Category Archives: Neuroscience

Method of the Year 2010: Optogenetics

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The time to celebrate methods has come and this year we have chosen to devote our end of year special feature to Optogenetics.

While neuroscientists will hardly need any introduction to this booming technology, recent developments have shown that this technique can go beyond controlling the activity of neurons in the brain and has the potential to open new avenues of experimentation across multiple other biological fields as well.

The term optogenetics was only coined 4 years ago but the technology has already matured to the point that it is having a substantial impact on basic biological research. Because of the transformative effect that it has already had in neuroscience studies and the excitement of its future prospects in other fields, it’s nomination as Method of the Year has not been a difficult one.

You can read more about this choice in the editorial of our January issue and access all the content of our special issue here.

We hope that you will share our excitement for this technology and we welcome any comments on our selection!

Brains at work

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Neuroscience is a field where much still needs to be learned and for that, technology development is increasingly necessary. Recent developments have greatly expanded our capacity to visualize the activity of neurons using genetically encoded fluorescent probes and optogenetic tools now enable precise modulation of this activity.

But the brain is contained in a protective skull and peeking into it is usually an invasive process. In this month’s editorial we discuss recent technical developments and future prospects that will take us a step closer to a minimally invasive form of ‘transcranial neuroscience’. Despite the big progress, much work remains but we are hopeful that with the right technology and motivation, the field will soon approach the holy grail of performing non-invasive cellular-level functional studies of the entire brain.

Any thoughts about this? Tell us what’s on your mind!

Trace some neurons, get a big check

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The idea of tracing the structure of stained neurons to obtain functional insights into in situ neural networks isn’t new and dates back over 100 years to Ramón y Cajal. Just recently I discovered that copies of his books have been digitized by Google and the illustrations are incredible. See for example Studien über die Hirnrinde des Menschen.

Even though software now exists to automate this process, it seems that the performance still isn’t good enough to replace manual tracing of image stacks of labeled neurons. Neuroanatomists often spend days to months manually tracing the structures rather than rely on the software that currently exists for automating the process.

Two big players in the neuroscience field have decided to do something about this. On April 9th the Allen Institute for Brain Science and the Janelia Farm Research Campus of the Howard Hughes Medical Institute announced the DIADEM Challenge. The acronym is derived from Digital Reconstruction of Axonal and Dendritic Morphology. I wonder how long it took to come up with that one.

Over the next year groups and individuals are invited to download image stacks of real data and use their algorithms to create digital reconstructions of the neurons and submit them for evaluation. Five finalists will be invited to compete in a final round at the Janelia Farm Research Campus. The organizers will award a $75,000 cash prize to the winner whose algorithm performs the best. The results will be submitted for publication in a special issue of the journal Neuroinformatics.

The hope is that the competition will encourage the advances in automated neuronal tracing that will be required for researchers to construct a functional atlas of the brain — one of the principle goals of the research at Janelia Farm.

It is encouraging to see a competition devoted to a small community like this. Nature Methods previously argued that such competitions would be valuable for improving algorithms in such specialized applications. I’m excited to see that it is happening and wish the organizers and competitors are successful.

Idiosyncrasies of the human CMV promoter

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A Correspondence in the May issue of Nature Methods points to the fact that the widely used human cytomegalovirus promoter shows dramatic differences of expression in various cell types.

The Correspondence focuses on potential problems associated with CMV in the brain in relation to a paper by Wickersham and Callaway who respond to the criticism.

Share your experience with CMV in neurons or other cell types by adding your voice to the discussion.