University at Buffalo (UB)
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Rates
Instrumentation rates for university investigators are listed below. Users outside the university are charged double the rates of university users. Payments can be made through Interdepartmental invoice, check, or revenue transfer.
| Instrument | Rate |
|---|---|
Microscopes | $40/hr |
| Microscopes (after 8+ hr consecutive reservation) | $20/hr |
| BD LSR Fortessa | $40/hr |
| BD FACSAria Cell Sorter | $60/hr |
| ScanCo MicroCT | $30/hr |
| RS 2000 Small Animal Irradiator | $50/hr |
| BioRad CFX96 Connect and Touch | $30/run |
| PerkinElmer IVIS Lumina LT | $20/hr |
| BioRad ChemiDoc | $10/hr |
Acknowledgements
To demonstrate the importance of this facility to research at UB and aid in the procurement of future equipment, we ask users to please acknowledge the Optical Imaging and Analysis Facility in your publications, and to inform the facility director at the time of publication.
Stay informed
To receive occasional updates about the facility, including any new instrumentation or changes to existing instrumentation, please join the facility listserv, oiaf-list@listserv.buffalo.edu. For instructions on how to join, please click the link below.
Principle Equipment
The facility currently houses four optical microscopes: an Andor Dragonfly spinning disk confocal microscope, an inverted Zeiss AxioObserver fluorescent microscope, and an upright Zeiss AxioImager fluorescent microscope. We also have a BD Fortessa cell analyzer, a BD FACSAria cell sorter, a ScanCo µ100 microCT, and a PerkinElmer IVIS Lumina LT.
The Andor Dragonfly spinning disk confocal microscope is mounted on an inverted Leica microscope base. This microscope is designed for long-term live-cell imaging, having both temperature and CO2 controls, as well as a focus drift correction system to maintain focus over long periods. Additionally, with the high sensitivity sCMOS camera, fast filter wheel, and piezo stage, this microsocpe is able to acuire large multi-channel volumetric images very quickly.
Four available solid state laser lines (nm): 405, 488, 561, 635
Four available emission filters: 420-470, 500-540, 580-605, 640-740
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)
The BD FACSAria Fusion cell sorter is equipped with five lasers and can sort cells into four separate tubes based on up to eighteen 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:
Ultra-violet Laser: 355 nm excitation
- BUV395 (---; 378/12)
- BUV496 (410 LP; 515/30)
Violet Laser: 405 nm excitation
- Pacific Blue, DAPI (---; 450/50)
- AmCyan (505 LP; 525/50)
- BV605 (600 LP; 610/20)
- BV650 (635 LP; 670/30)
- BV711 (690 LP; 710/50)
- BV786 (750 LP; 780/60)
Blue Laser: 488 nm excitation
- FSC
- SSC
- FITC, GFP (505 LP; 530/30)
- PerCP-Cy5.5 (690 LP; 710/50)
Yellow-green Laser: 561 nm excitation
- PE (---; 586/15)
- PE-Texas Red (600 LP; 610/20)
- PE-Cy5, PE-Vio670 (635 LP; 670/30)
- PE-Cy5.5 (690 LP; 710/50)
- PE-Cy7, PE-Vio 770 (750 LP; 780/60)
Red Laser: 640 nm excitation
- APC (---, 670/30)
- APC-R700, Vio R720(690 LP; 710/50)
- APC-Cy7, APC-Vio 770 (750 LP; 780/60)
The ScanCo µCT 100 is a high-resolution computed-tomography scanner for non-living samples. The scanner is capable of resolutions down to 3.5 µm. The instrument can hold up to 12 sample holders at a time to perform batch scanning. The facility has two of each of the cylindrical sample holders with the following internal diameters (in mm): 8, 12, 17, 32, 46, 71, 84, 99.
The PerkinElmer IVIS Lumina LT is a live animal topographic imager capable of imaging most small rodents, or small objects. This system performs best when imaging luminescent transgenic rodents, but is also capable of fluorescent imaging. For fluorescence, the IVIS has ten 30 nm bandwidth excitation filters covering the full spectrum from 415 nm to 760 nm, and four emission filters:
- GFP (545/60)
- DsRed (612/75)
- Cy5.5 (732/75)
- ICG (842/65)
Any prospective user of the IVIS instrument must be listed as personnel on an approved IACUC protocol. This IACUC protocol must also contain the standard procedure for the IVIS imager (available on our additional resources page: link). This information will be verified by the facility director prior to IVIS use.
Additional Equipment
The facility currently has:
- An RS 2000 Small Animal Irradiator
- Two gel/blot imagers (Bio-Rad ChemiDoc and GelDoc)
- A qPCR system (Azure Cielo 6)
- A microplate reader (BioTek Synergy HT)
- A NanoDrop One Spectrophotometer
- A Bio-Rad Experion Automated Electrophoresis System
Analysis
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, open source 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. It is also very versatile and can work on nearly any type of image data.
CellProfiler is another free, open source image analysis package designed to easily automate the processing and analysis of cell images.
QuPath is an open source package designed for the analysis of whole slide images from slide scanners. However, it can work on traditional microscopy images and features powerful trainable pixel and object classifiers.
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.
Floreada is a free online web app for flow cytometry analysis. While still early in development, this web app is very easy to use and provides many of the most common features used in cytometry data analysis. You can view their youtube channel for tutorial videos.
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. This software does not work on FCS 3.1 files, only 2.0 and 3.0. Additionally, 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.
Useful Links
Image Analysis
Microscopy
Micro CT
Flow Cytometry
Hours
Monday-Friday
9 a.m. to 5 p.m.
Location
406 Biomedical Research Building
Dr. Andrew McCall
Director of South Campus Confocal Microscopy and Flow Cytometry Facility
Office of the Dean
