Imaging
In depth 3D imaging
One of the challenges in biological imaging is to visualize in depth and in three dimensions biological structures and living organisms. CERT provides the tools and expertise to perform this type of analysis. Amongst such tools, the SPIM, the result of research by CERT and other Toulouse laboratories, remains a unique platform instrument to probe biological samples in 3D.
Lightsheet Zeiss Z7
System description
The Z7 illuminates an entire plane of the sample with a sheet of light at depth.
These acquisitions are combined to produce a 3D image of the sample. The fluorescence emitted by the sample is detected at 90° to the illumination plane.
Specifications :
Detection objectives:
5X Neofluar NA 0.16
20X Neofluar NA 1
Illumination sources:
488nm laser
515nm laser
561nm laser
638nm laser
Detectors :
2 x PCO.Edge 4.2 monochrome camera (sCMOS ) 2048x 2048 pixel, 6.5µm pixel size
Incubation:
Temperature and C02 control
Applications :
- 3D depth imaging
- In vivo imaging
- Multi-channel, multi-plane Z, multi-view imaging with 360° sample rotation
MacroSPIM (unavailable)
System description
The MacroSPIM, a macroscope based on light sheet excitation, enables rapid optical sectioning of whole tissues and organs to be visualized in 3D and in depth, after transparentization.
It offers multiview acquisition possibilities, opening up new perspectives in biological observation. This unique equipment, based on a development carried out in Barcelona (IRB), is now available to the entire scientific community at CERT.
Specifications :
Objectifs :
2x
5x
Zoom from 1X to 8X
Lasers :
405nm
488nm
561nm
642nm
Detectors :
2x ORCA Flash 4 camera (sCMOS) 2048×2048 pixels, 6.5µm pixel size
Applications :
- 3D depth imaging
- Tissue and large sample imaging
Imagerie spectrale
Spectral imaging coupled with linear unmixing can be used to detect and differentiate between fluorophores with overlapping spectra. It is also possible to isolate autofluorescence from the sample.
Confocal/Multiphoton Zeiss LSM880
System description
Upright confocal microscope coupled to a multiphoton laser for imaging on fixed samples (slide-lamellar) or “living” samples (explants, animal models).
It also enables label-free imaging thanks to detection of the second harmonic generation (SHG) and third harmonic generation (THG) signal.
Specifications:
Stand :
AxioExaminer ( straight stand, maximum distance: 11cm)
Objectives:
2.5X Fluar NA 0.12
10x Plan ApoChroma NA0.45
20x Plan ApoChroma NA 1
25x Plan Neofluar NA 0.8
40x ApoChroma NA 1.1
Detectors :
– 2 lateral PMTs
– 1 PMT central GaAsP spectral detector (32 high-sensitivity detectors)
– 1 NDD detector (380-400 and 580-600 detection)
Lasers:
– Argon 458, 488 and 514 nm
– DSSP 561nm
– Helium/Neon 633nm
– Ti/Sa Discovery ( Coherent) 690 – 1300 nm
Applications :
- Confocal and multiphoton imaging
- Live imaging (explants and animal models)
- Simultaneous acquisition of up to 10 channels (8 GaAsP + 2 PMTs)
- Simultaneous spectral acquisition from 391 to 749 nm
- Label Free imaging: Simultaneous second and third harmonic generation (SHG and THG)
- Multi-position and mosaics
Real-time imaging
Wide field AxioObserver Zeiss
System description
Videomicroscopy enables long-term dynamic monitoring of “living” 2D samples.
Our systems are equipped with incubation chambers enabling long kinetic acquisitions in multi-position or mosaic, in fluorescence and transmission (Bright Field and Phase Contrast).
Specifications :
Objectives:
5X Fluor NA 0.25
10X Achromat NA 0.25 PH1
10X Neofluar NA 0.3
20X Neofluar NA 0.5 PH2
40X Apochroma NA 0.95
63X Apochroma NA 1.4
Detector :
Axiocam 506 mono monochrome camera (ZEISS CCD) 2752 x 2208 pixel, 4.54µm pixel size
Incubation:
Temperature and C02 control
Fluorescence filter cubes :
DAPI
GFP
Yellow
DsRed
Cy5
Sample holders available:
Multi-well plate insert
Universal insert
4-slide insert
Applications :
- 2D live imaging
- Multi-channel
- Multi-position and mosaics
Incucyte S3
System description
The incucyte S3 is an automated imaging and analysis system for monitoring cell evolution in a temperature-controlled environment.
The system can be used to monitor cells for up to several weeks on different plates, thanks to the multiple locations available.
