# MSCA AGILE


## Posts

- [AGILE: When Art and Science Break Their Boxes](https://www.msca-agile.eu/agile-when-art-and-science-break-their-boxes/): AGILE explores the intersection of art and science, inviting multidisciplinary artists to collaborate with researchers. Through residencies and dialogue, scientific inquiry transforms into music, visual art, poetry, and performance. Discover how knowledge can be translated across mediums and how art can illuminate science. Join us in this dynamic space of experimentation and shared imagination.

## Pages

- [Cookie Policy](https://www.msca-agile.eu/cookie-policy/): This page provides comprehensive information about how we use cookies on our website to enhance your browsing experience, improve website performance, and deliver personalized content. Cookies are small text files that are stored on your device when you visit our site. They help us understand how visitors interact with our website, allowing us to offer a smoother and more efficient user experience. In the table below, you will find detailed information about each type of cookie we use, their purpose, and how long they remain on your device. We are committed to respecting your privacy and providing transparency about the […]
- [Trainings and Meetings](https://www.msca-agile.eu/trainings-and-meetings/): TRAININGS AND MEETINGS AGILE Training Programme & Network-Wide Events The AGILE project offers a comprehensive and structured training programme combining scientific excellence, transferable skills development, and career-oriented activities. Throughout the project, Early Stage Researchers benefit from network-wide conferences, specialized technical workshops, online courses, and dedicated career days in both academia and industry. From advanced microscopy imaging and machine learning applications in plant sciences to FAIR data management, critical thinking, entrepreneurship, and project management, the programme is designed to provide interdisciplinary expertise and foster innovation. These activities, delivered by leading partner institutions across Europe, ensure high-quality training, collaboration, and professional growth […]
- [Sitemap](https://www.msca-agile.eu/sitemap/): Sitemap
- [Legal notice](https://www.msca-agile.eu/legal-notice/): LEGAL NOTICE     1. Website Publisher This website (the “Website”) is published by MSCA AGILE. Funded by the European Union under Grant Agreement No. 101226536 – AGILE. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union. 2. Publication Director The Publication Director is: Name: Frédéric PONTVIANNEPosition: Coordinator of the AGILE consortiumContact: contact@msca-agile.eu 3. Hosting Provider The Website is hosted by: Hosting Provider Name: HOSTINGER operations UABRegistered Office: Švitrigailos str. 34, Vilnius 03230 LithuaniaTelephone: +37064503378Website: https://www.hostinger.com 4. Intellectual Property All content on this Website, including but not limited to text, images, graphics, […]
- [Integration of spatiotemporal image analysis results into OMERO, a scalable and FAIR data management framework](https://www.msca-agile.eu/individual-research-projects/integration-of-spatiotemporal-image-analysis-results-into-omero-a-scalable-and-fair-data-management-framework/): INDIVIDUAL RESEARCH PROJECT 13 Integration of spatiotemporal image analysis results into OMERO, a scalable and FAIR data management framework Home / Blog / Parent Category / Category / Page Title Abstract The ingestion of analysis results in scalable and efficient open formats, and the development of tools to efficiently query these analysis results, are critical challenges to the democratisation of image analysis. To address these challenges, we will focus on the storage of analytical results allowing queries without loading in memory all the results associated with an analysis, by contributing to the development of analytical pipelines (ChromTrack3D workflows) and the […]
