Development Of 3D Micrometer-Resolution Cardiac Tissue Meshes And Their Validation Using Image Processing Methods H/F

INRIA

Development of 3D micrometer-resolution cardiac tissue meshes and their validation using image processing methods
Le descriptif de l'offre ci-dessous est en Anglais
Type de contrat : CDD

Niveau de diplôme exigé : Thèse ou équivalent

Autre diplôme apprécié : MSc in science or engineering

Fonction : Chercheur contractuel

A propos du centre ou de la direction fonctionnelle

The Inria center at the University of Bordeaux is one of the nine Inria centers in France and has about twenty research teams.. The Inria centre is a major and recognized player in the field of digital sciences. It is at the heart of a rich R&D and innovation ecosystem: highly innovative SMEs, large industrial groups, competitiveness clusters, research and higher education players, laboratories of excellence, technological research institute...

Contexte et atouts du poste

Within the framework of the EuroHPC MICROCARD-2 project (project ID 101172576), a collaboration between 10 partner institutions in France, Germany, Italy and Norway, with the aim to develop exascale-capable software and meshes to perform macroscopic numerical simulations with microscopic resolution of the electrophysiology of the heart muscle.

Travel expenses for missions benefiting the project are covered within the limits of the scale in force.

Mission confiée

Assignments :

The recruited person will propose methods to efficiently segment confocal microscopy data of cardiac tissue, perform segmentations, and build three-dimensional (3D) tetrahedral meshes from these segmentations, with the help of mesh creation and remeshing software developed in our Center.

For a better knowledge of the proposed research subject :

A state of the art, bibliography and scientific references are available https://microcard.eu.

Collaboration :

The recruited person will be in connection with Dr Mark Potse and his group, with the Carmen team, the IHU Liryc, and the developers of the mmg3d software.

Responsibilities :

The person recruited may direct an intern for a period of a few months.

Principales activités

Main activities (5 maximum) :

- implementing and operating image segmentation methods forcardiac tissue samples across scales, from the microscale (confocal microscopy) to the nanoscale (electron tomography)
- building tetrahedral meshes from segmentations
- developing methods to validate artificial tissue meshes already developed by our team: quantifying connectivity, cell volume distribution, cell dimensions, cross-sectional shapes, ...
- incorporating other cell types (endothelium, fibroblasts, myofibroblasts)
- comparison of algorithmic choices during meshing (mesh quality, runtime,parallelisation/scaleability)

Additional activities (3 maximum) :

- working with our colleagues at IHU Liryc to setup sample preparation and confocal imaging/analysis workflows
- presentation of plans, background, and results in team meetings and project meetings
- preparing publications

Compétences

Technical skills and level required : Linux, bash or similar shell, shell scripting, Python, ITK, VTK, basic knowledge of C or C++.

Languages : English (required), French (appreciated)

Relational skills : Ability to work in a team, to collaborate responsively

Other values appreciated : An appetite for interdisciplinary collaboration, experience with Paraview, Gmsh, and deep-learning methods for pattern recognition.

Avantages

- Subsidized meals
- Partial reimbursement of public transport costs
- Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
- Possibility of partial teleworking and flexible organization of working hours
- Professional equipment available (videoconferencing, loan of computer equipment, etc.)
- Social, cultural and sports events and activities
- Access to vocational training
- Social security coverage

Rémunération

Salary based on education and professional experience from 3085 euros (The amount shown is before deductions for mandatory social security contributions and income tax).