The offer, accessible by online reservation, is aimed at all research players (IBPS, P6 campus, public research organizations, private companies).

- ZEISS 980 FAST-Airyscan II upright microscope coupled to FLIM Becker&Hickl

- ZEISS 980 FAST AIryscan II inverted coupled to FLIM Becker&Hickl

- Upright confocal microscope Leica TCS SP5 AOBS 

- Inverted confocal microscope/resonant scanner Leica TCS SP5 AOBS 

- Upright Biphoton/confocal microscope / resonant scanner Leica TCS SP8 MPII

- Phaseview Alpha 3 Lightsheet Microscope

- SPINNING DISK /ILAS II upright microscope

- NIKON TIRF/inverted Video Microscope

- Macro-apotome

- VYB Analyzer

- MACSQuant Analyzer

- 3 data processing and analysis stations with ImageJ, Huygens, Metamorph, Volocity, FlowJo, Venturi-One

To contact please send an email to :

imagerie.ibps@listes.upmc.fr

Offers may include conception monitoring, follow-up, realization, analysis and result analysis of possible experimental strategies on our equipment.

Type of offers :

• Observation sessions for autonomous users : Autonomous use of equipment, attribution of a user account, data availability.
• Engineer-assisted observation session : Image acquisition monitored by an engineer, attribution of a user account, data availability.
• Long-term collaborative project

- Assistance with sample preparation (clarification, immunolabeling advice, etc.)

- Three-dimensional imaging from the cell to the whole organism

- Life Imaging 

- Photomanipulation (FRAP, Photoconversion, Photoablation)

- Spectral imaging

- Fluorescence Lifetime Imaging

- Image restoration and analysis: Co-localization analysis, deconvolution (wide-field,    confocal, spinning disc, multiphoton), 3D reconstruction...

Development of clarification protocols for complex biological samples:

A biological sample is composed of different molecules with refractive indices varying between 1.33 (water) and 1.56 (proteins). The sample is therefore opaque because the light used for imaging is strongly scattered, making deep imaging very difficult. Therefore, complex biological samples must be made transparent to allow volume imaging. Over the past ten years, we have observed a revolution in volumetric imaging of complex samples thanks to the clarification technique.

Clarification makes it possible to observe internal structures present in opaque and thick biological samples, called complex (tissues, organs or small embryos). It makes volumetric optical observation accessible. The principle of clarification consists in homogenizing the differences in refractive index, in order to obtain transparent biological specimens.

Clarification methods must be adapted to each biological sample, which explains the multitude of protocols. The method used will depend on the nature of the sample, its size, the rate of auto-fluorescence, its complexity and the desired fluorescent labeling.

We are developing, in collaboration with research teams, new low-toxic clarification protocols, allowing the imaging of tissues, small embryos and spheroids of multiple biological organisms (mice, chicken, fruit fly, xenopus, axolotl, grass snake, sea dogfish, etc.).

In addition, we offer training to guide the user in the multitude of protocols that exist, starting from a theoretical introduction to the range of existing techniques and observation methods ending with the prerequisites for a suitable data analysis.

Optimization of 3D resolution: 

We have worked to implement confocal super-resolution by optimizing sample preparation (Fouquet et al., 2015), followed by developing a workflow of optimisation of acquisition parameters and systematic deconvolution of images in order to substantially double the lateral and axial resolution in confocal microscopy (Lam et al., 2017). 

We arena studying the improvement of axial resolution in thick fixed samples (mouse brain, zebrafish, etc.) immunolabeled or carrying fluorescent proteins in complex biological samples and in depth. 

We are currently developing confocal super-resolution thanks to the acquisition of two ZEISS 980 Fast Airyscan II and the deconvolution of data from this type of imaging. We are also studying the artifacts of this kind of image processing.

Development of spatial analysis tools: 

The facility team has proven expertise in the analysis of cellular events such as co-localization (Bolte and Cordelières, 2006, Cordelières and Bolte, 2014).

In the past, we used “JaCoP”, a plugin for ImageJ. This analysis tool is restricted because it is based on intensities. This is the reason why we have recently developed a more advanced tool for the analysis of cellular structure associations based on object detection and 3D spatial relationship analysis. This automated tool is called DiAna (Distance Analysis, Gilles et al., 2017) and was designed in collaboration with Dr. T Boudier (Centuri, Marseille). 

A new ImageJ plugin project aims now to facilitate the study of dendritic spines. This work is done in collaboration with N. Heck and T. Boudier and takes advantage of two recognized ImageJ plugins, 3D ImageJ Suite and SNT. Its purpose is to study the morphological characteristics of spines based on a semi-automatic approach and by exploiting their shapes in 3D for more precise results.

The facility has a strong partnership with the Jean-Perrin Laboratory (UMR CNRS/SU 8237), a constituent unit of the IBPS. This laboratory mainly brings together physicists interested in the challenges of biology. He has recognized expertise in optical instrumentation for biology, and was notably a pioneer in the development of light sheet microscopy for functional imaging.

As part of the attachment of the Jean Perrin laboratory to the IBPS, the IBPS imaging facility is thus a stakeholder in several federative instrumental projects associating several sites of the LUMIC network (Brain and Spinal Institute, ICM and L Institute of Vision, IdV), which aim to set up new innovative imaging systems (high spatial and temporal resolution light sheet microscopy). These have recently been supported by IDF and GIS-IBISA funding

It is Thomas Panier (IR-SU) who is responsible for the instrumentation projects.

The IBPS imaging facility is part of the national networks GDR IMABIO and rt-mfm (France LAM, Organization des Assises RTmfm, Communication Manager). In addition, the facility coordinates the imaging and cytometry network of Sorbonne- University LUMIC (Susanne Bolte, operational manager).

The imaging platform is a strong player in training at local, national and international level: 

CNRS Corporate Training: Clarification for three-dimensional imaging of complex biological objects, annual 

CNRS-MiFoBio: 7 Workshops on confocal super-resolution, clarification and spatial analysis. 

CNRS IFSEM-training: Processing and analysis of microscopy images using ImageJ software, Level I: Initiation, annual 

INSERM workshops: 

Workshop 241: Live imaging of morphogenesis in 4D: probes, microscopy techniques and Quantification 

Workshop 264: Tissue clearing, sample preparation, 3D imaging and data analysis