- [Characterisation of peripheral light-induced transcription clusters](https://www.msca-agile.eu/individual-research-projects/characterisation-of-peripheral-light-induced-transcription-clusters/): INDIVIDUAL RESEARCH PROJECT 14 Characterisation of peripheral light-induced transcription clusters Home / Blog / Parent Category / Category / Page Title Abstract The three dimensional arrangement of the genome in the nuclear space likely plays a significant role in transcriptional regulation. Our goal is to understand whether and how the 3D organisation of transcription contributes fast responses to the environment. Using 3D STED imaging we identified Light Induced Transcription Clusters (LITC) enriched at the nuclear periphery of plant cells exposed to light. The project aims at: (Obj1) quantifying LITC distribution relative to the nuclear pore complex, in wild-type and in […]
- [Integration of spatiotemporal image analysis tools into Fractal, a scalable and FAIR (Findable, Accessible, Interoperable, Reproducible) analysis platform](https://www.msca-agile.eu/individual-research-projects/integration-of-spatiotemporal-image-analysis-tools-into-fractal-a-scalable-and-fair-findable-accessible-interoperable-reproducible-analysis-platform/): INDIVIDUAL RESEARCH PROJECT 15 Integration of spatiotemporal image analysis tools into Fractal, a scalable and FAIR (Findable, Accessible, Interoperable, Reproducible) analysis platform Home / Blog / Parent Category / Category / Page Title Abstract The two main challenges standing in the way of democratizing bioimage analysis in plant biology are 1) the availability of algorithms carrying out complex analysis tasks across spatial and temporal dimensions, and 2) the integration of these algorithms into frameworks making them accessible to all researchers, regardless of their computational expertise. Recognizing the power of modern image analysis methods and the value of the next-generation image […]
- [Quantifying the light and Temperature driven association of phyB photobodies with chromatins](https://www.msca-agile.eu/individual-research-projects/quantifying-the-light-and-temperature-driven-association-of-phyb-photobodies-with-chromatins/): INDIVIDUAL RESEARCH PROJECT 12 Quantifying the light and Temperature driven association of phyB photobodies with chromatin Home / Blog / Parent Category / Category / Page Title Abstract phytochrome B photobodies (phyB PBs) are phase-separated dynamic compartments that form or dissipate in response to light and temperature changes1. phyB PBs regulate transcription, however their functional association with target genes has never been demonstrated. (Obj1) we will quantify phyB PBs features (size, intensity) and positioning relative to target loci and other nuclear compartments (heterochromatin and periphery) in intact leaf nuclei, comparing different light (Red versus Far-Red) and temperature (21℃ versus 30℃) […]
- [Understanding peri-nuclear actin organisation in response to environmental stresses and its effect on nuclear architecture](https://www.msca-agile.eu/individual-research-projects/understanding-peri-nuclear-actin-organisation-in-response-to-environmental-stresses-and-its-effect-on-nuclear-architecture/): INDIVIDUAL RESEARCH PROJECT 11 Understanding peri-nuclear actin organisation in response to environmental stresses and its effect on nuclear architecture Home / Blog / Parent Category / Category / Page Title Abstract Plant cell nuclei undergo striking changes in size and shape under environmental stress, processes closely linked to the organization of the actin cytoskeleton. This PhD project aims to uncover how peri-nuclear actin organisation regulates nuclear architecture and mediates responses to environmental stress, with a focus on heat stress. Obj. 1: Characterize peri-nuclear actin organization under normal conditions using lattice-SIM and spinning disk confocal microscopy. A novel fluorescent reporter line developed […]
- [Analysing the structure and molecular mechanism of the NE-ER interface in plants](https://www.msca-agile.eu/individual-research-projects/analysing-the-structure-and-molecular-mechanism-of-the-ne-er-interface-in-plants/): INDIVIDUAL RESEARCH PROJECT 10 Analysing the structure and molecular mechanism of the NE-ER interface in plants Home / Blog / Parent Category / Category / Page Title Objectives ER structure and functionality are influenced by temperature and heat stress. This also affects the structure and organization of the ER-nuclear interface, which impairs protein transport to the nucleus. In this project we address the hypothesis that under heat stress, ER shaping proteins modify properties of the nuclear envelope (NE) resulting in changes in membrane tension and with this in structural changes of Nuclear Pore Complexes (NPC). Therefore, we will analyse heat-stress […]
