Blog

Quicker whole-brain imaging in Nature Methods

Malin Sandström — Tue, 17 Jan 2012 12:15:00 +0100

The collaborators just published a paper in Nature Methods (available online January 15) describing how their microscopy method, serial two-photon (STP) tomography, enables automated high-throughput imaging of fluorescently labeled mouse brains. A typical whole mouse brain scan is reported to take 6.5 to 8.5 hours, while a scan at the maximum resolution takes 24 hours - in any case quick enough to potentially, as the researchers put it "transform the emerging field of systematic whole-brain anatomy, until now limited to dedicated atlas-generation initiatives, into a routine methodology".

If this turns out to be a true prediction, we are likely to see many comparably small and diverse data sets in the hands of many different groups and labs, some years from now. And a corresponding increased need to compare data sets with each other and with reference atlases, to integrate data for combined queries, and to describe and publish both data and analysis methods. We of course hope that the tools and services INCF and the Task Forces, especially those in Digital Brain Atlasing and in Datasharing, are developing will be useful in this regard, and that we also can help support and complement the community-developed tools already out there.

Have you identified a problem or barrier that you think we can help you and your scientific field or subfield with? Be sure to let us know in the comments!

(Figure: Figure 1a-c from the paper, showing method scheme and 2D/3D views of the resulting brain scans. Reused with permission from Nature Methods)

Links:

1. T Ragan et al (2012) "Serial two-photon tomography for automated ex vivo mouse brain imaging" Nature Methods, doi:10.1038/nmeth.1854

2. Cold Spring Harbor Laboratory press release, January 12, 2012

INCF at SfN 2011

Malin Sandström — Tue, 13 Dec 2011 13:50:00 +0100

As in previous years, the INCF exhibit booth at the annual SfN meeting was well attended. Our co-location (see map) with other neuroinformatics projects and initiatives helps - visitors interested in our activities are likely interested in our booth neighbors, and vice versa - and probably also our hosted program of live neuroinformatics demos. (Though we suspect that our comfy sofa might also be a contributing factor.)

This year we added a satellite workshop to our schedule, "Neuroshare revisited" on November 12, for a discussion on the state of Neuroshare and possible future developments to the format in order to improve and facilitate access to neurophysiological data. It was organized through the INCF Program on Standards for Datasharing, and we invited data acquisition system vendors, data analysis software developers, and users to talk about needs and problems - it turned out to be a very interesting discussion. The group agreed that extending Neuroshare would be a worthwhile endeavor.

We devoted a full day of our neuroinformatics demo program to digital brain atlasing. Representatives from the INCF Program on Digital Brain Atlasing held a "Walk-in Registration Clinic" for researchers with rodent data and an interest in sharing them through the Program's infrastructure. We were even visited by George Paxinos (yes, that Paxinos)!

Our other two scientific programs were also represented - the Program on Ontologies of Neural Structures through the "Adopt a Neuron" campaign which was also presented in our booth during a demo, and the Program on Multiscale Modeling through a demo of a reference implementation in progress for NineML (the Network Interchange for Neuroscience ML). And there were many other interesting demo contributions from Programs, Nodes and the scientific community - you can see them all here.

This dazzling array of new information - posters, lectures, exhibitors and a constant flow of brief tweeted updates - and many interactions with scientific community from all over the world is what makes the SfN week one of the high points of our year, and this year was no exception. Unfortunately, there is never any way to see all that is potentially interesting at SfN. But some key lectures have been saved for posterity in video format on SfN's YouTube channel - for instance the Kavli minisymposium on legal implications of neuroscience advances.

James Gee, Ilya Zaslavsky, George Paxinos and Luis Ibanez.

NI2011: Little more than a week to go before the Neuroinformatics 2011 Congress

Malin Sandström — Fri, 26 Aug 2011 11:15:00 +0200

Abstract Book

We have just made the 2011 Abstract book, with abstracts for all keynotes, workshops, demos and posters, available as a pdf for browsing and download (including a handy clickable index at the end!)

Satellite Workshop on September 3

The Congress kicks off already September 3 with the satellite workshop "Toward a Global Neuroinformatics Infrastructure" organized in collaboration with the IEEE Engineering in Medicine and Biology Society at their yearly meeting EMBC, held at the Boston Marriott Copley Place Hotel. The workshop will include presentations from the leaders of large neuroscience infrastructure projects from around the world:

Sean Hill: "Building an informatics infrastructure for multiscale neuroscience data integration"

Jan Bjaalie: "Spatial data integration - an infrastructure for data driven atlasing"

David Van Essen: "The Human Connectome - an infrastructure for brain connectivity analyses"

Mitsuo Kawato: "Understanding the brain by building the brain: infrastructure for modeling the brain and manipulating the mind"

Main meeting September 4-6

The main meeting will feature 5 keynote lectures, 8 spotlight presentations of selected demos and posters, 12 workshop speakers, 35 demos and and 130 posters, as well as the INCF US Node Special Symposium (with another 9 lectures) on the afternoon of the last meeting day, September 6. The same day, September 6, also offers lunch seminars sponsored by BIRN. All details can be found on the meeting web pages.