Specifications :
Objectives:
4x
10x
20x
Channels:
-Phase contrast
-Fluorescence Green ( Ex : 440-480nm, Em: 504-544nm)
-Fluorescence Red ( Ex : 565-605nm, Em: 625-705nm)
Incubation :
Temperature 37°C and 5% CO2
Sample holders available :
6 multi-well plate slots
Modalities available:
– Standard
– Image Lock
– Scratch Wound
– Whole Well
– Dilution Cloning
– Chemotaxis
Applications :
- 2D live imaging
- Short and long time-lapse acquisition ( days, weeks)
- Multi-channel
- Quantitative analysis of cell proliferation, migration and invasion rates.
Other equipments
Wide field Eclipse Ti NIKON
System description
The NIKON Eclipse Ti allows 2D sample acquisition in a variety of formats, thanks to its long working distance lenses.
Thanks to its color camera, this system is ideal for acquiring histological markings and malassez slides.
Specifications :
Objectives :
2X Achromat NA 0.1
4X Plan Fluor NA 0.13 PHL
10X Plan Fluor NA 0.3 PH1
20X Plan Fluor NA 0.45 PH1
40X Plan Fluor NA 0.6 PH2
Detector :
Nikon Ds Ri1 color camera 1280 x 1024 pixel, 6.45 µm pixel size
Fluorescence filter cubes :
DAPI
GFP
Cy3
Cy5
Sample holders available:
Multi-well plate insert
Universal insert
4-slide insert
Applications :
- Multi-channel
- Imaging staining (B-Gal, Trypan blue, eosin)
MacroFluo
System description
This system allows acquisitions over wide fields of view and long working distances, enabling the handling of large samples.
This system is a good choice for examining the effects of a genetic defect or transgenic modification on living models, petri dishes or tissues.
Specifications :
Objectives:
0.5X Plan Apo
2X Plan Apo
5X Plan Apo
Detector:
CoolSNAP HQ2 monochrome camera 1392 x 1040 pixel, 6.45 µm pixel size
Fluorescence filter cubes :
DAPI
GFP
N3
FarRed
Applications :
- Animal (Drosophila, zebrafish, mouse) and large sample (tissue) imaging
- Petri dish acquisition
- Leica CM1950 Cryostat – Frozen thin sections – Faculty of dental surgery
- Microtome HM340E – Paraffin thin sections – Faculty of dental surgery
- Vibroslice Campden 5100mz – Thick cuts in agarose – Incere
- Vibroslice Campden MA752 – Thick sections in agarose – Faculty of dental surgery
Cytometry
Flow cytometry
Fortessa X20 - BD Biosciences
The Fortessa X20 is equipped with 5 lasers: 488nm blue, 405nm purple, 355nm UV, 640nm red, 561nm yellow-green, which can read 19 parameters. It is equipped with a 96-well plate changer. The platform is also equipped with DIVA, Flowlogic and Kaluza analysis software, which can be used on site under reservation conditions.
MACSQuant - Miltenyi
The MACSQuant is equipped with 3 lasers: 405nm, 488nm and 640nm, which can read 10 parameters. This cytometer is also equipped with a plate changer, a marking and automatic dilution module. It allows to standardize experiments.
Cell sorting
ARIA Fusion - BD Biosciences
The sorter proposed, an ARIA Fusion (BD Biosciences), is housed under sterile environment and is equipped with 4 lasers: 561nm yellow-green, 407nm violet, 633nm red, 488nm blue, able to read 18 parameters.
This sorter is also equipped with the following accessories:
- 4 ways sorting
- Sorting in tubes of 1.5ml, 2ml, 5ml, 15ml
- Nozzle of 70µm, 85µm, 100µm
- Refrigeration module at the entrance and at the exit of the sorting process.
Imaging Flow Cytometer
Image Stream X Mark 2 - Merck Luminex
The platform has an imaging flow cytometer: Image Stream X Mark II (Merck-Luminex). This apparatus is equipped with 3 objectives (20x, 40x and 60x), 3 lasers (405nm, 488nm and 642nm) and a camera. It can read 6 parameters simultaneously.
The image files consisting of tens of thousands of cell images can be routinely analyzed using the IDEAS software. This Software can analyse up to 500 morphometric and photometric parameters for each cell image using patented algorithms. The software is present on the platform and can be used under reservation conditions.
Mechanobiology – AFM BioFab
Mécanobiologie-AFM
NanoWizard® II de JPK
Coupled with a Zeiss inverted fluorescence microscope
Bioscope Catalyst de Bruker
Coupled with a Nikon inverted fluorescence microscope
- Original AFM-Photonic couplings
- Force spectroscopy in air and in liquid with tips functionalized using surface chemistry.