- [Elucidating the role of cold-induced spatial clustering at the FLC locus during Polycomb-mediated gene silencing](https://www.msca-agile.eu/individual-research-projects/elucidating-the-role-of-cold-induced-spatial-clustering-at-the-flc-locus-during-polycomb-mediated-gene-silencing/): INDIVIDUAL RESEARCH PROJECT 9 Elucidating the role of cold-induced spatial clustering at the FLC locus during Polycomb-mediated gene silencing Home / Blog / Parent Category / Category / Page Title Abstract Investigate the functional connection between physical clustering and epigenetic silencing of the major flowering regulator FLOWERING LOCUS C (FLC) locus. Our previous findings revealed that cold-induced epigenetic silencing of FLC is accompanied by the physical clustering of FLC alleles7, suggesting a coordinated mechanism linking chromatin organization with gene expression regulation. Here, we will: (Obj1) Investigate the relationship between clustering and transcriptional output by measuring FLC nascent transcript levels (using […]
- [Imaging cellular heterogeneity in nuclear RNA bursting triggered by Phosphate status variations](https://www.msca-agile.eu/individual-research-projects/imaging-cellular-heterogeneity-in-nuclear-rna-bursting-triggered-by-phosphate-status-variations/): INDIVIDUAL RESEARCH PROJECT 8 Imaging cellular heterogeneity in nuclear RNA bursting triggered by Phosphate status variations Home / Blog / Parent Category / Category / Page Title Abstract We want to unravel the variability of the transcription (RNA bursting) between cells of the root during Phosphate homeostasis variation. Combining whole-mount roots growing in a microfluidics system, enabling fine-tuning Pi parameters and MS2/MCP labelling, we will access live, dual imaging (spinning disk microscopy) of the nascent RNAs with a cellular resolution1. 3D single molecule RNA FISH1,2 will be used to validate the results obtained by a distinct approach. Different algorithms (developed […]
- [Characterizing altered 3D chromatin organization in Arabidopsis pds5 mutants](https://www.msca-agile.eu/individual-research-projects/characterizing-altered-3d-chromatin-organization-in-arabidopsis-pds5-mutants/): INDIVIDUAL RESEARCH PROJECT 7 Characterizing altered 3D chromatin organization in Arabidopsis pds5 mutants Home / Blog / Parent Category / Category / Page Title Abstract This project focuses on characterizing changes in spatial chromatin organization in the Arabidopsis pds5 mutants that alter chromatin compartmentalization and form prominent Topologically Associating Domains (TADs) across the genome. Using ploidy-sorted nuclei, which allows us to exclude potential variations amongst nuclei due to endoreplication, we aim to achieve the following objectives: (Obj1) with FISH, to measure the distance between lamin-associated domains (LADs) and the nuclear periphery in pds5; (Obj2) with immunostaining, to characterize the spatial […]
- [Comparative chromatin analysis of supernumerary and standard chromosomes](https://www.msca-agile.eu/individual-research-projects/comparative-chromatin-analysis-of-supernumerary-and-standard-chromosomes/): INDIVIDUAL RESEARCH PROJECT 6 Comparative chromatin analysis of supernumerary and standard chromosomes Home / Blog / Parent Category / Category / Page Title Objectives Compare the spatial distribution and chromatin composition of standard A chromosomes (As) and supernumerary B chromosomes (Bs) of rye. To determine if supernumerary chromosomes have a preferential or nonrandom distribution, (Obj1) we will analyse the relative position of As and Bs in intact root nuclei of tissue sections labelled using chromosome painting and imaged using 3D super-resolution (SIM) and Imaris-based image analysis (S1). To determine whether B chromosomes have a different epigenetic setup than As, (Obj2) […]