INCF Task Force meetings September 7-8

Taking advantage of the fact that a large part of our community is present in Boston, after the main meeting we are also organizing meetings for many of the Task Forces associated with the INCF Scientific Programs, including a cross-Task Force hackathon at MIT on September 8.

INCF at CNS*2011 (part 2)

Malin Sandström — Fri, 29 Jul 2011 15:35:00 +0200

We can now, based on empirical testing in the form of the CNS*2011 reception, conclude that the Stockholm City Hall is just about a comfortable fit for some five hundred mingling conference attendees - where they fit the additional eight hundred people at the 1300-guest Nobel banquet will remain a mystery.

CNS*2011 attendees in the Stockholm City Hall's Golden Hall.

One of the high points of the CNS*2011 meeting are the poster sessions - this year, almost four hundred posters were presented in three intense poster sessions.

Among the work presented we found one of the first posters produced from the EuroSPIN Erasmus Mundus program, which offers joint doctoral degrees in neuroinformatics and is offered by a consortium consisting of four universities in INCF member countries: National Centre for Biological Science, Bangalore, India; University of Edinburgh, UK; Albert Ludwig University of Freiburg, Germany, and KTH in Sweden . We also found a poster on CoCoMac 2.0, a macaque brain atlas with an interface built on the INCF Scalable Brain Atlas.

Left: Oliver Muthmann, EuroSPIN PhD student, and Jeanette Hellgren Kotaleski, EuroSPIN Program Coordinator. Right: Rembrandt Bakker, explaining the CoCoMac 2.0 poster to Hermann Cuntz.

For the INCF Multiscale Modeling program, one of the most important events at CNS*2011 was the workshop Emerging standards in network modeling, which served as an update on the state of the art in the field, as well as the release of the initial version of the model description language NineML. Documentation and tutorials for NineML can be found at the INCF Software Center NineML pages.

INCF at CNS*2011 (part 1)

Malin Sandström — Sun, 24 Jul 2011 15:30:00 +0200

Stockholm at this time of year is at its most beautiful - and also at its emptiest, when many inhabitants are spending their vacations elsewhere. The 500+ conference attendees at CNS*2011, the second largest CNS conference ever, are certainly noticeable where they mill around on the campus of the Royal Institute of Technology, and they fill its largest lecture hall to the absolute limits.

Prof. Ivan Soltesz lectures in front of a full auditorium at CNS*2011

The meeting began yesterday, July 23rd, with tutorials - we filmed one of them, and hope to be able to make the material available within a few weeks, in collaboration with the OCNS.

The main meeting days started today July 24th, with the "INCF Distinguished lecture" given by Dr Ivan Soltesz (and, as the name hints, sponsored by us), titled "Functional network connectivity of the control and epileptic hippocampus". He and his lab are working on some truly fascinating biological neural network studies with medical applications, combining experimental work and large-scale, anatomically and biophysically realistic modeling - for instance this recent PNAS study on the importance of "hubby" cells in the epileptic rat dentate gyrus, which shows how a small number of highly interconnected granule cells are able to change the dynamics of the network so that it becomes hyperexcitable and prone to epileptic seizures (see also the accompanying commentary by Dr Astrid Prinz). Several different probable candidates for such hub cells have been shown to exist.

Start of the conference season

Malin Sandström — Thu, 23 Jun 2011 10:40:00 +0200

This Saturday, June 25, our summer conference season starts in earnest, with our satellite workshop on Neuroimaging Data Sharing and Data Access in Quebec, just before the launch of HBM*2011. The workshop has been greeted with much interest and is full - close to 100 attendees - with a waiting list. The following week, June 26-30, we will be present as exhibitors at HBM*2011, in booth 104.

Two weeks later, July 14-18, we will exhibit at the 8th IBRO World Congress of Neuroscience in Florence. Since we have recently become a member of IBRO, we are looking forward to meeting the IBRO community. Come meet us in booth 35!

Less than a week after IBRO, the CNS*2011 conference opens its doors in our hometown Stockholm. We have an exhibitor table, we are organizing a workshop on Emerging standards in network modeling on July 27, and we are also one of the local co-organizers - you'll meet us in various places during the conference days July 23-28.

