The DIVA (Data Integration and Visualization in Virtual and Augmented Environments) project aims to create environments for data treatment that leverages Virtual Reality (VR), human data interaction and automated algorithmic treatment. It is a joint initiative between the Institut Pasteur and the Institut Curie. Key to our segmentation approach is the relation between user intervention and data treatment. It is tailored to handle data in limited quantities, possibly very noisy, and to allow rapid and robust learning of the required procedures to extract relevant information from data.
Development of the proposed segmentation tool will use an in-house software platform that is designed to load any type of image stack (e.g. microscopy image or MRI/CT scan) into a VR environment. The platform generates entire scenes allowing real-time interaction with data (i.e. representation modifications, annotations and projections of data). Currently the platform is available in alpha version at both DIVA host institutes.
More information on applications of the DIVA project is available at the following address: https://research.pasteur.fr/en/project/data-integration-and-visualisation-in-augmented-and-virtual-environments/
We are proposing a 1-year postdoctoral fellowship (renewable for 1 year) financed by the DIM-ELICIT for a motivated candidate. They will be expected to contribute to our efforts of designing segmentation procedures for noisy data coming from microscopy and biomedical images. The envisioned approach will join Bayesian pixel feature learning (within the VR environment) and amortized active membrane segmentation to direct interaction with data by the user. Strong experience in programming is required and previous experience in pixel classification and segmentation is recommended. The approach will be tested on large-scale multi modal images of neurons (e.g. via light sheet and 2-photons approaches) and if times permits, on CT scans of breast and hepatic cancers.
The successful candidate will be working directly with both designers and coders of the DIVA platform: Mohamed El Beheiry and Sebastien Doutreligne. They will be working directly with various members of the team of Jean-Marie Lledo to test the approaches on experimental data. They will join a highly multidisciplinary lab where physicists and computer scientists combine approaches to question random walks of biomolecules in cells and study relations between neural architecture and behavior in the drosophila larva. Finally, the successful candidate will have privileged access to multiple GPU clusters in the Institut Pasteur and custom platforms in the lab.
For a physicist: statistical physics or condensed matter physics.
For a computer scientist: Bayesian inference, variational inference, segmentation and optimization
Scripting language experience: Bash, Python
Nice to have Skills
Institut Pasteur (Paris)
Interested candidates should contact Jean-Baptiste Masson (email@example.com) and Maxime Dahan (Maxime.Dahan@curie.fr) with their CV, a brief motivation letter and 2 letters of recommendation.