- [Role of nuclear lamina in Rabl chromosome configuration](https://www.msca-agile.eu/individual-research-projects/role-of-nuclear-lamina-in-rabl-chromosome-configuration/): INDIVIDUAL RESEARCH PROJECT 5 Role of nuclear lamina in Rabl chromosome configuration Home / Blog / Parent Category / Category / Page Title Abstract Interphase chromosome organization is an important factor linked with chromatin states, gene expression and cell cycle stages. Understanding chromosome organization in cereals with large genomes is still in its infancy. We developed means of exploring dynamic chromosome organization in the small grain temperate cereal model barley, and aims to explore the role of nuclear lamina in the establishment and maintenance of Rabl chromosome configuration. (Obj1) Quantify the temporal and spatial relationships between centromeres (CENH3) and nuclear […]
- [Cell-cycle regulation of DNA repair](https://www.msca-agile.eu/individual-research-projects/cell-cycle-regulation-of-dna-repair/): INDIVIDUAL RESEARCH PROJECT 4 Cell-cycle regulation of DNA repair Home / Blog / Parent Category / Category / Page Title Abstract This IRP aims to determine how the plant DNA damage response (DDR) changes during the cell cycle. To examine the role of reparative mechanisms during replication and outside of it, we will utilize PCNA1 protein, showing the distinct pattern in G1/G2 and S phases, genotoxic stress (zeocin/camptothecin – applied via root microfluidic), DDR deficient lines (atr, fas1) and DDR marker proteins MRE11/PARP1. (Obj1) Quantification of PCNA1 association with DNA repair factors MRE11 and PARP1 in wild-type (WT) and mutant […]
- [Connecting Chromosomes and the Nuclear Envelope: Mechanisms Shaping Meiotic Prophase Organization](https://www.msca-agile.eu/individual-research-projects/connecting-chromosomes-and-the-nuclear-envelope-mechanisms-shaping-meiotic-prophase-organization/): INDIVIDUAL RESEARCH PROJECT 3 Connecting Chromosomes and the Nuclear Envelope: Mechanisms Shaping Meiotic Prophase Organization Home / Blog / Parent Category / Category / Page Title Abstract Upon entry into meiotic prophase, chromosome ends become anchored to the nuclear envelope (NE), establishing dynamic connections between the nucleus and the cytoplasmic microtubule network. These connections are mediated by NE-spanning transmembrane protein complexes that assemble into specialized structures known as attachment plates (APs). The formation and regulation of APs are crucial for ensuring the recognition and pairing of homologous chromosomes. When this attachment process is defective, it leads to abnormal chromosome dynamics, […]
- [OMERO embedding and Optimisation of Biom3d, an image analysis tool using deep-learning networks](https://www.msca-agile.eu/individual-research-projects/omero-embedding-and-optimisation-of-biom3d-an-image-analysis-tool-using-deep-learning-networks/): INDIVIDUAL RESEARCH PROJECT 2 OMERO embedding and Optimisation of Biom3d, an image analysis tool using deep-learning networks Home / Blog / Parent Category / Category / Page Title Abstract Neural networks, employing deep learning (DL), have become essential for high-throughput image analysis. However, DL tools should be made accessible to a broader scientific community, including plant biologists. In line with the FAIR (Findable, Accessible, Interoperable, Reusable) principles, (Obj1) we aim to implement new image analysis functionalities into Biom3d, a modular framework based on DL networks initially designed to quantify nuclear shape and chromatin organization. (Obj2) To facilitate the use of […]
- [Chromatin mobility induced by temperature changes](https://www.msca-agile.eu/individual-research-projects/chromatin-mobility-induced-by-temperature-changes/): INDIVIDUAL RESEARCH PROJECT 1 Chromatin mobility induced by temperature changes Home / Blog / Parent Category / Category / Page Title Objectives Heat stress affects heterochromatin organization and nuclear movement, but the impact remains unknown at the gene scale. This IRP investigates how nuclear and chromosomal positioning affect gene mobility and transcriptional activity. Measure will be performed under control and heat stress conditions, in wild-type and in plants impaired in two mutants affected in temperature sensing and adaptation (hsfA2 and hsp101). This project will greatly benefit from a comprehensive collection of Arabidopsis thaliana lines tagged at hundreds of individual locations […]
