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The cytometry platform: expertise and reliability at the service of research

The cytometry platform aims to support researchers in setting up robust and reproducible experiments. It constitutes a reference space where technical expertise and scientific support combine to guarantee the quality and reliability of data.

Founded in 1976 with the creation of the Immunology Center, the Cytometry Service operates with two engineers, Sylvain Bigot (department manager) and Laurence Borge. Scientific responsibility is assured by Cyrille MionnetThe service is assisted by a steering committee, made up of advanced users, which meets every month.

Our services are structured around four axes:

Development of data processing and preparation workflows, integrating quality control, compensation and standardization, for reliable analyses whatever the software environment.

Design and optimization of multiparametric panels, in order to produce data that can be used in conventional and multidimensional analyses.

Provision of validated protocols, covering the essential steps of sample preparation, antibody titration and the study of key cellular processes such as apoptosis and the cell cycle.

Standardization and monitoring of instruments, ensuring the stability and comparability of acquisitions over time.

The main missions of the service are as follows:

  • Cell sorting under biological conditions of any type of cells in any medium: 1.5 ml to 15 ml tube or multi-well plates (96 or 384 wells). Sorting is carried out under conditions optimizing cell viability.
  • Quality control and maintenance of instruments.
  • User training: Users are trained to become self-sufficient on all of the department's analyzers. The training consists of two modules: a theoretical module and a practical module on an analyzer. Beginner users are then assisted in starting their own experiments.
  • Advice and assistance for cytometry experiments, data analysis and cell sorting.
  • Evaluation of new cell analysis and sorting technologies to maintain cytometry at the highest level in the department.
  • Development and optimization of analyzers and sorters: modification of instruments for optimal detection of fluorescent probes and proteins.

The service has an online booking calendar and a network of servers for secure data storage.

Training

Beyond these services, the platform places training and support for users at the heart of its mission. It ensures that best practices are transmitted and applied, thus guaranteeing methodological rigor and reproducibility of results. Training adapted to the needs and cytometry level of each user is offered by the platform: Conventional multiparametric cytometry, spectral cytometry, cell sorting.

Open Science

Through this approach, the platform contributes directly to the scientific excellence of research projects and to strengthening the quality of data generated in cytometry.

Projects

Project
2025
DECrypting of the Tissue Instruction of Plasmacytoid Dendritic Cells in Homeostasis and Viral Infections (DECITIP)

Project: DECITIP Plasmacytoid dendritic cells (pDCs) excel in the production of type I and III interferons (IFN), […]

Elena TOMASELLO
Pierre MILPIED
Project
2025
Circulating precursors and niche requirements for LysoDC differentiation (LysoDiff)

Our health depends on a delicate balance between immune defense against pathogens and tolerance to […]

Hugues LELOUARD
Marc BAJENOFF
Project
2025
The role of the maternal diet in embryonic immune system development

Project: CholControl You are what your mother ate Transgenerational impact of maternal diets via the regulation of RORγt activity […]

Serge VAN DE PAVERT
Project
2025
Lymphoid Tissue inducer cell ontogeny

Lymph nodes are formed in the embryo by Lymphoid Tissue Inducer (LTi) cells. LTi cells arise not from the yolk […]

Serge VAN DE PAVERT
Project
2025
Innate immune cells in the central nervous system

Innate immune cells are essential partners of the central nervous system, supporting both homeostasis and repair. Within the brain, perivascular […]

Serge VAN DE PAVERT
Project
2025
Treating Liver Metastases

Project: TREATLIVMETS Liver metastases occur in nearly 50% of cancer patients, particularly in […]

Eric VIVIER
Project
2025
Treating Breast Cancer

Project: Treating Breast Cancer Breast cancer is the most frequently diagnosed cancer in women in […]

Emilie NARNI-MANCINELLI
Project
2025
Role of plasmacytoid dendritic cells in disease-associated behavior (DC) induced during viral infections or obesity (pDCComp)

Project: pDCComp Individuals infected with viruses or suffering from inflammatory diseases develop a set of behavioral disorders […]

Elena TOMASELLO
Project
2025
Role of interactions with dendritic cells in maintaining NK cell functions in tumor conditions

Project: PLBIO 2024 Coordinator: Thierry Walzer, CIRI, Lyon. Other participant: Nathalie Bendriss-Vermare, CRCL, Lyon. Abstract: Natural Killer cells […]

