PhD/Postdoctoral/Sabbatical researcher position

Neuronal morphology using image analysis

(FAPESP fellowship)

Luciano da F. Costa and Roberto M. Cesar Jr.

NAP e-Science

University of São Paulo, Brazil

(Published on April/2014)


    Neurons can be understood as cells with morphology adapted to make long- and short-term connections.  Since the pioneering studies of Santiago Ramon-y-Cajal, several types of neuronal categories have been identified by taking into account respective morphological characteristics.  Interestingly, several of these morphological types have been found to correspond to electrophysiological categories. However, despite the recent intensification of related researches, there is still no agreement with respect to the number of neuronal categories in the natural world.

    The Neuromorpho open repository incorporates several resources in neuronal morphology, including a database with over 10.000 tridimensionally reconstructed neuronal cells of various types and animals, contributed by several research laboratories worldwide.   Neuromorpho also includes resources for obtaining several measurements
    of the neuronal morphology.

    We are looking for PhD/post-doctoral/Sabbatical candidates to apply for a FAPESP fellowship (see the conditions below) to develop research based on this data. The project will be developed under the co-supervision (PhD, Postdoc) / collaboration (Sabbatical) of professors Luciano da F. Costa and Roberto M. Cesar Jr. The current project aims at investigating systematically how neuronal cells can be effectively classified into the several established types  (e.g. pyramidal, ganglion, interneurons, etc.) while using diverse alternative supervised and unsupervised pattern recognition approaches such as  knn, SVM, and neuronal networks.  This investigation will involve cross-validations using the Neuromorpho cells and possibly open environments such as Weka.  In addition, we will also investigate how these neuronal cells can be recognized while taking into account portions of their structure (e.g. branches) and/or diverse 2D projections.

    It is expected that the results of these investigations will provide interesting implications in basic neuroscience research as well as pave the way to integration into the WWW, allowing query submissions, which may be developed also during this project.

    The successful candidate will actively participate in R&D and also in team activities such as organization of seminars, short courses, study group meetings and co-supervision of undergraduate and graduate students. All these activities are related to the Research Support Centers NAP e-Science of the University of São Paulo.

Required qualifications / skills
  • Undergraduate/Graduate degree with strong background in computation (Computer Science, Engineering, Physics, Math or proven ability to design and implement computer algorithms/systems)
  • Research experience in one or more of the following areas: signal/image processing, image analysis, pattern recognition/analysis, machine learning, multivariate data analysis
  • Oral and written communication skills (English)
    Additional desired qualifications/skills
    • Knowledge of statistical data analysis
    • Proven ability to design data analysis experiments and evaluate their results
    • Programming skills
Application procedure and schedule
    Application deadline: We accept applications on a rolling basis.
    Required documents:
    • CV
    • Summary of the MSc/doctoral thesis and other relevant works
    • Names, positions and emails of two people that may provide you with references

    Fellowship conditions: The selected candidate will apply for a fellowship from FAPESP (São Paulo Research Foundation) with the one of the following conditions: PhD (3-4 years, fellowship US$ 16K/year plus US$ 4.9K/year for  for travel expenses such as attending to conferences); Postdoc (2-4 years, fellowship US$ 30K/year plus US$ 4.5K/year for travel expenses such as attending to conferences); Sabbatical (1 year, fellowship US$ 50K-70K/year ). All fellowships may cover expenses for moving to São Paulo/Brasil (including flight tickets). PhD and Postdoc fellowships may apply for an extra period (4 months to 1 year) to do part of the research in any top research university abroad (FAPESP BEPE fellowship). Medical care at the University of São Paulo hospital is also available. The Sabbatical fellowship includes health insurance for non-brazilians.

    Please email applications and inquiries to Prof. Roberto M. Cesar Jr.:
      Subject: NAP/USP Postdoc application
NAP e-Science

    NAP e-Science supports initiatives that are concerned with computational issues derived from the big data phenomenon, in several areas such as Astronomy, Bioinformatics, Systems Biology, Oceanography, Biomedicine, among others, by developing methods and creating tools to facilitate data storage, data mining, data analysis and data visualization.

USP - University of São Paulo

  IFSC/USP - Institute of Physics of São Carlos

IME/USP - Institute of Mathematics and Statistics