Equipment and Software

Cellular Imaging Equipment and Software

All microscopes are equipped with high-resolution objective lenses and digital cameras to produce the highest quality images and time-lapse movies.

LaVision Biotec UltraMicroscope II fluorescence lightsheet microscope (Saban 538)

Lightsheet microscopy is capable of imaging large specimens, such as whole mouse embryos and organs, in 3D rapidly and at high resolution.  In this technique, a thin sheet of light is used to optically slice through a clear specimen.  A 3D image is built by moving the sheet sequentially through the depth of the specimen while a synchronized camera captures an image of each optical section.  Utilization of sCMOS camera technology, with its high sensitivity and fast data transfer rate, allows for short exposure times and much faster acquisition times than point-scanning confocal. Since illumination is orthogonal to the direction of image capture, each plane is illuminated only once and the specimen does not suffer from photobleaching.  Additionally, the UltraMicroscope II is unique in its ability to image specimens cleared with organic solvents for superior clarity over aqueous techniques.  Superb specimen clarity combined with minimal photobleaching and a high numerical aperture long working distance lens allow the UltraMicroscope to generate high-resolution images at increased depth, up to about 6 mm; it can accomodate specimens up to 1.2 x 1.2 x 0.6 cm.   It is equipped with a zoom body to easily change between acquiring fast broad-view images and achieving single-cell resolution (down to 0.5 microns/pixel).  It has four sets of excitation (ex.) laser lines and emission (em.) filters for fluorescence imaging:

  • 405 nm ex./440-480 nm em. for blue dyes such as DAPI and CFP
  • 488 nm ex./500-500 nm em. for green dyes such as Alexa Fluor 488, FITC, GFP, and YFP
  • 561 nm ex./590-650 nm em. for red dyes such as Alexa Fluors 546 and 561, Cy3, rhodamine, RFP, tdTomato, and mCherry
  • 640 nm ex./665-695 nm em. for far-red dyes such as Alexa Fluors 633 and 647, Cy5 and TO-PRO-3

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Zeiss LSM 710 Inverted Confocal Microscope (Saban 338)

  • Specializes in confocal and three-dimensional fluorescence imaging
  • Acquisition of up to three fluorescence channels simultaneously
  • Laser lines: 405, 458, 488, 514, 561 and 633 nm
  • DIC/Nomarski imaging simultaneous with fluorescence
  • Capable of advanced analytical techniques like FRAP, FRET and spectral unmixing
  • 35mm Petri dish warmer available for live cell imaging

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Leica DMI6000B Inverted Microscope (Smith Tower 1030B)

  • Versatile microscope that can image virtually any specimen on a slide or culture dish/plate
  • DIC/Nomarski and phase-contrast optics
  • Color CCD camera for histology and immunohistochemistry slides
  • Fast, ultra-sensitive high-resolution sCMOS camera for epifluroescence
  • Motorized stage for tiling/stitching large areas


Leica MZFLIII Stereo/Dissection Microscope (Saban 439)

  • Specializes in imaging of embryos and other whole specimens
  • Fluorescence
  • Reflected and transmitted light
  • Motorized focus (z) drive for “extended depth of focus” images

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Zeiss Axioplan Upright Microscope (Smith Tower 1030B)

  • Specializes in color brightfield imaging
  • Color CCD camera
  • Also capable of standard blue, green and red fluorescence

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Zeiss Axio Observer Inverted Confocal, Epifluorescence and Color Transmitted Light Microscope (Saban 448)

  • Versatile microscope that can image virtually any specimen on a slide or culture dish
  • LSM 700 confocal scanner with laser lines of 405, 488, 555 and 639 nm
  • Color CCD camera for histology and immunohistochemistry slides
  • Sensitive high-resolution monochrome camera for epifluroescence
  • ApoTome structured illumination system
  • Capable of advanced analytical techniques like FRAP, FRET and spectral unmixing
  • DIC/Nomarski, and phase contrast
  • Motorized stage for tiling/stitching large areas
  • 35mm Petri dish warmer available for live cell imaging


CARV II Spinning Disk Live Cell Imaging Confocal (Smith Tower 322C)

  • Nipkow spinning disk confocal system with lamp-based excitation (no lasers) for gentler confocal imaging of live cells
  • Enclosed in environmental chamber to control temperature, CO2, and O2 for imaging live cells over extended time
  • Capable of standard blue, green, red and far red fluorescence in confocal or widefield mode
  • DIC/Nomarski and phase contrast


Image Processing Workstations and Software 
(Saban 543 and Smith Tower 322C)

  • Arivis Vision4D - for visualization and analysis of static and timelapse 3D images, including cell/particle tracking. Specialized for efficiently processing very large datasets, such as lightsheet images. 
  • MetaMorph – powerful 2D and 3D image processing and analysis including morphometry and movie making
  • AutoDeblur – for deconvolution of confocal images to reduce noise and increase resolution
  • Photoshop – image preparation for publication and presentation
  • FoveaPro – scientific image processing and analysis add-ons for Photoshop
  • ImageJ – versatile, customizable, open-source scientific image processing and analysis software.  The core’s Imaging Scientist can write custom software for ImageJ to suit your needs
  • MATLAB Image Processing Toolbox - fast, powerful programming environment for image processing