Travel grant reports 2012

Tomislav Milekovic - Brain Institute for Brain Science, Brown University

Visit Greece, June 2012, and meet several people who attended AREADNE 2012.

Travel report:
I would like to thank International Neuroinformatics Coordinating Facility for their generous support of my visit to Greece at the time of the AREADNE 2012 conference. The goal was to meet specific people, but also to discuss my own research. I received useful comments about the work I presented and was encouraged to continue the project and publish in the near future.

The AREADNE conferernce itself, which I attended when visiting Greece, consisted of 4 days of talks, 6 or 7 every day, with poster presentations during every evening for the first three days. I would like to single out three talks that were directly relevant to my current research projects. Dr. Prof. Eilon Vaadia presented the work of his lab which showed that monkeys can get volitional control of local field potential signals (LFPs) in the beta range (10-40Hz). This is of direct relevance to one of my projects where the same technique is used to give people with paralysis volitional control of their LFPs. Subsequent discussion with him provided me with ideas how to improve my experiments and results. Dr. Prof. John Pezaris gave a talk about information contained in the high frequency range of the LFPs (1000-6000Hz). Due to technical restrictions in data analysis, this part of the signal is often disregarded. His research shows that LFPs in this frequency range can contain highly stable tuning, while being as specific as the spiking rates of single neurons. This finding could provide an additional source of information to be used in designing Brain-Machine interfaces, the work being done in my research group. Another interesting lecture was given by Dr. Prof. Nicholas Hatsopoulos. He demonstrated that beta
oscillations in motor cortex behave like a planar wave. During the beginning of the movement, beta planar wave changes direction in such a way to propagate from proximal to distal neuronal representations in motor cortex. One possible explanation is that the wave represents sequential facilitation of muscles, which goes from proximal to distal muscles during most of the natural movements. This is of direct interest for my research projects, where LFPs in beta are investigated for providing information to drive brain-machine interface control.

Soon after my return from Greece, a travel report meeting was held, where I presented the most relevant discussions I had, and also reported on some of the talks, posters and discussions from the AREADNE 2012 conference to my colleagues. A lot of interest was given to the scientific results presented by Dr. Hatsopoulos during his talk. Due to good connections between my supervisor, Dr. Donoghue and Dr. Hatsopoulos, his former student, this interest will be easily
followed by personal contact. High amount of interest was shown in relation to Dr. Pezarisí talk as well, especially by Dr. Hochberg, one of my supervisors, who invited Dr. Pezaris to hold a lecture at Brown University. Therefore, my visit to Greece not only improved my research skills and experience, but could also kick-start other fruitful collaborations.

Grace Lindsay ñ BCCN Freiburgh, presently Columbia University

Visit Dr Andreas Hertz' lab at Bernstein Center Munich

Activities and accomplishments:
During my stay in Munich, Sept 2012, I met with Dr. Andreas Herz and several of his lab members to discuss their approach to model building. My main goal was to gain information as to how they approach building or improving on a model, and how they determine what scale is best (molecular, spiking models, firing-rate, etc) for specific datasets. I was also interested in learning the specifics of how they acquire their own data and incorporate data from other labs into their models.

Meeting with various lab members and learning about their projects, I was able to see the full scope of the work done in the Herz lab and how it spans many levels both in terms of what is being physically modeled and the phenomenon that are trying to be explained. There is also a huge variety in the complexity and parameter-space size of the model and it was beneficial to see how and why different levels of complexity and detail are used by different people for different modeling goals.

During my meeting with Dr. Herz, I was able to discuss with him the specifics of the project that I am currently starting wherein I will be obtaining electrophysiological data from primates and attempting to work on a model of attentional effects in both LIP and PFC. He gave me many insights into the initial stages of model building. Of particular note was the importance of working extensively with the raw data and gaining an intuition about it. Only through these measures can one decide what scale of modeling seems appropriate. Another benefit of visiting with members of the Herz lab was that I was able to learn about their development of the Cloud API system for storing, sharing, and annotating electrophysiological data. I got to experience a demonstration of its interface with Matlab. This system could be of great help for organizing my future experimental work.

Finally, while this was not the purpose of the travel grant, I did attend the INCF conference while in Munich. I just wanted to mention that I found the conference incredibly engaging and informative. As a result of it, I've been made aware of a wide range of neuroinformatics tools, as well as some of the challenges the field faces. It was a very valuable experience.

Jeremy Ullmann - University of Queensland, Centre for Advanced Imaging, Australia, Brisbane

The aim of this visit is to work on establishing a multi-modal atlas of the adult zebrafish brain.