Marc DALOD
Project
2025
To determine how dendritic cells promote effective anti-tumor NK and CD8 T responses in mouse models of breast cancer, spontaneously or in response to adjuvant administration

Project: ACLAMADABREC Partly through their effectiveness in activating natural killer (NK) cells and CD8 T lymphocytes […]

Marc DALOD
Project
2025
Computational deciphering and mathematical modeling of regulatory networks controlling plasmacytoid dendritic cell biology

Project: MITI Other participants: Magali Richard, LIG, Grenoble; Lionel Spinelli, CB2M hub of CIML. Summary: This project aims to […]

Marc DALOD
Project
2025
Accelerating our ability to understand and combat immunopathology caused by respiratory infections due to emerging viruses: from mouse models to patients to macaques

Project: UNFIRE Other participants: Ciphe (Ana Zarubica), Hospices Civils de Lyon and CIRI (Sophie Trouillet-Assant, Thierry Walzer), CoVir team […]

Marc DALOD
Marc BAJENOFF
Rejane RUA
Mauro GAYA
Philippe PIERRE
Project
2025
Contributions of non-coding genome-derived antigens to anti-tumor immune responses.

Project: PLBIO-25 Coordinator: Marianne BURBAGE, Institut Curie, Paris. Other participant: Andrew GRIFFITHS, ESPCI, Paris. The effectiveness of CD8 T lymphocytes […]

Nathalie AUPHAN-ANEZIN, PhD, HDR
Project
2025
A novel genetic screening approach to identify regulators of the biology of different types of human dendritic cells

Project: DCFUNDEVSCREEN Abstract: Studies in mice have shown the key antiviral/tumor role of plasmacytoid dendritic cells (pDCs) […]

Marc DALOD
Project
2025
Role of type I interferons and plasmacytoid dendritic cells in pulmonary immunopathology caused by respiratory viral infections

Project: RIPIREVI Other participants: CIPHE (Ana Zarubica and colleagues). Abstract: Type I interferons (IFN-Is) are essential for […]

Marc DALOD
Rejane RUA
Project
2025
LYMPHOMATLAS: an atlas of B-cell lymphomas at the single-cell level

Project: LYMPHOMATLAS Single-cell multi-omic studies in B-lymphomas have highlighted a […]

Sandrine ROULLAND
Pierre MILPIED
Project
2025
Discovery of a novel TSLP-induced regulatory axis in the pathogenesis of inflammatory skin diseases

Project: NRegSkin Project leader: Mei LI (IGBMC, Strasbourg). Other participants: Katia Boniface, Julien Seneschal (University of Bordeaux). Summary: The skin […]

Marc DALOD
Project
2025
CPC_profile: Characterization and Targeting of Cancer Precursor Cells (CPC) at the origin of relapses in B-cell lymphomas 

The progression of follicular lymphoma is marked by iterative cycles of remission and relapse, the latter usually resulting from the […]

Sandrine ROULLAND
Project
2025
Intracellular Carriers Against Resistant microOrganisms (ICARO)

Project: ICARO Current acellular vaccines are mostly effective against extracellular pathogens, but fail to induce a response […]

Hugues LELOUARD
Cyrille MIONNET
Project
2025
Respective immune inductive functions of epithelial tuft and M cells in relation to the gut-associated lymphoid tissue (PPTuft)

Project: PPTuft This project coordinated by Philippe Jay (IGF, Montpellier) in partnership with our team aims to determine the […]

Hugues LELOUARD
Project
2025
Myfunbat

Project: Myfunbat The project aims to define the diversity and functions of brown adipose tissue (BAT) macrophages, […]

Marc BAJENOFF
Project
2025
Endopos

Project: EndoPos The EndoPos project explores the role of the GDPD2 enzyme, produced in particular by pulp fibroblasts […]

Marc BAJENOFF
Project
2025
T-Mac 

Project: T-MAC The T-MAC project aims to understand how testicular macrophages and their niches contribute to the maintenance of […]

Marc BAJENOFF
Project
2025
NICHE

Project: NICHE The NICHE project explores the concept that macrophages (Macs) depend on local niches formed by […]

Marc BAJENOFF
Project
2025
Path Finder

Project: Path Finder This project aims to characterize the spatio-temporal development of type I dendritic cells (cDC1) in […]

