Job opening: 3D + time live imaging data analyst and software developer

The Tunicate embryology Research Team and the MRI core imaging facility in Montpellier, France, have an opening for a computer scientist in charge of the analysis of 3D + time fluorescence imaging data of living embryos of a class of marine invertebrates, the ascidians. The contract is for up to 4 years.

The selected candidate will use and further develop a tool for the automatic segmentation of fluorescence imaging data obtained using a light sheet microscope, ASTEC (Automated Segmentation and Tracking of Embryonic Cells) developed by the team and its collaborators (for an example output of ASTEC, watch the Video showing a segmented Phallusia embryo).

Missions:

– Use ASTEC to segment and track the imaging data collected by the team’s biologists. Perform statistical analyses of embryonic morphology (reproducibility between individuals and between species, phenotyping,…).

– Develop ASTEC’s ergonomics and man-machine interface to make the system as user-friendly as possible for biologist users. Participate in its deployment on the MRI imaging facility.

– Train biologist users in the use of the tool and set up and maintain a website presenting the system and its documentation to the scientific community.

– Improve ASTEC’s performance after finding its limits and the most important imaging parameters for the successful segmentation and tracking of cells.

Context:

The work will be carried out mainly within the tunicate development research team in Montpellier, Southern France. Frequent interactions will take place with the core facility’s engineers and with the computer scientists developing the core of ASTEC in the Morpheme, ICAR and MOSAIC teams.

Prerequisites:

– Undergraduate studies level in computer science, bioinformatics, applied mathematics, image analysis or physics
– Good knowledge of Python
– Knowledge in statistics
– Interest in biological image analysis
– Some training in biology would be a plus, but is not required
– A sufficient level in written / spoken English to interact daily with non-French speaking scientists. French knowledge not required

Contact:

Apply through the CNRS employment website. An informal contact can be established beforehand with the scientist in charge of the project, Patrick Lemaire, CRBM, patrick.lemaire@crbm.cnrs.fr

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