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.
SPIM
A new microscope based on a light sheet excitation, the SPIM (Selective Plane Illumination Microscope), allows rapid optical sectioning in 3D and in depth on living samples and offers multi-views acquisition opening new perspectives in biological observation. This unique equipment is now available to the entire scientific community.
Specifications
- 5X, 10X, 20X objectives lenses
- Laser 488, 532, 594nm
- CCD camera
- CO2 and temperature controlled
- Q-Switch Laser 532nm
Applications
- 3D imaging in depth
- Live dynamic analysis
- Photomanipulation
MacroSPIM
The MacroSPIM, a macroscope based on a light sheet excitation, makes it possible after optical clearing to visualize tissues and whole organs by rapid in depth 3D optical sectioning. This novel approach offers multi-view acquisition possibilities and opens up new perspectives in biological observation. This unique equipment, based on developments carried out in Barcelona (IRB), is now made available to the entire scientific community by CERT.
Specifications
- 2X, 5X objective lenses
- 1X to 8X zoom
- Laser 405,488, 561, 642nm
- CMOS camera
Applications
- 3D imaging in depth
- Tissue imaging
Spectral imaging
Biphoton
Specifications
AxioExaminer (straight stand) LSM 880 (Zeiss)
Maximum distance under the lens: 11 cm
Quasar spectral detection system with 2 lateral PMTs and 1 central GaAsP spectral detector composed of 32 high sensitivity detectors)
Laser 458, 488,514,561 and 633
Ti / Sa Chameleon Laser (Coherent)
Applications
Live imaging (explants, animal models)
Acquisition of up to 10 individual channels (8 GaAsP)
Simultaneous spectral acquisition from 391 to 749 nm
Free setting of the fluorescence emission window.
Confocal acquisition
SHG
Real-time imaging
Widefield live imaging microscope 2- AxioObserver Zeiss
Videomicroscopy allows long-term dynamic monitoring of “living” 2D samples.
Specifications
- 5X, 10X, 20X, 40X, 63X objectives lenses
- DAPI, GFP, Cy3 and Cy5 Filter sets
- CCD camera
- CO2 and temperature controlled
- ApoTome.2 module
Applications
- Live dynamic analysis
Other equipments
- 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
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.
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
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
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
- 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.