- Contact mode topography, tapping and quantitative imaging in air and liquid
BioFab
3D Fabrication : ZORTRAX INKSPIRE
- Printing Technology: UV LCD* – projecting a shape of a layer on the underside of the tank with liquid resin and curing the layer with a UV lamp
- Layer Thickness: 25, 50, 100 microns
- Pixel size: 50 microns (0.05 mm)
- Build Volume: 132 x 74 x 175 mm [2.9 x 5.2 x 6.9 in]
- Supported Formats: .cws, .zcodex, .sl1, .zip
- Operating Temperature: 20 – 30˚ C
- Software Bundle: Z-SUITE 2®
- Supported File Types: .stl, .obj, .dxf, .3mf, .zcodex
2D Lithography
Gesim soft lithography machine (Micro-Contact Printing – µCP)
Soft UV-NIL (Inking, Drying, Molecular deposition, UV curing)
Plasma oxygen microwave DIENER Pico & MEMMERT oven
Microscope droit avec champ sombre
Spin coater (LAURELL WS-650-SZ)
Biological culture
2 MSC (Microbiological safety cabinet) with carbon filter for solvents
2 Incubators and 1 reactor
Data management, processing and analysis
Logiciels de traitement et d’analyse
Software for biological data processing and analysis
Specifications | Applications |
| 3 Imaris licences (Bitplane) | 3D & 4D modeling, 2D & 3D tracking |
| 2 Amira licences (ThermoFisher) | 3D modeling, 3D & 4D image processing |
| 1 Vision 4D licence (Arivis) | 3D & 4D modeling, pixel & object classification |
| Matlab licence server (Mathworks) | Pixel & Object classification, workflow & automatic image processing, GUI implementation, database implementation |
| 3 NIS elements licences(Nikon) | 3D & 4D modeling, 2D & 3D tracking, Volume analysis, High content analysis |
| Ilastik open-source software | Pixel & Object classification |
| Fiji open-source software | 2D, 3D & 4D image processing, Pixel & Object classification, 2D & 3D tracking, automatic image processing |
| Python open-source software | Pixel & Object classification, GUI implementation, database implementation |
| Graphpad Prism Licences | Statistical analysis of biological data |
| 3 Flowlogic licences | Flow Cytometry analysis |
| 5 Kaluza licences | Flow Cytometry analysis |
| 1 INSPIRE licence | Imaging Flow Cytometry analysis |
High Content Screening analysis software
Specifications
- 1 HCS Studio licence (ThermoFisher)
- 2 Harmony licences (Operetta)
Applications
- Real time acquisition and visualization of 2D, 3D et 4D images
- Automated high content analysis (Apoptosis, Cell cycle, cell proliferation, Cell viability, Neurite, outgrowth, protein synthesis)
- Visual and quantitative analysis of 2D, 3D and 4D cell models
Stations d’analyse
2 dedicated workstations Dell Precision T7910
Specifications
- Intel Xeon CPU E5-2680 V4
- NVIDIA Quadro K6000 12GB graphics cardApplications
- 256GB of RAM
- Windows 10 operating system (64-bit)
Applications
- Modeling, image visualization
- Image analysis
- Image processing
- GPU & CPU computing
Genomics / Transcriptomics
Samples quantification and quality control
NanoDrop 2000 ® (Thermofisher Scientific)
Quantification and purity control based on sample absorbance
UV-visible (190-840nm) measurements
Micro-volumes sampling (1-2µl)
Transcriptomic analysis
GeneAtlas system microarray – Affymetrix
FX96 Touch Real-Time PCR System- Biorad
StepOnePlus™ Real time PCR – Biorad
Système LightCycler® 480 plateforme PCR – Biorad
Fluxomic
In vivo fluxomic module
Specifications
Gas anesthesia tables (TEM SEGA) for animal catheterization
Device for perfusion on vigil mice (syringe pumps, tether, swivels)
Thermostatic chamber
Applications
- In vivo isotope tracing (perfusion models, intraperitoneal injection, …)
- Collection of biofluids, tissues, organs
In vitro fluxomic module
Specifications
- In vitro metabolism quenching system
- Controlled oxygen atmosphere chamber (X-Vivo)
Applications
- In vitro isotope tracing (2D and 3D cell models)
- Collection of the endometabolome and exometabolome
Jacques Rouquette
Head of CERT
- provides advice in the development of multi-color panels,
- provides user training,
- assists users in the analysis and interpretation of their results,
- supports users in setting up research and development projects, in the form of collaboration.