- [Virginie UHLMANN](https://www.msca-agile.eu/network/virginie-uhlmann/): Virginie UHLMANN Assistant Professor in Bioimaging and Data Analysis BioVisionCenter Director ORCID link : 0000-0002-2859-9241 Website links : Profil and BioVisonCenter IRP : Integration of spatiotemporal image analysis tools into Fractal, a scalable and FAIR (Findable, Accessible, Interoperable, Reproducible) analysis platform Institute University of Zürich, Switzerland Research thematic Microscopy image analysis Research My research group focuses on the development of novel algorithms to quantify complex visual phenotypes from microscopy data and on the application of these methods to biological discovery. Our contributions span both modality- and scale-agnostic image quantification methods leveraging state-of-the-art machine learning, as well as tailored computational pipelines developed […]
- [Célia BAROUX](https://www.msca-agile.eu/network/celia-baroux/): Célia BAROUX PD Dr., Group Leader Department of Plant and Microbial Biology, University of Zurich ORCID link : 0000-0001-6307-2229Website links : Research IRP : Characterisation of peripheral light-induced transcription clusters Institute Chromatin Dynamics and Quantitative Microscopy for Plant Sciences, University of Zürich, Switzerland Research thematic Chromatin dynamics, 3D genome organization & quantitative microscopy in plants Research My research group investigates the three-dimensional organisation and dynamic behaviour of chromatin in plant nuclei, aiming to understand how chromatin structure influences cellular transitions during development and in response to environmental cues. Plants exhibit remarkable nuclear plasticity — the genome’s spatial arrangement changes throughout the […]
- [Jean-Marie BUREL](https://www.msca-agile.eu/network/jean-marie-burel/): Jean-Marie BUREL Dr., Group Leader Faculty of Life Sciences, University of Dundee ORCID link : 0000-0002-1789-1861 Website links : OME IRP : Integration of spatiotemporal image analysis results into OMERO, a scalable and FAIR data management framework Institute Faculty of Life Sciences, University of Dundee, United Kingdom Research thematic Image Data standard, Software development, FAIR data. Research My research focuses on developing open-source technologies to build the data management and integration tools needed to make imaging data a first-class resource for the next generation of life sciences research. We develop and release data models, file format translators and data management software. […]
- [Kasper VAN GELDEREN](https://www.msca-agile.eu/network/kasper-van-gelderen/): Kasper VAN GELDEREN Independent research group leader ORCID link : 0000-0001-7809-2812Website links : Laboratory IRP : Quantifying the light and Temperature driven association of phyB photobodies with chromatins Institute Centre for Organismal Studies, Heidelberg, Germany Research thematic Plant light perception and signalling, phase separation and condensate formation, plant developmental plasticity. Research My group focuses on the regulation of light perception and signalling in the plant nucleus. Phytochrome photoreceptors are crucial red light sensors affecting plant developmental plasticity. They can be found in almost all of the cells of the plant body, and within these cells, they cluster into subnuclear phase separated […]
- [Joseph MCKENNA](https://www.msca-agile.eu/network/joseph-mckenna/): Joseph MCKENNA BBSRC Discovery Fellow, Assistant Professor ORCID link : 0000-0003-4838-6048Website links : Research IRP : Understanding peri-nuclear actin organisation in response to environmental stresses and its effect on nuclear architecture Institute School of Life Sciences, University of Warwick, United Kingdom Research thematic Plant Cytoskeleton and Organelle Organisation and Dynamics Research We uncover how plant cells are built, organised, and rapidly rewired under stress, by decoding the dynamic behaviour of the cytoskeleton and organelles. Using cutting-edge super-resolution microscopy, spinning disk confocal imaging, and proximity labelling proteomics we map how cellular architecture is assembled and controlled in living plant cells. Our long-term […]
