Skip to main content


Where do I start?

Much information for new users can be found in an entire section of this web site dedicated just to you.
Head on over to the New User Information section.

How do I sign up to use a microscope?

ALL CISR microscopes are available ONLY to those who have been trained in their use by a member of the RESOURCE STAFF. After training, you will be able to through iLab and use the microscopes as needed. Detailed instructions on microscope use can be found on most Equipment pages.

How much will this cost?

CISR SERVICE PRICES [as of December 1, 2022]

LSM 510 Confocals, scope time$42.00 / hour
Confocal, scope time$49.00 / hour
Widefield, scope time$42.00 / hour
TEM, scope time$106.00 / hour
ESEM, scope time$57.00 / hour
Live Imaging, Extended Hours
(special permissions)
$32.50 / hour
Nikon Center of Excellence
Nikon Spinning Disk, scope time$32.50 / hour
Nikon SIM Super Resolution, scope time$32.50 / hour
Nikon STORM Super Resolution, scope time$32.50 / hour
Nikon TIRF, Multi-Excitation$32.50 / hour
LIGHTSHEET Microscopes
Zeiss Z.1 Lightsheet$32.50 / hour
Lattice Lightsheet$32.50 / hour
SOPi Lightsheet$32.50 / hour
Embed (Spurr's)$53.95 / capsule
Freeze Substitution$105.00 / sample
Thick section$56.20 / block
Thin section$109.50 / block
Negative stain, material only$6.00 / grid
Immunolabel, material only$20.00 / kit
ESEM prep, material only$10.00 / stub
Sputter Coater$10.00 / each
CPD$10.00 / each
TEM grid box$5.25 / each
Technical Help
Imaging for hire, training, protracted help$64.25 / hour
Analysis Workstations$6.35 / hour

When are the microscopes available?

*Payment for service is processed through VU iLab using billing information set-up by each individual laboratory prior to receiving service. An iLab account with current billing information is required. The CISR is supported, in part, by 5 NIH-funded Research Center Grants. Accordingly, members of the following Centers may be eligible to receive assistance to pay for service with a “scholarship” number: VICC, DRTC, DDRC, MMPC, and VVRC. Please contact your Center administration for details.

** Services provided to non-Vanderbilt University investigators requires a completed, current “Research Core Services Agreement.” Services are limited to non-clinical research samples. Commercial customer prices will be adjusted to equal 1.6 times the service rates in the table above.

All CISR microscopes are in secured rooms, most requiring a VU ID badge for entry. CISR light microscopes are available for use 24/7. TEM and SEM are available Monday through Friday 9:00 a.m. – 6:00 p.m. with use after hours or on weekends limited to users with extensive experience who have undergone additional training.

Please remember that ALL scopes should be reserved before use through the online iLab calendar reservation system.

Will you help me plan my experiment?

For new experiments or for inexperienced researchers it is best to consult with CISR staff to insure that specimen preparation is optimized and to ensure you have a through understanding of microscope use. A brief meeting and/or training sesstion between the Resource staff and the researchers laboratory to iron out details can be arranged by contacting anyone on our Staff page. This meeting can help determine feasibility, provide suggestions for optimal use of the resource, and, if appropriate, alert the resource staff to unique details of specimen preparation for your project.

How do I prepare my samples for light microscopy?

That depends on the sample, the fluorophore, and the information desired, but here are a couple of examples: a tissue staining protocol, and a cell staining protocol. Some notes on coverslips can be found here, and some information on anti-fade reagents and mounting media is located here.

How do I prepare my samples for EM?

Samples must be fixed prior to submission. Please see the Tips for Fixation Procedures for EM question on this page. If you have samples for immunolabeling or any other specialized protocol, please discuss your project with EM staff prior to sample preparation.

Fixation is typically achieved with a 2.5% glutaraldehyde solution in 0.1 M sodium cacodylate buffer. Fixation should be initiated at room temperature. Tissue should be fixed in a solution volume of at least ten times the sample volume. Specimen vials pre-filled with fixative solution are available for users in the refrigerator of the Processing Lab located in room T-3208 of MCN.

Larger volumes of fixative and buffer are available for whole-animal perfusion fixation (recommended). Please contact a member of our staff to arrange for pick up.

Samples for SEM must also be fixed. Typically these samples will be processed in the critical point dryer by EM staff and mounted for examination in the SEM.

Do you have any tips for fixation procedures for EM?

To maintain ultrastructure, specimens must be fixed rapidly after the oxygen supply has been cut off. The specifics of fixation (fixative, concentration, time, temperature) and the buffering medium will vary for specific experiments. However, in general, fixation will involve buffered aldehydes which cross link proteins, carbohydrates, and to a certain extent lipids. The fixatives will cross link similar molecules that surround the sample (body fluids, cell culture medium, etc. ) so the sample should be washed briefly in a buffered solution before fixation.

Aldehyde fixatives penetrate tissue slowly, so samples must be small (less than 0.5 mm on two sides). For large specimens, mincing the sample directly in fixative after washing works best. This can be done by placing a drop of fixative on dental wax or parafilm and placing the excised and washed sample in the drop of fixative and then mincing with fresh razor blades. The EM staff can show you how this is done.

Cold depolymerizes cytoskeletal elements, so whenever possible, buffer washes, fixatives, and sample should be at room temperature or warmer to initiate fixation. For temperature sensitive samples, such as enzyme cytochemistry, the samples can be briefly warmed placed in fixative and then, after a minute, re-cooled. To store fixed samples for more than a few hours, the specimen should be placed on ice or in the refrigerator after fixation. For storage of samples more than a few days before processing, the fixative should be replaced with buffer after 24 hours

How do I submit my EM samples?

All samples must now go through the EM online laboratory information management system located here. Please contact a member of our staff if you experience any problems or need access to the system.

Please note that specimens for EM processing should be fixed prior to submission and kept refrigerated until submitted. EM fixative and wash buffer can be obtained from the refrigerator in the Processing Lab located at T-3208 MCN.

How do I save my data?

Typhon is a very large, very fast disk storage system available to all registered Cell Imaging Shared Resource users, and is the core’s preferred location for storing image files. View instructions for accessing Typhon.

For Nikon microscopes in the CISR/Nikon COE in T-2216 MCN, the NCOEstore is available as well.  View instructions for accessing the NCOEstore.

Where do I get relevant software?

The free LSM Image browser is here.

The free NIS-Elements Viewer is here.

The free Olympus Viewer is here.

The free ZEN browser is here.

How do I get help with advanced imaging techniques?

Answer: Just ask!

CISR staff members are available to assist you with FRET, FRAP, time lapse, image tiling, and many, many other specialized procedures. Extended help may be subject to additional charges, but most answers are free. We are always ready to help.