Flow cytometry, Light microscopy, Electron microscopy, Image analysis




ImagoSeine is the service and R&D (Research & Development) platform in imaging of the Institut Jacques Monod.

ImagoSeine is a member of the national infrastructure of imaging platforms France-BioImaging and the Euro-BioImaging network.

It offers and develops high-level services for the visualisation and analysis of the structure, dynamics, interactions and functions of biological samples.

To do this, the Institut Jacques Monod’s ImagoSeine platform brings together flow cytometry, electron microscopy and photonic microscopy resources in a single location.

  • Flow cytometry allows qualitative and quantitative multiparametric and multicolour analysis, as well as high-throughput cell sorting, based on the size, granularity and fluorescence intensity of suspended elements.
  • Electron microscopy allows the ultrastructural analysis of the cell and its components. It includes transmission microscopy and sample preparation at room temperature or at low temperature.
  • Photonic microscopy allows the visualisation and analysis of the structure and dynamic processes at the cellular (prokaryotic and eukaryotic) and tissue levels. It offers expertise and innovative equipment, allowing observations from the single molecule to the scale of an organism.

The Institut Jacques Monod’s ImagoSeine platform is open to the entire national and international scientific community, both public and private.

ImagoSeine is supported by the following organisations:



We are a team of engineers, coming from different disciplines (biology, physics, computer science), working on the interface of microscopy with biology.
We propose :

  • the orientation of users towards the most suitable equipment for their project
  • the assistance in the design of tools: molecular biology, protein labeling, choice of labels and fluorophores, analysis protocols…
  • the assistance in setting up the experiment: definition of controls, operating procedures, precautions to be taken with respect to potential artifacts
  • the possible supervision of the users for the realization of the experiments
  • the provision of functional and calibrated equipments
  • the training of users for an autonomous use of the equipments
  • the taking in charge of the acquisitions for the non autonomous users
  • the assistance to the treatment and analysis of the obtained data
  • assistance in the interpretation and presentation of the results.




The ImagoSeine imaging platform offers 3 types of services in photonic microscopy, cytometry and electron microscopy:

1 – Independent use of equipments and reagents

The autonomous user is previously trained by the platform staff on certain equipment or for the performance of certain operations (see Training). He/she benefits from extended use time slots (see Access times) and adapted rates (autonomous rate). During the sessions reserved for autonomous use (see Reservation), the platform’s engineers can be called upon for specific questions, or in the event of technical problems (malfunctions or defects in the equipment), during the platform’s normal opening hours, depending on their availability. If necessary, the autonomous user can book a session with assistance (advice, in-depth training). The autonomous user is responsible for the quality and management of the results he/she has obtained. A “session follow-up book”, located next to each device, must be filled in at each session. Documents (user’s manual, tutorials, …) are made available to the users and can be consulted on site. During the service, the autonomous user is responsible for the equipment provided. He/she must follow the rules for starting up, using, closing and storing the equipment and reagents used.  The team leader agrees to pay the full cost of repairs in the event of damage due to improper use of equipment. Any independent user who has not used equipment for more than one year or since the update of equipment (hardware, software) will have to undergo additional training. The status of autonomous user is subject to the appreciation of the platform staff and can be reviewed without notice. An autonomous user cannot train another user under any circumstances.

2 – The assisted session

The assisted session is conducted in the presence of the platform’s staff. It is proposed within the framework of the implementation of known protocols in standard experimental conditions, decided with the user, and does not have an inventive character. The engineers of the platform involved guarantee the quality of the results, provided that the use is made according to their recommendations, under the conditions fixed in agreement with the user. The session with assistance is subject to prior reservation (see Reservation), depending on the availability of the platform’s equipment and engineers and only during the normal opening hours (see Access hours). It is subject to “assisted” pricing.

3 – The collaborative project

This is the case when the user’s project requires the support of one or more platform engineers for occasional or regular assistance or for the development of a technique or technology for the user’s applications, or of a data acquisition or processing protocol. The platform’s engineers involved in the project guarantee the quality of the results obtained and their restitution (samples, data). The stages of a project can be carried out in the presence or absence of the user, depending on what has been decided beforehand between the user and the engineers involved. In the second case they are not subject to a particular reservation. Project invoicing may be subject to special pricing, based on an estimate, depending on the equipment used for the project. Billing will be based on actual hours used. The rate applied will be the “assisted users” rate.