- [Verena KRIECHBAUMER](https://www.msca-agile.eu/network/verena-kriechbaumer/): Prof. Verena KRIECHBAUMER Professor of Plant Sciences and Biotechnology ORCID link : 0000-0003-3782-5834 Website links : Research Group and staff page Brookes Kriechbaumer IRP : Analysing the structure and molecular mechanism of the NE-ER interface in plants Institute School of Biological and Medical Sciences, Oxford Brookes University, United Kingdom Research thematic Endomembrane Structure and Function Research My research explores how the organisation and dynamics of plant cell membranes control growth, development and stress responses. We focus on the endoplasmic reticulum (ER) as a central hub for protein folding, lipid metabolism and inter-organelle communication. By combining cell biology, molecular genetics and advanced live-cell […]
- [Stefanie ROSA](https://www.msca-agile.eu/network/stefanie-rosa/): Stefanie ROSA Associate Professor ORCID link : 0000-0002-8100-1253 Website links : Research Group and staff page Stefanie Rosa IRP : Elucidating the role of cold-induced spatial clustering at the FLC locus during Polycomb-mediated gene silencing Institute Department of Plant Biology, Swedish University of Agricultural Sciences, Swedish Research thematic Chromatin Dynamics & Genome Integrity Research My group investigates how chromatin dynamics within the plant nucleus shape gene expression and preserve genome integrity. Because nuclear processes are often heterogeneous across cells, we are moving beyond population-averaged measurements toward quantitative, single-cell and single-molecule approaches. A key part of our work is therefore to develop and […]
- [Laurent NUSSAUME](https://www.msca-agile.eu/network/laurent-nussaume/): Laurent NUSSAUME CEA Research Director ORCID link : 0000-0002-9445-2563Website links : EBMP IRP : Imaging cellular heterogeneity in nuclear RNA bursting triggered by Phosphate status variations Institute BIAM, Saint Paul lez Durance, FRANCE Research Our research focuses on Phosphate: a main mineral macro-nutrient for plants. We study its uptake and associated signaling pathways. We combine genetics, molecular biology, plant physiology, radio-imaging and cellular biology. For such a purpose, we have developed state-of-the-art technologies such as live cell transcriptomics imaging using MS2/MCP system coupled with microfluidics (Hani et al., 2021) and a novel reporter system facilitating dynamic study of protein/protein interactions in […]
- [Chang LIU](https://www.msca-agile.eu/network/chang-liu/): Chang LIU Professor ORCID link : 0000-0003-2859-4288 Website links :  Research IRP : Characterizing altered 3D chromatin organization in Arabidopsis pds5 mutants Institute Institute of Biology, University of Hohenheim, Germany Research thematic Chromatin organization Research My research focuses on understanding how the vast length of eukaryotic DNA is hierarchically organized within the tiny space of the nucleus, and how this 3D chromatin architecture regulates essential processes such as transcription, DNA replication, recombination, and repair. I am particularly interested in how chromatin packing shapes long-range interactions and links epigenomic and transcriptomic landscapes to genome topology. In plants, where genomes are highly dynamic […]
- [Andreas HOUBEN](https://www.msca-agile.eu/network/andreas-houben/): Andreas HOUBEN Research Group Leader ORCID link : 0000-0003-3419-239XWebsite links : Research IRP : Comparative chromatin analysis of supernumerary and standard chromosomes Institute IPK Leibniz Institute, Germany Research thematic Comparative chromatin analysis of supernumerary and standard chromosomes Research The group’s research focus is the biology of chromosomes, specifically aiming to explore the regulation, organization, segregation and evolution of the mitotic, meiotic and interphase chromosomes of both model, wild and crop species. Such knowledge has the potential to increase the efficiency of the crop breeding process. We are currently I Analyzing both the organization and dynamics of cell-cycle-dependent chromatin in nuclei and […]