Dr. Mario Wullimann, Ludwig Maximilians-Universit‰t, Munich Germany

Activities and Accomplishments: 
During September 2012 I visited Dr. Wullimann to work on establishing a multi-modal atlas of the zebrafish brain. During the two weeks I was there we were able to make significant progress in the development of a population-based atlas by 1) establishing a stereotaxic space for the zebrafish brain; 2) segmenting over 80 structures on a minimum deformation model, a significant improvement over the previous atlas; and 3) discuss which immunohistochemical markers will be incorporated into the atlas. In addition, I was able to interact with Dr. Wullimann lab group and gave a presentation on some of my previous research. Finally, we had lengthy discussions on: the continued progress of the project; where to publish a journal paper; and how to best disseminate the data once the project is completed in early 2014.

Douglas M. Bowden, MD - University of Washington, Seattle, USA

To further interoperability between the INCF-sponsored BrainInfo and other INCF web-based resources for the dissemination of neuroscientific information.

Activities and accomplishments: 
Attended sessions of the INCF Neuroinformatics Conference and Workshops of the PONS and Atlasing Task Forces in Munich, Sept. 9-14, 2012.

a) Presented a poster on steps taken to facilitate the use of NeuroNames as a source of Standard Nomenclature for natural language tagging/indexing of neurodata Synonyms to let Users query systems using any neuroanatomical terminology. URLs to give Users one-click access to definitions and illustrations at BrainInfo NeuroNames is now available in XML, Excel and UMLS formats.
b) Presented a poster on adaptation of the INCFís Waxholm Mouse Brain Atlas to BrainInfo/NeuroMaps for mapping data to Waxholm space and for editing images for publication, presentation and archival purposes.
c) Established contact with representatives of the Allen Brain Atlas, SenseLab, GenePaint, Scalable Brain Atlas, CoCoMac and others to further interoperability between their resources and the BrainInfo portal.
d) Pursued discussions with staff of the NIF on the translation of NeuroNames in to OWL.

Added value for the INCF:
In 2008 the INCF contracted with the University of Washington (UW) and the University of California San Diego (UCSD) to sponsor the transfer of the BrainInfo website and NeuroNames from UW to servers of the Neuroscience Information Framework (NIF) at UCSD. Since then we have worked toward consistency between the neuroanatomical ontology of NeuroNames, the neuroanatomical ontology of NIFSTD and nomenclature of NeuroLex. This yearís conference and workshops gave us the opportunity to support the international coordinating mission of INCF by establishing contact with other teams from the US, Europe and Australia in efforts to establish interoperability between BrainInfo and five other neuroscience resources.

Mehran Ahmadlou, Pedriatric Neurorehabilitation Research Centrum, Tehran, Iran


To visit and collaborate with Dr. F Vialatte and Dr K Hiyoshi in Laboratoire SIGMA, ESPCI Paris Tech.

Activities and accomplishments:

During March to May 2012 an earlier started project with Dr F Vialatte and Dr K Hiyoshi was finished in Paris. The goal was to develop a new EEG signal analysis real-time software. Using this software, the underlying mechanisms of emotional judgments were to be investigated. Paired audio-visual stimuli were used and presented to subjects with three emotional valences, either two with similar valences (for example Happy-Happy) or with different valences (e.g. Happy-Angry). EEG signals were recorded from subjects, and the analysis was performed by computing the synchronization of the EEGs and conditions congruent vs. non-congruent stimuli. The obtained results demonstrate functional connectivity at the alpha band EEG, amd this could be used as a predictive tool. The results of the project has been prepared to submit to a conference ( Also the plan is to publish a journal paper, and put the related programs and matlab-files on a public website.


Espen Hagen and Torbjørn Bæko Ness, Norwegian Univ of Life Science, Ås, Norway


Attending the NeuroInformatics.NL Workshop on Structure, Function and Modeling of Dendrites, and visit Dirk Schubert and Rembrandt Bakker at Donders Institute for Brain, Cognition and Behaviour, UMC Nijmegen.

Activities and accomplishments:

We, Torbjørn Ness and Espen Hagen, attended on January 20 the NeuroInformatics.NL 2012 Workshop Series on “Structure, Function and Modeling of Dendrites” held at Vrije Univeriteti Amsterdam Medical Center (VUmc), for details and program see

We there gave a talk on our ongoing activities of modeling local field potentials titled “Modeling the Effect of Neuronal Dendritic Structure on Potentials Recorded by Multi-Electrode Arrays (MEAs)”.

In the next days we travelled to Nijmegen for a three-day visit in Dirk Schubert’s research group (Radboud University Nijmegen Medical Centre, Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, see first and foremost to discuss ongoing research activities where we analyze and model electrophysiological recordings obtained in vitro recordings from rat slices on multi-electrode arrays. We have for some time received such data, and during our visit we were able to participate in the experimental procedures of preparing the in vitro recordings.

In addition, we participated in their group activities such as Journal Club, we also gave a talk presenting our activities and tools that we develop, and had discussions with different people about problems forward modeling of local-field potentials, inverse problems in neurophysiology and continued and future research projects.