René-Marc Mège – +33 (0)157278067 –

Jean-Marc Verbavatz – +33 (0)157278004 –

Flow cytometry:

Electron microscopy:

Photonic microscopy:

Platform members ImagoSeine :

Nicolas VALENTIN Engineer, Flow Cytometry Manager
Rémi LE BORGNE Engineer, Head of Electron Microscopy
Catherine DURIEU Electron microscopy engineer
Xavier BAUDIN Engineer, Head of Photonic Microscopy
Nicolas MOISAN Photonic microscopy research engineer
Thomas RIOS Photonic microscopy engineer

How to proceed


1) Contact us by email to make an appointment with our team.

Flow cytometry:

Electron microscopy:

Light microscopy:

2) During this meeting it is necessary that the person in charge of the project is present and that you provide us with the important information (purpose of the experiment, type of samples, markers, support…).

It will be decided whether your project requires collaboration, service or training on one of the devices.

3) Register on the platform’s booking site.

You must have a valid professional email address. Once your information has been validated by the platform, your identifier (first name.surname) will be activated to connect you.

4) Create your password to connect to the booking site on this page. Once connected, download the charter, print and sign the last page.


Use of equipment and services

Only after the signed charter has been received can the services take place. Make requests for equipment training and collaborative projects once you are logged on to the booking site with the “Request” tab.

Charter to download from the reservation site


The use of the platform’s equipment is subject to a fee (see our rates). The rates are calculated to cover the maintenance and updating of the platform’s equipment.

A detailed statement of the services provided will be sent to you each month. In return, you must send a purchase order to the Institute’s accounting department.


ImagoSeine Flow cytometry core facility user fees


ImagoSeine Light Microscopy User Fees


For time laps acquisitions, the price is divided by 2 between 8pm and 9am and during the weekend.


