The Optical Imaging and Analysis Facility provides training and use on a variety of optical equipment for both the University and external users including microscopes, flow cytometers, gel imagers, and qPCR systems. The equipment is available for all to use, and I am happy to consult any users on optimizing the equipment for their experiments, as well as analyzing generated data.
Instrumentation rates for university investigators with funding to support research and for users such as industries outside the university are listed below. Payments can be made through Interdepartmental invoice, check, or revenue transfer.
|BD LSR Fortessa||$30/hr|
|BD FACSAria Cell Sorter||$45/hr|
|BioRad CFX96 Connect and Touch||$30/hr|
The facility currently houses three optical Zeiss microscopes: a LSM 510 confocal microscope, an inverted AxioObserver fluorescent microscope, and an upright AxioImager fluorescent microscope.
The Zeiss LSM 510-Meta point scanning confocal microscope is mounted on an inverted microscope base. It currently has six laser excitation lines, two single-channel PMT detectors, and a multispectral detector. With the current laser configuration, UV excitation is not possible on this microscope. Thus, staining protocols with DAPI or Hoechst should be modified for other nuclear stains. The monomeric cyanine nucleic acid stains provide many strong alternatives; TO-PRO 3 is recommended for any protocol with a far-red dye.
Available laser lines (nm):
Detector 1 emission filters:
Detector 2 emission filters:
The Zeiss AxioImager is an upright widefield fluorescent microscope ideal for thin slide mounted samples. In addition to the monochrome camera for fluorescent imaging, this scope also has a color camera ideal for imaging histological sections.
Available filter sets:
The Zeiss AxioObserver is an inverted widefield fluorescent microscope with a custom-built incubation chamber allowing for extended live cell imaging. This chamber is also allows for CO2 or other air tank attachments, should a controlled atmosphere be desired.
Available filter sets:
The BD LSRFortessa flow cytometer is a highly sensitive fluorescent cell analyzer equipped with four laser lines.
Each available laser line has its own set of long-pass (LP) dichroic mirrors and bandpass filters configured for the most commonly used dyes:
Violet Laser: 405 nm excitation
Blue Laser: 488 nm excitation
Yellow-Green Laser: 561 nm excitation
Red Laser: 640 nm excitation
The facility currently has:
While the facility does not presently have dedicated analysis computers available to users, there are many freely available data analysis applications that we are happy to help users with as much as we are able.
ImageJ/FIJI is a free software package for analyzing 2D or 3D microscopy images. While not as intuitive as some of the available commercial software, it does offer extensive documentation and a large plugin database, making it a very powerful image analysis tool.
Vaa3D is a free, open source image analysis platform designed specifically for 3D datasets, and is particularly well suited to 3D data visualization.
ZEN lite is a basic image processing only version of their ZEN acquisition software. The movie exporter of ZEN lite can generate smaller sized, higher-resolution videos than other freely available image analysis software.
FCSalyzer is a free open source java application for analyzing flow cytometry data. While this software is still in its early stages, it already offers most of the processing and analysis capabilities as the major software packages. They also have several tutorial videos available.
Flowing Software is a freely available application for flow cytometry data. While a bit more complex than its paid counterparts, it has a number of tutorial videos to get users started. While this software does work on current datasets, the development of Flowing Software has stopped, and the source code was never released, thus there will likely be no future updates.
FlowJo and FCSExpress are the most commonly employed paid flow cytometry applications available. Both are powerful, user-friendly data analysis tools that are more likely to receive regular updates, and will provide support to their users.
9 a.m. to 5 p.m.
406 Biomedical Research Building