Scientific Software Developer / PhD student (project Neuron Cofund Micronet)


Scientific Software Developer / PhD student

Laboratory of Neuroinformatics at the Nencki Institute of Experimental Biology, is seeking a Scientific Software Developer / PhD student in a JTC ERA-NET NEURON grant. You will become part of a cutting edge EU-funded endeavor focused on investigating cortical microcircuitry after traumatic brain injury. In the project, we will use the most advanced technologies available for visualizing how and when nerve cells lose connections after trauma and regain the ability to communicate with each other. A successful candidate will contribute to research in the areas of novel high throughput, efficient and reliable methods for quantitative analysis of whole-brain optical imaging using light-sheet fluorescence microscopy (LSFM) and similar types of microscopy, with emphasis on automated cell segmentation and counting, tract tracing, registration in 3D brain atlas space. This full-time position is funded for three years and offers a possibility of obtaining a PhD degree.

The key responsibilities include:

  • Establishing a computational environment and novel methods for managing and processing large scale imaging data (of the order of terabytes). Creating a dedicated file format and related server software for rapid access to the images.
  • Developing machine-learning approaches for detection, classification and analysis of labeled cells somata and extraction of axonal bundles and fibers. Using these methods to conduct high throughput analyses of microscopy imaging data to investigate neuronal plasticity as well as long-range and local microcircuitry rewiring.
  • Creating efficient and robust intra- and cross-modal registration methods for coregistration of imaging data between distant imaging modalities. Also, utilizing techniques of computational neuroanatomy to improve coregistration accuracy.

Essential selection criteria and qualifications:
We are looking for a highly motivated and skilled candidate with a recent academic MSc degree (or about to obtain such) in physics, mathematics, computer science or closely related field with a strong focus on computational aspects of high throughput image processing. The candidate should be a result-driven team player, have good communication skills in English (both oral and written) and posses the majority of the qualifications listed below:

  • Coding skills in Python (additional C++ would be an advantage) including popular scientific libraries. Software engineering skills, documented experience in projects involving multiple developers. Experience with high performance computing.
  • Knowledge of image processing algorithm design, including machine learning methods, neural networks and texture analysis. Documented experience in working with biomedical images.
  • Experience in interdisciplinary projects involving neurobiology, computational neuroanatomy, image registration and methods of spatial integration of imaging data will be highly regarded. Knowledge of the anatomy of the central nervous system will be considered a strength, but is not a requirement.

Application should include:

  • A letter of application,
  • Resume,
  • Source code of the solutions to the tasks below (the more the better) and a report summarizing developed code and the outcomes,
  • A letter of reference.

The deadline for applications is Sunday, 30th April 2017. You don’t have to solve all tasks, however applications with no solutions will not be considered. Please send applications and to

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