ImagoSeine Electronic Microscopy User Fees


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Xie, J., Najafi, J., Le Borgne, R., Verbavatz, J.-M., Durieu, C., Sallé, J., & Minc, N. (2022). Contribution of cytoplasm viscoelastic properties to mitotic spindle positioning. Proceedings of the National Academy of Sciences of the United States of America, 119(8), e2115593119.
Dussouchaud, A., Jacob, J., Secq, C., Verbavatz, J.-M., Moras, M., Larghero, J., Fader, C. M., Ostuni, M. A., & Lefevre, S. D. (2022). Transmission Electron Microscopy to Follow Ultrastructural Modifications of Erythroblasts Upon ex vivo Human Erythropoiesis. Frontiers in Physiology, 12, 791691.
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Gonzalez Curto, G., Der Vartanian, A., Frarma, Y. E.-M., Manceau, L., Baldi, L., Prisco, S., Elarouci, N., Causeret, F., Korenkov, D., Rigolet, M., Aurade, F., De Reynies, A., Contremoulins, V., Relaix, F., Faklaris, O., Briscoe, J., Gilardi-Hebenstreit, P., & Ribes, V. (2020). The PAX-FOXO1s trigger fast trans-differentiation of chick embryonic neural cells into alveolar rhabdomyosarcoma with tissue invasive properties limited by S phase entry inhibition. PLoS Genetics, 16(11), e1009164.
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Déjardin, T., Carollo, P. S., Sipieter, F., Davidson, P. M., Seiler, C., Cuvelier, D., Cadot, B., Sykes, C., Gomes, E. R., & Borghi, N. (2020). Nesprins are mechanotransducers that discriminate epithelial-mesenchymal transition programs. The Journal of Cell Biology, 219(10), e201908036.
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Gaston, C., De Beco, S., Doss, B., Pan, M., Gauquelin, E., D’Alessandro, J., Lim, C. T., Ladoux, B., & Delacour, D. (2021). EpCAM promotes endosomal modulation of the cortical RhoA zone for epithelial organization. Nature Communications, 12(1), 2226.
Canever, H., Carollo, P. S., Fleurisson, R., Girard, P. P., & Borghi, N. (2021). Molecular Tension Microscopy of E-Cadherin During Epithelial-Mesenchymal Transition. Methods in Molecular Biology (Clifton, N.J.), 2179, 289–299.
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Brossas, C., Valton, A.-L., Venev, S. V., Chilaka, S., Counillon, A., Laurent, M., Goncalves, C., Duriez, B., Picard, F., Dekker, J., & Prioleau, M.-N. (2020). Clustering of strong replicators associated with active promoters is sufficient to establish an early-replicating domain. The EMBO Journal, 39(21), e99520.
Mukherjee, R. N., Sallé, J., Dmitrieff, S., Nelson, K. M., Oakey, J., Minc, N., & Levy, D. L. (2020). The Perinuclear ER Scales Nuclear Size Independently of Cell Size in Early Embryos. Developmental Cell, 54(3), 395-409.e7.
Bruzzone, L., Argüelles, C., Sanial, M., Miled, S., Alvisi, G., Gonçalves-Antunes, M., Qasrawi, F., Holmgren, R. A., Smibert, C. A., Lipshitz, H. D., Boccaccio, G. L., Plessis, A., & Bécam, I. (2020). Regulation of the RNA-binding protein Smaug by the GPCR Smoothened via the kinase Fused. EMBO Reports, 21(7), e48425.
de Vanssay, A., Touzeau, A., Arnaiz, O., Frapporti, A., Phipps, J., & Duharcourt, S. (2020). The Paramecium histone chaperone Spt16-1 is required for Pgm endonuclease function in programmed genome rearrangements. PLoS Genetics, 16(7), e1008949.
D’Ambrosio, J. M., Albanèse, V., Lipp, N.-F., Fleuriot, L., Debayle, D., Drin, G., & Čopič, A. (2020). Osh6 requires Ist2 for localization to ER-PM contacts and efficient phosphatidylserine transport in budding yeast. Journal of Cell Science, 133(11), jcs243733.
Joly, N., Beaumale, E., Van Hove, L., Martino, L., & Pintard, L. (2020). Phosphorylation of the microtubule-severing AAA+ enzyme Katanin regulates C. elegans embryo development. The Journal of Cell Biology, 219(6), e201912037.
Coppin, L., Jannin, A., Ait Yahya, E., Thuillier, C., Villenet, C., Tardivel, M., Bongiovanni, A., Gaston, C., de Beco, S., Barois, N., van Seuningen, I., Durand, E., Bonnefond, A., Vienne, J.-C., Vamecq, J., Figeac, M., Vincent, A., Delacour, D., Porchet, N., & Pigny, P. (2020). Galectin-3 modulates epithelial cell adaptation to stress at the ER-mitochondria interface. Cell Death & Disease, 11(5), 360.
Borne, F., Kovalev, A., Gorb, S., & Courtier-Orgogozo, V. (2020). The glue produced by Drosophila melanogaster for pupa adhesion is universal. The Journal of Experimental Biology, 223(Pt 8), jeb220608.
Thai, L.-P.-A., Mousseau, F., Oikonomou, E., Radiom, M., & Berret, J.-F. (2020). Effect of Nanoparticles on the Bulk Shear Viscosity of a Lung Surfactant Fluid. ACS Nano, 14(1), 466–475.
Pizon, V., Gaudin, N., Poteau, M., Cifuentes-Diaz, C., Demdou, R., Heyer, V., Reina San Martin, B., & Azimzadeh, J. (2020). hVFL3/CCDC61 is a component of mother centriole subdistal appendages required for centrosome cohesion and positioning. Biology of the Cell, 112(1), 22–37.
