Bio Medical Research Building South Campus.

Optical Imaging and Analysis Facility

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.

On this page:


Instrumentation rates for university investigators and for users outside the university, such as industries, are listed below.  Payments can be made through Interdepartmental invoice, check, or revenue transfer.

Instrument Rate


BD LSR Fortessa $30/hr
BD FACSAria Cell Sorter $45/hr
BioRad CFX96 Connect and Touch $30/run

The facility will be updating its instrumentation rates starting August 1st, 2019 to those listed below. Additionally, at this time, users outside the university will be charged double the rates of university users.

Instrument Rate


Microscopes (8+ hr consecutive reservation) $20/hr
BD LSR Fortessa $40/hr
BD FACSAria Cell Sorter $60/hr
BioRad CFX96 Connect and Touch $30/run

Stay informed

To receive occasional updates about the facility, including any new instrumentation or changes to existing instrumentation, please join the facility listserv, For instructions on how to join, please click the link below.

Microscopes & Flow Cytometer

The facility currently houses three optical Zeiss microscopes: a LSM 510 confocal microscope, an inverted AxioObserver fluorescent microscope, and an upright AxioImager fluorescent microscope.

View Details About Microscopes

Zeiss LSM 510 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):

  • Argon laser: 458, 477, 488, 514
  • DPSS: 561
  • HeNe: 633

Detector 1 emission filters:

  • Short Pass: 685
  • Band Pass: 480-520; 500-530; 500-550

Detector 2 emission filters:

  • Long Pass: 505; 575
  • Band Pass: 500-520; 500-550; 535-590; 575-615; 650-710
Zeiss Axiolmager Microscope.

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 (links to Zeiss filter specifications): 

Zeiss AxioObserver Microscope.

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 (links to Zeiss filter specifications): 

View Details About Flow Cytometer and Cell Sorter

BD LSRFortessa flow Cytometer.

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

  • Pacific Blue  (---, 450/50)
  • AmCyan (505 LP; 525/50)
  • Qdot 605 (600 LP; 600/10)
  • Qdot 655 (635 LP; 670/30)

Blue Laser: 488 nm excitation

  • FSC
  • SSC
  • FITC, GFP (505 LP; 515/20)
  • PerCP-Cy5.5 (685 LP; 695/40)

Yellow-Green Laser: 561 nm excitation

  • PE (---, 582/15)
  • PE-Texas Red, mCherry (600 LP; 610/20)
  • PE-Cy5 (635 LP; 660/20)
  • PE-Cy5.5 (685 LP; 710/50)
  • PE-Cy7 (750 LP; 780/60)

Red Laser: 640 nm excitation

  • APC (---, 670/30)
  • Alexa 700 (685 LP; 730/45)
  • APC-Cy7 (750 LP; 780/60)
BD FACS Aria cell sorter.

The BD FACSAria cell sorter is equipped with three lasers and can sort cells into four separate tubes based on up to nine fluorescent markers.

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

  • Pacific Blue, DAPI  (---, 450/40)
  • AmCyan (502 LP; 530/30)

Blue Laser: 488 nm excitation

  • FSC
  • SSC
  • FITC, GFP (502 LP; 530/30)
  • PE (556 LP; 575/26)
  • PE-Texas Red (595 LP; 610/20)
  • PerCP-Cy5.5 (655 LP; 695/40)
  • PE-Cy7 (735 LP; 780/60)

Red Laser: 640 nm excitation

  • APC (---, 660/20)
  • APC-Cy7 (735 LP; 780/60)

Additional Equipment

The facility currently has:

  • Two gel/blot imagers (Bio-Rad ChemiDoc and GelDoc)
  • Two qPCR systems (Bio-Rad CFX96 touch and connect)
  • A microplate reader (BioTek Synergy HT)
  • A NanoDrop One Spectrophotometer


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.

Image Analysis

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.

Cytometry Analysis

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.