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FACILITIES AND OTHER RESOURCES
University of Idaho
IBEST Optical Imaging Core Facility
The IBEST Optical Imaging Core (OIC) is a core facility dedicated to creating
opportunities for high-resolution imaging and high-throughput characterization of biological
processes. IBEST has consolidated 4 fluorescent-based microscopes, a Fluorescent Activated
Cell Sorter and analysis software programs into one core facility that is available to all UI
investigators. An experienced microscopist provides expertise in experimental design, image
capture, cytometric acquisition and data analysis. With this infrastructure and staffing, the OIC is
able to support a diversity of research projects, including but not limited to, monitoring protein
translocation, visualizing viral movement and isolating of stem cells.
Core Facility Infrastructure
The IBEST Optical Imaging Core has instruments for imaging biological samples such as
individual cells, biofilms, tissue samples, and small organisms. There are 4 microscopes
available which provide stereoscopic, epifluorescent, confocal and multiphoton imaging. A Flow
Cytometer is available for high-throughput counting and sorting of cell populations. Two
separate computers are available for data analysis. A small refrigerator and small incubator are
also located in the laboratory. These instruments occupy 636 sq. feet of laboratory in Life
Science South 450. The OIC Director’s office in Life Science South 447B is 129 sq. feet. The
Core facility infrastructure is described in more detail below.
Fluorescent Stereo Microscopy
A Leica MZ16F Stereo Fluorescence microscope with DAPI, GFP and DsRed filter sets
provides imaging of surface structure of larger samples, such as nematodes, seeds and
flowering plants. Fluorescence and standard reflected white light imaging is achieved using a
Leica DFC420 color digital camera and Leica Application Suite software. Images can be easily
organized, adjusted, annotated and made ready for publication in the Leica Application Suite
software.
Epifluorescent and transmitted light microscopy
The Nikon Eclipse upright microscope has a monochrome digital camera for imaging in the
epifluorescent and transmitted/phase light modes.
The Nikon Eclipse has filter sets for standard DAPI, FITC and TRITC fluorescence, with
additional sets for Violet excitation and choices for different GFP emission requirements.
MetaMorph software (Molecular Devices) controls the Hamamatsu C4742-95 12-bit
monochrome camera and filter set movements. Further processing and annotation of images,
as well as counting and tracking of user-identified objects, can be done on the MetaMorph
program. Journals can be created to automate many of these routine measurement steps and
resulting data is logged directly to data management software.
A Leica upright Laborlux microscope with a color digital camera is available for true color
imaging of traditional histological samples.
Confocal and Multiphoton microscopy
The Olympus Fluoview upright microscope platform provides confocal imaging of fluorescent
labels within cells and tissue. The high energy of laser excitation, increased excitation options
with multiple laser lines and the pinhole aperture that reduces out of focus fluorescence, aid in
producing extremely high resolution images.
Laser options on the Olympus Fluoview are 405, 440, 488, 515, 559 and 635nm. The
Fluoview ASW acquisition and analysis software controls the microscope shutters and imaging
system. There are 3 fluorescence detectors and 1 for transmitted light. A dye database
provides an automated approach to image acquisition, while parameters such as image
resolution, optical section thickness and speed of capture are user defined. Image processing
and annotation, as well as basic object measurements, can be made in the Fluoview ASW
package.
The Olympus Fluoview also has a Coherent Ultra 2 multiphoton tunable laser ranging from
690-1040nm. The longer wavelengths of the multiphoton laser allow for deeper penetration into
samples and reduced damage to live tissue. The multiphoton laser allows imaging of samples
that are up to a few hundred microns thick, such as biofilms and brain slices. The Fluoview
ASW software also runs this acquisition mode.
Flow Cytometry and Sorting
The BD FACSAria Flow Cytometer has a blue and red laser and characterizes samples for
Side Scatter, Forward Scatter and multiple fluorescent markers. Sorting can be done into up to
4 tubes or multiple-well plates. FACS Diva Software runs the cytometer and performs
performance checks. Data management tools and a variety of data export options are also
included in the FACS Diva software.
Data Analysis Software
Each microscope has an acquisition program that can be used for basic image adjustments
and annotations to prepare images for publication. Additional user defined morphometric
measurements, such as shape, size, or optical density are provided in the NIS-Elements BR
and MetaMorph programs, available on the Dell XPS Studio Image analysis computer. Journals
can be created in MetaMorph for automation of repetitive measurements and direct logging of
data to a data management program. The Imaris program provides excellent 3-dimensional
visualizations of confocal and multiphoton z-series images.
A separate Dell XPS computer station is provided for detailed analysis of data from the Flow
Cytometer using the FlowJo (TreeStar Corporation) software. FlowJo facilitates automation of
repetitive analytical steps and produces statistics tables and graphical reports.