Casanova, M., Moscatelli, M., Chauvière, L. É., Huret, C., Samson, J., Liyakat Ali, T. M., Rosspopoff, O., & Rougeulle, C. (2019). A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans. Nature Communications, 10(1), 5652.
Basquin, C., Ershov, D., Gaudin, N., Vu, H. T.-K., Louis, B., Papon, J.-F., Orfila, A.-M., Mansour, S., Rink, J. C., & Azimzadeh, J. (2019). Emergence of a Bilaterally Symmetric Pattern from Chiral Components in the Planarian Epidermis. Developmental Cell, 51(4), 516-525.e5.
Mercier, A., Clairet, C., Debuchy, R., Morais, D., Silar, P., & Brun, S. (2019). The mitochondrial translocase of the inner membrane PaTim54 is involved in defense response and longevity in Podospora anserina. Fungal Genetics and Biology: FG & B, 132, 103257.
Antunes, J. C., Benarroch, L., Moraes, F. C., Juenet, M., Gross, M.-S., Aubart, M., Boileau, C., Caligiuri, G., Nicoletti, A., Ollivier, V., Chaubet, F., Letourneur, D., & Chauvierre, C. (2019). Core-Shell Polymer-Based Nanoparticles Deliver miR-155-5p to Endothelial Cells. Molecular Therapy. Nucleic Acids, 17, 210–222.
Lipp, N.-F., Gautier, R., Magdeleine, M., Renard, M., Albanèse, V., Čopič, A., & Drin, G. (2019). An electrostatic switching mechanism to control the lipid transfer activity of Osh6p. Nature Communications, 10(1), 3926.
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Davì, V., Chevalier, L., Guo, H., Tanimoto, H., Barrett, K., Couturier, E., Boudaoud, A., & Minc, N. (2019). Systematic mapping of cell wall mechanics in the regulation of cell morphogenesis. Proceedings of the National Academy of Sciences of the United States of America, 116(28), 13833–13838.
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Frapporti, A., Miró Pina, C., Arnaiz, O., Holoch, D., Kawaguchi, T., Humbert, A., Eleftheriou, E., Lombard, B., Loew, D., Sperling, L., Guitot, K., Margueron, R., & Duharcourt, S. (2019). The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium. Nature Communications, 10(1), 2710.
Duriez, B., Chilaka, S., Bercher, J.-F., Hercul, E., & Prioleau, M.-N. (2019). Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase. Nucleic Acids Research, 47(10), 5155–5169.
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Chen, T., Callan-Jones, A., Fedorov, E., Ravasio, A., Brugués, A., Ong, H. T., Toyama, Y., Low, B. C., Trepat, X., Shemesh, T., Voituriez, R., & Ladoux, B. (2019). Large-scale curvature sensing by directional actin flow drives cellular migration mode switching. Nature Physics, 15, 393–402.
Cianciolo Cosentino, C., Berto, A., Pelletier, S., Hari, M., Loffing, J., Neuhauss, S. C. F., & Doye, V. (2019). Moderate Nucleoporin 133 deficiency leads to glomerular damage in zebrafish. Scientific Reports, 9(1), 4750.
Van de Walle, A., Plan Sangnier, A., Abou-Hassan, A., Curcio, A., Hémadi, M., Menguy, N., Lalatonne, Y., Luciani, N., & Wilhelm, C. (2019). Biosynthesis of magnetic nanoparticles from nano-degradation products revealed in human stem cells. Proceedings of the National Academy of Sciences of the United States of America, 116(10), 4044–4053.
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Lacroix, B., Letort, G., Pitayu, L., Sallé, J., Stefanutti, M., Maton, G., Ladouceur, A.-M., Canman, J. C., Maddox, P. S., Maddox, A. S., Minc, N., Nédélec, F., & Dumont, J. (2018). Microtubule Dynamics Scale with Cell Size to Set Spindle Length and Assembly Timing. Developmental Cell, 45(4), 496-511.e6.
October 2022: New LSM980 Airyscan2 scanning confocal and two-photon module available as part RH26B.
Latest generation Zeiss confocal, equipped for live experiments, allowing simultaneous spectral separation and FRAP experiments. The Airyscan 4Y module allows a 50% increase in resolution compared to a conventional confocal and an increase in acquisition speed. The two-photon microscopy module allows for more in-depth observation of samples.
September 2022 : New ELYRA7 Super-Resolution microscopy system in RH22B room.
Microscope allowing PALM and dSTORM experiments for localization accuracy down to 20nm.  Lattice SIM experiments allowing a 3D resolution increase of two times the theoretical limit and compatible with the living. TIRF experiments to observe events at the interface between the cell membrane and its substrate.
June 2022: New FLIM and FCS module on the confocal LSM980 in room RH20B1.
The FLIM technique allows studying the fluorescence lifetime in the sample, which gives information on its biological state as well as the interaction between proteins by the FLIM-FRET technique. FCS techniques allow the study of the mobility of fluorescent molecules.
September 2021: Upgrade of the CSU X1 FRAP spinning disk and UV Photoablation in RH20B9.
The spinning disk X1 FRAP has a new laser bench (405nm, 445nm, 488nm, 561nm, 642nm) as well as the possibility to do FRAP with the 5 lasers and photoablation by pulsed UV.