After these three events, it is a month to go to the great finale - our own Neuroinformatics Congress in Boston, September 4-6. We are actually starting a day early, September 3, with a workshop during the last day of the EMBC conference; Toward a Global Neuroinformatics Infrastructure which includes talks by four world leaders of neuroinformatics and a concluding panel discussion. The registration fee for this last day of EMBC will be significantly discounted for Neuroinformatics Congress attendees.

And then? We start looking forward to meeting you all at SfN*2011 in Washington DC in November, of course.

Python in Neuroscience workshop at EuroSciPy

Malin Sandström — Wed, 01 Jun 2011 15:55:00 +0200

EuroSciPy, the cross-disciplinary gathering focused on the use and development of the Python language in scientific research, is organized for the fourth year in a row, and is growing steadily. New for this year is the organization of two satellite conferences, centered around Python use in the physics and neuroscience communities.

The Python in Neuroscience workshop aims at bringing together researchers who develop software tools in different branches of neuroscience in order to share ideas, concepts, tools and to foster collaborative projects based on Python language. The organizers are asking for contributions in the form of a one page abstract, and submission is open until June 8.

Possible topics for contributions include large parts of the neuroinformatics field:

tools for neural simulation
electrophysiology data analysis
data management and databasing in neuroimaging and neuroscience
stimulus generation
neuroimaging data processing
workflows and pipelines for data processing
massive computation facilities for simulation and data analysis in neuroscience
visualization tools in neuroscience and neuroimaging

Read more on the workshop web page, http://pythonneuro.sciencesconf.org/, or contact the organizers on pythonneuro@sciencesconf.org.

So why has the Python language reached such a prominent position in the neuroscience field? Dr. Raphael Ritz, INCF Scientific Officer and involved in the organization of the workshop, explains:

"Python is a simple yet powerful, fully object-oriented, open source scripting and programming language. Lead by the increased maturity of 'numpy' and 'scipy' in particular, it has become a serious competitor as a platform for scientific computing. Consequently, more and more neuroscience labs and projects are switching to Python for managing their computational tasks - be it data acquisition or analysis, stimulus generation or delivery, visualization or animation, modeling or simulation etc. Due to Python being open source and platform independent it is also easy to share code across laboratories and groups which has let to a flourishing ecosystem of libraries and tools tailored to tasks as found in doing neuroscience research."

New German-Japanese funding initiative

Malin Sandström — Wed, 25 May 2011 11:15:00 +0200

The Japan Science and Technology Agency (JST), the Bundesministerium für Bildung und Forschung (BMBF) and the Deutsche Forschungsgemeinschaft (DFG) have announced the implementation of a new programme for joint funding of German-Japanese cooperative research in computational neuroscience.

Citing from the call text: "This initiative focuses on the funding of collaborative research projects that bring together scientists and engineers with complementary experience and training in the experimental and theoretical neurosciences. Proposals for research projects should describe collaborations that bring together the complementary expertise needed to achieve significant advances on challenging interdisciplinary problems. They should include collaborations among computational and/or modelling experts, theorists, and experimental neuroscientists or engineers. Computational research supported under this initiative must relate to biological processes and should lead to hypotheses that are testable in biological studies."

The application deadline is August 8, 2011.

INCF Nodes Workshop May 10-11, 2011

Malin Sandström — Mon, 16 May 2011 17:01:44 +0200

Last week, 33 representatives from 14 of the 16 INCF National Nodes met in Stockholm for the fourth Nodes Workshop. This meeting's theme was "Neuroinformatics Infrastructure". The INCF Secretariat presented its visions for global neuroinformatics infrastructure, and each Node was asked to give a brief overview of their country's current neuroscience infrastructure status. Breakout discussion sessions collected input and ideas on data sharing, infrastructure needs, and teaching and training aspects of neuroinformatics.

As usual, the meeting also afforded plenty of opportunities for discussion and networking between the participants - over coffee, during the poster session and at lunch and dinner. We look forward to meeting you all again next time!

Welcome to the INCF Blog!

Malin Sandström — Wed, 04 May 2011 09:52:35 +0200

This is the inaugural post of the new INCF blog, where we plan to highlight neuroinformatics news, events and resources - big and small. If there is something you would like to see featured or discussed here, you are very welcome to contact us on blog@incf.org with your feedback.

You can follow the blog via several syndication options: RSS, ATOM, and RDF.

We will of course still publish newsflashes and newsletters, and post short updates to our Twitter feed and our Facebook page. Important things will likely show up in several of these channels.