Multimodal Animal Imaging Center


Dr. Sylvain Le Marchand

Zeiss 780 Confocal and Brüker Micro-CT Training and Appointments

Associate Scientist

Phone: (302) 831-3441

Office: DBI 123

Dr. Jeffrey Caplan

Brüker Micro-CT Training and Appointments

Associate Scientist

Phone: (302) 831-3403

Office: DBI 117B


Zeiss LSM 780 Confocal Microscope

The Zeiss LSM 780 is an upright confocal (objectives are above the sample) that enables confocal, spectral, and multiphoton excitation imaging. The non-descanned detection system can be used for two-photon excitation fluorescence or detection of second harmonic generation (SHG) in the forward and reverse directions. The 780 is particularly well-suited for intravital imaging of small animals.


-Confocal imaging.

-Spectral imaging with linear unmixing. It can be used to remove background autofluorescence or for multicolor imaging when spectral overlaps between colors cannot be separated with standard confocal microscopy.

-Multiphoton excitation microscopy. It can be used to image up to 10x deeper than confocal microscopy. The upright configuration, non-descanned detection system and the Z-deck add-on are ideal for intravital imaging of small animals. The system is also ideal for reverse and forward detection of second harmonic generation (e.g. can be used to image collagen fibers).

-Confocal reflection microscopy. It can be used to image collagen fibers and surface microtopography.


-Fluorescence Correlation Spectroscopy imaging. It provides quantitative data on concentrations, diffusion coefficients, molecular transport and interactions.

-Tile scanning to image a large field at high resolution.

Objectives: 10x/0.3, 20x/0.75, 40x/1.2 W, 40x/1.4 Oil. Other objectives available in the room: 20x/0.6, 20x/1 W, 40x/0.8 W, 63x/0.9 W, 63x/1.4 Oil.

Laser lines: 405 nm, 458 nm, 488 nm, 514 nm, 561 nm, 633 nm, 690-1040nm.

Detectors: a 32-channel ultra-sensitive spectral GaAsP PMT (Gallium Arsenide Phosphide PhotoMultiplier Tube) detector (i.e. ChS in Zen), two multi-alkali PMT detectors (Ch1 & Ch2), two non-descanned GaAsP PMT detectors, and one transmitted PMT (T-PMT) for contrast imaging (Bright Field, Differential Interference Contrast, Phase).

Operating software: Zen 2.3 SP1

Location: CBBI (Center for Biomedical and Brain Imaging) #244C

Contact person: Dr. Le Marchand

Brüker SkyScan 1276 Micro-CT

The SkyScan 1276 is a high performance, stand-alone, fast, desktop in vivo micro-CT with continuously variable magnification for scanning small laboratory animals (mice, rats, hamster, etc.) and biological samples.



The Brüker SkyScan 1276 Micro-CT features a combination of high resolution, big image size, round/spiral scanning, reconstruction, and low dose imaging. The image field of view (up to 80 mm wide and more than 300 mm long) allows full body mouse and rat scanning. The variable magnification allows scanning bone and tissue samples with high spatial resolution down to a 2.8 µm pixel size. Variable X-ray energy combined with a range of filters ensures optimal image quality for diverse research applications from lung tissue to bone with metal implants. Further, the SkyScan 1276 in vivo micro-CT administers low radiation dose to the animals allowing multiple scans in longitudinal pre-clinical studies without the risk of unwanted radiation-induced side effects. The system can perform scanning with continuous gantry rotation and in step-and-shoot mode with the fastest scanning cycle of 3.9 sec.

The SkyScan 1276 allows reconstructing non-invasively any cross section(s) through the animal body with possibilities to convert reconstructed datasets into realistic 3D-images and to calculate internal morphological parameters including specific bone structural parameters.


  • 3.9 second shortest scanning cycle
  • 2.8 micron highest nominal resolution
  • Maintenance-free 20-100 kV micro-focus X-ray source, automatic 6-position filter changer
  • 11 Mp cooled X-ray camera
  • Continuously variable magnification with smallest pixel size of 2.8 micron
  • Possibility to resolve object details of 5-6µm with more than 10% contrast
  • Scanning in circular or spiral (helical) trajectory
  • GPU-accelerated and world's fastest InstaRecon® 3D reconstruction
  • Full body mouse and rat scanning, 80mm scanning diameter, >300mm scanning length,
  • Step-and-shoot and continuous gantry rotation with shortest scanning cycle of 3.9 sec.
  • Integrated physiological monitoring (breathing, movement detection, ECG) for time-resolved 4D microtomography
  • Software for 2D/3D image analysis, bone morphology and realistic visualization
  • On-screen dose meter to estimate accumulated dose and dose rate
  • Export results to 3D printers to create magnified physical copy of scanned objects
Location: CBBI (Center for Biomedical and Brain Imaging) 244A

Contact person: Sylvain Le Marchand and Jeffrey Caplan