- [Aleš PEČINKA](https://www.msca-agile.eu/network/ales-pecinka/): Aleš PEČINKA Assoc. prof., Dr., Group Leader Centre of Plant structural and Functional Genomics ORCID link : 0000-0001-9277-1766 Website links : Profil IRP : Role of nuclear lamina in Rabl chromosome configuration Institute Institute of Experimental Botany, Czech Academy of Sciences, Czech Republic Research thematic Chromatin functions, 3D genome organization, genome stability, Arabidopsis, barley Research My research group focuses on the analysis of chromatin functions in regulating 3D organization and dynamics of chromosomes, control of gene expression in the context of plant breeding and meintenance of genome stability. Our favorite model plants include Arabidopsis and barley. While nuclear genome carries most […]
- [Martina DVOŘÁČKOVÁ](https://www.msca-agile.eu/network/martina-dvorackova/): Martina DVOŘÁČKOVÁ Senior researcher Chromatin Molecular Complexes, group of J. FajkusMendel center for plant genomics and proteomics ORCID link : 0000-0001-5998-6159 Website links : Profil IRP : Cell-cycle regulation of DNA repair Institute CEITEC MU, Brno, Czech Republic Research thematic chromatin stability, DNA repair during cell cycle Research We focus on how plant cells maintain genome integrity, through the coordinated regulation of DNA repair, chromatin assembly, and cell cycle progression. Using advanced live-cell imaging, we visualize DNA repair processes in real time across defined cell cycle phases, employing Arabidopsis PCNA1 as a marker of the early DNA damage response in wild-type […]
- [Mathilde GRELON](https://www.msca-agile.eu/network/mathilde-grelon/): MathildeGRELON INRAE Research Director, Group leader Mechanisms of meiotic recombination team (MEIOME) ORCID link : 0000-0003-3695-4984Website links : Research Team IRP : Connecting Chromosomes and the Nuclear Envelope: Mechanisms Shaping Meiotic Prophase Organization Institute IJPB, INRAE Versailles, France Research thematic Chromosome dynamics during meiosis Research Meiosis is the specialized cell division that generates haploid cells and underpins sexual reproduction. Using complementary approaches in genetics, molecular biology, cytology, and advanced live-cell imaging, our team investigates the molecular and cellular mechanisms that govern meiotic progression in plants. A major focus of our work is the dynamic behavior of chromosomes during meiotic prophase and […]
- [Christophe TATOUT](https://www.msca-agile.eu/network/christophe-tatout/): Prof. ChristopheTATOUT Professor of Plant epigenetics and bioinformatics ORCID link : 0000-0001-5215-2338 Website links : Research Group IRP : OMERO embedding and Optimisation of Biom3d, an image analysis tool using deep-learning networks Institute iGRED, Clermont-Ferrand, France Research thematic Chromatin and nuclear dynamics Research My research focuses on developing standardized, FAIR-compliant workflows for bioimage data handling from acquisition and storage to analysis. Using OMERO as a data management platform, integrated with HPC resources at our data center, I develop methods of image analysis on plant nuclei microscopy datasets to study chromatin and nuclear dynamics in plants. Our recent developments focused on a reproducible […]
- [Frédéric PONTVIANNE](https://www.msca-agile.eu/network/frederic-pontvianne/): FrédéricPONTVIANNE CNRS Research Director ORCID link : 0000-0002-2913-4104Website links : Research and team CODED IRP : Chromatin mobility induced by temperature changes​ Institute iGRED, Clermont-Ferrand, France Research thematic Chromatin organization and dynamic in plant Research My research group focuses on developing tools that can be used in microscopy to study the position and expression of genes with a single-cell and allelic resolution. To this end, we have adapted the ANCHOR system (NeoVirTech®) in plants to monitor the position of a single locus in the genome (Meschichi et al., 2021). We are currently I Creating a collection of A. thaliana lines with a […]
- [Recruitment](https://www.msca-agile.eu/recruitment/): Application closed Final decisions to be announced by the end of June 2026
