Engineer - Cytometry Data Analysis

Background

The Luxembourg Institute of Health (LIH) is a public biomedical research organisation focused on precision health. Its research aims to turn scientific excellence into concrete benefits for patients, with cancer and immunological disorders as priority disease areas.

The National Cytometry Platform (NCP) belongs to the Integrated Biobank of Luxembourg (IBBL), within LIH’s Translational Medicine Operations Hub (TMOH). The NCP pairs state-of-the-art single-cell technologies with careful experimental design and advanced data analysis. It serves researchers in Luxembourg and international collaborators, and runs training in cytometry and high-dimensional data analysis.

The NCP’s flow, spectral, mass and imaging cytometry instruments generate ever larger and more complex datasets. To make the most of them, the NCP is recruiting an engineer who will combine data analysis with the management of part of the instrument park. You will join a multidisciplinary team of engineers, scientists and technicians led by Antonio Cosma, Head of the NCP.

The Role

You will be the NCP’s reference engineer for data analysis and production software at the platform. Half of your time will go high-dimensional data analysis and supporting users with data analysis. The other half covers managing and operating some of the core facility’s instruments, alongside user support and training.

You will accompany LIH research groups, clinical studies and external partners from study design to publication-ready results. Recent NCP work includes a stepwise deep-immunophenotyping pipeline, an OMIP database of optimised panels, and IPerGlio, which combines immunomics and AI for personalised glioblastoma care.

Key Accountabilities

Data analysis and software support (about half of the time)

• Quality control and pre-processing: Check data quality, review unmixing and compensation, and apply transformation, normalisation and batch correction across large multi-batch studies.
• High-dimensional analysis: Perform clustering, dimensionality reduction and automated gating on flow, spectral, mass and imaging cytometry data, and interpret the results with users.
• Statistics: Apply sound statistical frameworks: differential abundance and state testing, mixed and longitudinal models, compositional approaches and multiple-testing control.
• Software support: Manage the production software at the NCP (e.g., FlowJo, OMIQ, Cytolution, CellEngine, Infinicyt, Qlucore, GraphPad Prism, Tableau) and support users in applying it.
• Analysis workflows: Set up, validate and document standardised workflows and templates in this software; evaluate new tools before they enter routine use.
• Data management: Organise data and metadata following FAIR principles and community standards (e.g., MIFlowCyt), in line with LIH data-protection (GDPR) and AI-use policies.

Instruments, users and platform (about half of the time)

• Instrument management: Take charge of some of the core facility’s instruments: daily QC and performance tracking, preventive maintenance with vendors, troubleshooting, scheduling and consumables.
• Instrument operation: Run sample acquisition and cell sorting for user projects, and train users to operate the instruments independently.
• Study design: Advise users on experimental design, sample size, batch layout (barcoding, reference samples, controls) and the analysis plan.
• Reporting: Deliver clear analysis reports, publication-quality figures and interactive dashboards, and contribute to scientific publications.
• Training: Train users in cytometry data analysis through one-to-one support, courses and workshops; write user guides and SOPs.
• Panel design and quality: Contribute to panel design and assay validation, and apply the ISO 9001 quality management system.
• Technology watch: Follow new computational methods, including AI-based approaches, and share expertise in the international cytometry community (e.g., ISAC, CYTO).

Key Skills, Experience and Qualifications

Required

• Education: Master’s or engineering degree, in bioinformatics, computational biology, biostatistics or data science, or in biomedical sciences with a strong computational component.
• Experience: At least 2 years of hands-on analysis of high-dimensional cytometry data (spectral flow and/or mass cytometry), ideally in a core facility or translational research setting.
• Instrument experience: Hands-on experience operating flow, spectral or mass cytometers, or cell sorters.
• Software: Proficiency in commercial analysis platforms such as FlowJo, OMIQ, Cytolution, CellEngine or Infinicyt.
• Cytometry analysis: Practical command of compensation and spectral unmixing review, batch correction, clustering (e.g., FlowSOM, PhenoGraph), dimensionality reduction (UMAP, t-SNE) and gating strategies.
• Biology: Good understanding of immunology.
• Communication: Ability to explain analysis choices and results clearly to biologists and clinicians, orally and in writing.

Assets

• Experience performing cell-based assays.
• Analysis of imaging mass cytometry (IMC) and/or other spatial biology data, or of image data (e.g., QuPath, histoCAT, Fiji, IDEAS for ImageStream).
• Compositional data analysis, Bayesian or machine-learning methods applied to single-cell data.
• Interactive dashboards (e.g., Tableau).
• Experience in a service environment and with quality management (ISO 9001).

Personal skills

• Service-oriented, rigorous and well organised, able to run several projects in parallel.
• Self-driven and able to work independently, while enjoying teamwork and teaching.

Language skills

• Fluent English, written and spoken.
• Knowledge of another EU language (e.g., French, German or Luxembourgish) is an asset.

Gender Equality

The LIH is an equal opportunities employer, fully committed to removing discriminatory barriers — not only those related to gender — in the recruitment and career progression of our staff.

The LIH is attentive to gender representation among its leadership staff and aims to eliminate obstacles to recruitment and promotion of female leaders and their career development.