution whole-brain staining for electron microscopic circuit reconstruction” by Shawn Mikula and Winfried Denk in Nature Methods. Published online April 13 2015 doi:10.1038/nmeth.3361


High-resolution whole-brain staining for electron microscopic circuit reconstruction

Currently only electron microscopy provides the resolution necessary to reconstruct neuronal circuits completely and with single-synapse resolution. Because almost all behaviors rely on neural computations widely distributed throughout the brain, a reconstruction of brain-wide circuits—and, ultimately, the entire brain—is highly desirable. However, these reconstructions require the undivided brain to be prepared for electron microscopic observation. Here we describe a preparation, BROPA (brain-wide reduced-osmium staining with pyrogallol-mediated amplification), that results in the preservation and staining of ultrastructural details throughout the brain at a resolution necessary for tracing neuronal processes and identifying synaptic contacts between them. Using serial block-face electron microscopy (SBEM), we tested human annotator ability to follow neural ‘wires’ reliably and over long distances as well as the ability to detect synaptic contacts. Our results suggest that the BROPA method can produce a preparation suitable for the reconstruction of neural circuits spanning an entire mouse brain.

“High-resolution whole-brain staining for electron microscopic circuit reconstruction” by Shawn Mikula and Winfried Denk in Nature Methods. Published online April 13 2015 doi:10.1038/nmeth.3361

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  1. Looking at the photo the brain looked like some largish crawling insect, but I hope the mapping of it will be followed by further investigations accounting for the (supposed) changeability of it as the personality grows, accumulate experiences, but in particular individuate more unfortunate states of mind and hopefully how to redress that.

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