- [Homepage](https://www.msca-agile.eu/): Advanced Training for Next Generation Scientists in Spatio-Temporal Imaging of Plant Cells Marie Skłodowska-Curie Doctoral Network Légende à mettre Transforming plant science through quantitative imaging Understanding how plants grow and respond to their environment requires insights from the molecular level to the entire organism. Quantitative microscopy provides this opportunity. Supported by the Marie Skłodowska-Curie Actions programme, the AGILE project offers interdisciplinary doctoral training in imaging and computational analysis focused on plant systems. Researchers investigate the structure and function of plant cell nuclei, uncovering principles that influence growth, development and adaptation to environmental changes with FAIR principles. Findable Accessible Interoperable Reusable A […]
- [Contact](https://www.msca-agile.eu/contact/): Contact us We will respond as soon as possible. Email contact@msca-agile.eu
- [News and Outreach](https://www.msca-agile.eu/news-and-outreach/): News and Outreach Home / Blog / Parent Category / Category / Page Title Stay up to date with the latest developments of the project.This News page brings together our most recent articles, announcements, achievements, events, and key updates. Here you will find insights into ongoing research activities, milestones, collaborations, and highlights that showcase the project’s progress and impact. Uncategorized 24 février 2026 AGILE: When Art and Science Break Their Boxes AGILE explores the intersection of art and science, inviting multidisciplinary artists to collaborate… Read More
- [Individual Research Projects](https://www.msca-agile.eu/individual-research-projects/): Chromatin mobility induced by temperature changes Clermont-Ferrand (France) / Frédéric PONTVIANNE / iGRED OMERO embedding and Optimisation of Biom3d, an image analysis tool using deep-learning networks Clermont-Ferrand (France) / Prof Christophe TATOUT / iGRED Connecting Chromosomes and the Nuclear Envelope: Mechanisms Shaping Meiotic Prophase Organization Versailles (France) / Mathilde GRELON / INRAE Cell-cycle regulation of DNA repair Brno (Czech Republic) / Martina DVOŘÁČKOVÁ / CEITEC MU Role of nuclear lamina in Rabl chromosome configuration Olomouc (Czech Republic) / Aleš PEČINKA / Centre of Plant Structural & Functional Genomics Comparative chromatin analysis of supernumerary and standard chromosomes Gatersleben (Germany) /Andreas HOUBEN […]
- [Network](https://www.msca-agile.eu/network/): NETWORK Internationally Recognised Leadership and Excellence in Research Training​ Highly skilled and internationally recognised leaders will mentor the Early Stage Researchers. Beyond their academic excellence, our supervisors have extensive experience guiding BSc, MSc, and PhD students. Scientists in charge Coordinator Frédéric PONTVIANNE Centre National de la Recherche Scientifique(CNRS) Prof. Christophe TATOUT Université Clermont Auvergne(UCA) Mathilde GRELON Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement(INRAE) Martina DVOŘÁČKOVÁ Masarykova Univerzita(MU) Aleš PEČINKA Ustav Experimentalni Botaniky AV CR(IEB) Andreas HOUBEN Leibniz Institute of Plant Genetics and Crop Plant Research(IPK) Chang LIU Universitaet Hohenheim(UHUH) Laurent NUSSAUME Commissariat à l’Energie Atomique et aux Énergies […]
- [Research](https://www.msca-agile.eu/research/): Légende à mettre Research Quantitative microscopy imaging Légende à mettre Légende à mettre Home / Blog / Parent Category / Category / Page Title Quantitative microscopy imaging holds transformative potential in plant sciences by uncovering structural and functional principles at unprecedented spatial and temporal scale revealing how plants adapt their growth and physiology to environmental changes. Despite its promise, this approach bridging studies at the molecular and organismal levels remains underutilised due to the need for adapting imaging methods and image analysis tools designed for animal models to plant systems and a lack of specialised training programs. The “Advanced Training […]

## Optional

- [Agent (MCP protocol)](websites-agents.hostinger.com/www.msca-agile.eu/mcp)

[comment]: # (Generated by Hostinger Tools Plugin)