Implementation Of An Open-Source 3D Data Hub Of 3D Cell Reconstructions And Meshes H/F

INRIA

Implementation of an open-source 3D data hub of 3D cell reconstructions and meshes
Le descriptif de l'offre ci-dessous est en Anglais
Type de contrat : CDD

Niveau de diplôme exigé : Bac +5 ou équivalent

Fonction : Ingénieur scientifique contractuel

Niveau d'expérience souhaité : De 3 à 5 ans

A propos du centre ou de la direction fonctionnelle

The Inria research centre in Lyon is the 9th Inria research centre, formally created in January 2022. It brings together approximately 410 people in 20 research teams and research support services.

Its staff are distributed in Villeurbanne, Lyon Gerland, and Saint-Etienne.

The Lyon centre is active in the fields of software, distributed and high-performance computing, embedded systems, quantum computing and privacy in the digital world, but also in digital health and computational biology.

Contexte et atouts du poste

We are looking for an engineer to join the AIstroSight project team for a fixed-term 18-month contract. The overall goal of the team is to develop innovative digital methods to further our understanding of the brain and find new treatments for brain diseases.

Based at the Pierre-Wertheimer Neurological Hospital in Lyon Est (Hospices Civils de Lyon, HCL), the team leverages applied mathematics and computer science in close collaboration with clinicians and neuroscience/imaging partners.

The engineer will report to Dr. Audrey Denizot, principle investigator of the project and a permanent researcher of the team, and will receive technical supervision from Dr. Jan-Michael Rye, an experienced permanent engineer of the Services d'Expérimentation et de Développement (SED) at Inria Lyon assigned to AistroSight's research projects. He has already established the technical and architectural foundation of the data hub as the team's lead developer.

Mission confiée

This project aims to design a domain-specific data hub to share 3D electron microscopy (EM) datasets and to develop open-source tools to quantify their structural properties and facilitate their use for computational modeling studies. It aims to contribute to unraveling the structural determinants of cell function at the nanoscale and to the use of more realistic meshes for cell digital twins.

The emergence of Digital Twins promises to revolutionize biology and medicine1. By mirroring the behavior of the modeled system, digital twins of diseased cells would allow personalized and improved drug discovery. This starts at the cellular level, where drugs interact with their cellular targets. Given that a cell's function is tightly linked to its shape2 and that recent computational works suggest that the nanoscopic intracellular landscape influences cell dynamics3,4, there is an increasing interest to simulate biochemical processes in realistic high-resolution 3D cell shapes.

Electron microscopy (EM) provides the highest resolution of 3D cell reconstructions. Recent technical advances such as cryo- and volume EM have yielded isotropic reconstructions of cells and organelles at an unprecedented spatial resolution (3)5. Open access to these reconstructions will prove invaluable to researchers to 1. quantify the geometrical properties of biological entities of interest in various (patho-)physiological conditions, 2. simulate biochemical processes within those detailed 3D structures and infer causal links, and 3. generate realistic synthetic datasets. However, most cell reconstructions derived from EM are not shared publicly, which prevents their usage in computational studies.

To address this challenge, our aim is to develop an interactive open-access web portal of 3D reconstructions derived from EM following the principles of the FAIR data (findable, accessible, interoperable, and reusable): the CELLular Architecture and Reconstructions Database (CELLARD). Once deployed, we will 1. leverage user feedback to adapt CELLARD to user needs ; 2. improve CELLARD's functionality by developing open-source Application Programming Interfaces (APIs) ; 3. conduct modeling studies to leverage structural information from CELLARD's reconstructions and showcase their use.

To determine the needs of researchers and collect initial datasets, we are working closely with EM experts, who have already shared EM images and 3D reconstructions with us and given us critical feedback on the metadata necessary and sufficient to describe datasets.

References
- Masison, J. et al. A modular computational framework for medical digital twins. Proceedings of the National Academy of Sciences118, e2024287118 (2021).
- Prasad, A. & Alizadeh, E. Cell Form and Function: Interpreting and Controlling the Shape of Adherent Cells. Trends in Biotechnology37, 347-357 (2019).
- Denizot, A., Castillo, M. F. V., Puchenkov, P., Calì, C. & De Schutter, E. The Ultrastructural Properties of the Endoplasmic Reticulum Govern Microdomain Signaling in Perisynaptic Astrocytic Processes. Glia74, e70091 (2026).
- Bell, M., Bartol, T., Sejnowski, T. & Rangamani, P. Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium. The Journal of General Physiology151, 1017-1034 (2019).
- Peddie, C. J. et al. Volume electron microscopy. Nat Rev Methods Primers 2, 1-23 (2022).

Main objectives of the mission

The mission is divided into the following three distinct goals, in order of priority:
- Finalize the implementation of the web portal
- Deploy the platform with datasets from partner laboratories, as well as ensure its administration and maintenance
- Develop APIs for visualization, synthetic mesh generation, and format/mesh conversions

In addition to these main tasks, the recruited candidate will be expected to share their expertise and carry out activities that benefit the research team or the institute's team of engineers.

Principales activités

- Finalize and validate elements already implemented (Aim 1)
- Deploy, administer, maintain, and populate the portal with various available datasets, in collaboration with IT (Aim 2)
- Improve the data hub based on user feedback (Aim 2)
- Explore methods and develop an API enabling the visualization of hosted 3D data (Aim 3)
- Implement a conversion tool between different file formats (e.g., surface meshes 3D simulation-ready meshes) (Aim 3)
- Explore methods and implement a tool generating realistic synthetic 3D objects (Aim 3)
- Collaborate with academic partners, in particular biologists (Aim 2)
- Participate in scientific valorization through publications and presentations (Aim 2)
- Develop and maintain technical documentation (Aim 1-2)
- Anticipate the future management of the project (Aim 1-2)

Collective activities such as:

- Training, seminars
- Promoting best practices in software engineering and experimentation
- Recruitment assistance and supervision
- Participation in project drafting, advice on development projects
- Representing the institute on technical matters

Compétences

The candidate should preferably hold a PhD or Master's degree in computer science and demonstrate skills or experience in most of the following areas:

- Experience with backend and frontend web technologies (e.g. Docker/Podman & Buildah, Flask, Gunicorn, HTTP APIs, HTML, CSS, JavaScript, Hugo, Bootstrap)
- Expertise in database/metadata management methods (e.g. metadata ontologies, CouchDB)
- Excellent programming skills in Python (modular design, documentation, unit testing, packaging, Git, etc.)
- Strong interest in biological applications
- Strong motivation for scientific research in an open science context
- Aptitude for working in a team and developing external collaborations
- Excellent command of English (oral and written)

Additional qualifications that will be valued include:

- Strong autonomy and a demonstrated ability to take initiative
- Sound, well-justified technical decision-making (trade-offs, documentation, rationale)
- Knowledge of cell biology
- Familiarity with 3D meshes and computational modeling workflows
- Previous contributions to open-source projects (code, documentation, community involvement)

Avantages

- Subsidizedmeals
- 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 teleworking (90 days / year) and flexible organization of working hours
- Social, cultural and sports events and activities
- Access to vocational training
- Social security coverage under conditions

Rémunération

Between2 692€ and 3 404€ gross / month (depending on experience and qualifications)