Marc BAJENOFF
Project
2025
Role of Border-Associated Macrophages in meningioma and stroke

Project: DeCoDis In the context of a European consortium, we are investigating the dynamics and function of border-associated macrophages […]

Rejane RUA
Project
2025
Investigating the role of endosomal dynamic modulators during immune dysregulation and neurodegenerative pathology – IMPACT Sensors

Project: IMPACT Sensors Other participants: IGBMC, Strasbourg (Nicolas Charlet-Berguerand) and Institut Curie, Paris (Franck Perez). Duration 2025 – […]

Evelina GATTI
Project
2025
Pathogenic mechanisms of HSPB8 mutations in neuromuscular diseases: the role of the ribosomal and protein quality control system and the integrated stress response.

Partner: University of Milan, Italy (Prof. Angelo Poletti, DISFEB) Frameshift mutations in HSPB8 cause neuromyopathies by disrupting […]

Evelina GATTI
Project
2025
MARCH-I dependent ubiquitination in innate and adaptive immunity: from characterization to manipulation.

CNRS – University of Melbourne Graduate Research Projects The project investigates the molecular interplay between the E3-ubiquitin ligase MARCH1 and […]

Evelina GATTI
Project
2025
MetaNiche (Spatial-SCENITH) Metabolic niches regulate hematopoiesis (MetaNiche, ANR-22-CE15-0015-02).

Bone marrow metabolic niches regulate hematopoiesis (MetaNiche, ANR-22-CE15-0015-02). Duration: 2023–2027 (42 months).Partners & funding amounts: Institut Curie (L. Perié), Institut […]

Rafael J ARGUELLO
Project
2025
Biomarkers established to stratify sepsis long-term adverse effects to improve patients' survivorship (BEATsep)

Full title & acronym: Biomarkers established to stratify sepsis long-term adverse effects to improve patients' survivorship (BEATsep).Duration: 2024–2029 (60 months).Partners […]

Rafael J ARGUELLO
Project
2025
IMAGINe – High Risk High Gain IMAGINe (France)

Targeting intratumor metabolic heterogeneity in neuroblastoma to develop innovative treatments (IMAGINe) Type: National.Duration: 2024–2029 (48 months).Partners & funding amounts: CRCM […]

Rafael J ARGUELLO
Project
2025
TALETE (Transcan-3 ERA-NET, Europe)

Targeting acute myeloid leukemia immunosuppressive microenvironment by combined IDO1 inhibition and PD-1 blockade Type: European.Duration: 2023–2027 (36 months).Partners & funding […]

Rafael J ARGUELLO
Project
2025
South-ROCK – SIRIC

South-Research On Cancer for Kids. INCA Pediacriex (France) Type: National (integrated cancer site).Full title & acronym: South-Research On Cancer for […]

Rafael J ARGUELLO
Project
2025
Neuroimmune regulations and viral infection

The host response to pathogens is orchestrated by the immune system and the nervous system, both present in […]

Sophie UGOLINI
Project
2025
Regulation of inflammation by the neurokine TAFA4

We have demonstrated that the neurokine TAFA4, produced by sensory neurons in the skin, can promote tissue repair […]

Sophie UGOLINI
Project
2025
Sensory neurons and immune regulation

Beyond the pain perception processes that are induced in the event of injury or infection of the […]

Sophie UGOLINI
Project
2025
Epic-SCENITH: regulators of metabolism and epigenetics in glioblastoma-associated myeloid cells

Duration: 2021–2025.Partners & funding amounts: APHM/La Timone (E. Tabouret); amount for team: 325 k€.Responsibilities: PI–coordinator (only beneficiary)Theme & content of […]

Rafael J ARGUELLO
Project
2025
INCa PL-Bio CARIBBEAN

Anti-GD3 CAR-NK cells to overcome therapeutic resistance in glioblastoma (Caribbean). Type: National.Duration: 2025–2029 (48 months).Partners & funding amounts: INP-APHM (E. […]

Rafael J ARGUELLO
Project
2025
GCselection: Redefining the selection criteria for B lymphocytes in germinal centers

The GCselection project, coordinated by Dr. Pierre Milpied (CIML), revisits the mechanisms of antibody maturation in centers […]

Pierre MILPIED
Mauro GAYA