Usage policy

The Center for Biologic Imaging (CBI) is one of the largest optical imaging centers in the country. Because of the richness of resources both in equipment and expertise, it cannot be considered a core in the classical sense in which services are billed to users. Only very rarely do we charge users to use the resources in the facility, rather we try to develop collaborative interactions with research teams such that funding is primarily derived from co-funded grants. We feel that this builds an intellectual camaraderie in which we as faculty within the center contribute to the research goals of investigators or teams of investigators such that an optimal experimental solution is achieved.

Importantly, we believe in a very open door philosophy in which we always try to provide access to expertise and equipment with minimal barriers. However, to do this and protect against abuse we expect users to respect our usage policies. Please read all the sections below. Usage of our equipment means that you agree to all terms in our Usage Policy.

We expect and require that if you are a new user of the center, the head of your lab will contact the center director (Simon Watkins) or one of the other faculty ( Claudette St. Croix, or Alan Watson) in the center directly.  Equally, if you are an established user interested in starting a new project or expanding an existing project, you should discuss it with the faculty in the Center with whom you have an established working relationship. In each case, you should feel free to contact the director at any time, if you have problems using the services and resources offered by the center. Unfortunately we are limiting access to instrumentation by undergraduates to widefield upright systems.  They are not permitted to use confocal, multiphoton, super-resolution systems or electron microscopes.

The reservation system is entirely computerized. We need to make sure that all users employ the scheduler (the computer sign up system) for all reservations. Note that the EM lab now additionally uses iLABS for service requests and billing — the full explanation is in the EM lab usage & billing changes section below.

Evening reservations are not time limited, this allows people to perform live cell experiments. You can start a reservation at 2pm or later (this is a 3 hour block 2pm-5pm) and run it into the evening/overnight. However, you must still sign up for the hours you intend to use. Commonly, people start experiments at 11pm or later so if you wish to run an overnight experiment book the entire period. Importantly you must clean up your experiment by 9am the following morning, this not only shows respect for the person who will follow you but also must be done to stay within our biohazard rules.

We do not allow adhoc usage. If you want to use a piece of equipment which is idle on walk up, please check the scheduler if it's available just sign up for it.

Cancelling and No-Shows

General

Changes in the CBI reservations policy: As you all know, the CBI is a very busy center and commonly it is quite difficult to get frequent and significant blocks of time on much of our instrumentation. For the last year we have been developing a new reservations system which gives priority to those users who have active funding or collaborative arrangements with the Center. For the large majority the impact should be positive as you find it easier to book time on microscopes.

We have chosen to implement this staged solution to give priority support to our PHS supported users who contribute to the center at a time when our instrumentation is very heavily booked and to ensure that reimbursements are sufficient to cover the significant cost of running the core components of the CBI. If you have any questions about this new strategy, feel that there is a better solution, or are concerned that your reservation limits are incorrect please contact one of the CBI faculty and we will work with you to solve any issues.

FY 26/27 Changes in the way the CBI EM lab works:

The CBI is a collaborative Research Center and we strive to build interactive, co-funded grants between individual user groups and the CBI faculty.  Last fall we had a stringent University audit where it became clear that we needed to move the EM component of our Center to a more traditionally supported (fee for service) resource.

For those of you who have collaborative grants with the Center and who only use EM in an occasional way this change in operation will have no impact at all as we have built the costs of using the EM lab into our budgets (this is the majority of you).  However, if you are using the EM facility without active collaborative grants with the Center we will need to bill you for the work (this unfortunately includes pending grants).

If there is a major expansion of the use of the EM components of the Center we will need to discuss our capabilities to absorb the costs.  If you are submitting grants that include significant EM we will need to attempt to itemize this in the budget.

As of September 1 2026 you can request services through iLABS for the EM lab, however all interactions still need to be requested through the usual channels (talking to a CBI faculty and working through the EM Lab Management (Jon and Mara), we can also provide you with the cost for using the services as needed.

The CBI EM lab iLABS page can be found here: Open the CBI EM lab iLABS page ↗

This change in operation is a matter of practical reality and cost management, the nature of your interactions with the center and its staff and faculty will not change.

At present (for the 2026 fiscal year)  the cost for each service is as follows:

TEM/SEM hourly:  $42 internal & $55 corporate

Per sample TEM (includes scope time): $366 internal & $475 corporate

Per sample Negative staining (Includes scope time): $184 internal & $239 corporate

Per Sample SEM (includes scope time): $317 internal & $411 corporate

Basic equipment hourly (ultra-microtome,critical point dryer): $25 internal & $33 corporate

Training and full staff assistance hourly: $104 internal & $136 corporate

***Hourly billing cannot be prorated to less than hourly units. Please make sure you are booking/requesting only the amount of time you will be using the instruments. If you only need the instrument for 20 minutes, you will be billed for the full hour***

The CBI imaging suite is a very very busy place, what we ask is that you show a responsible and courteous approach to using the equipment in the Center.

We recognize that some of our instruments are very heavily booked, and we are working hard to provide new instruments to offset the demand. Some tips to optimize your imaging sessions:

The CBI has extensive computing and workstation resources, we have multi-petabytes of storage space for data and several workstations available for use.  Each workstation is equipped with the primary processing and analysis packages available in the Center (NIS Elements, Imaris).  We do not offer support or training for Fiji/Image J.

There are two primary storage locations available for users:

The CBI is a very busy center working with close to 2000 individual researchers each year. Because of this we are very limited in our ability to manage the data generated by each individual group and we strongly encourage all users to take data with them when you finish an imaging session. All microscopes have USB3 ports open and available to plug personal storage devices into. We encourage everyone to bring portable drives with them each time they come to work in the Center.

Each lab uses a lab specific login to access our workstations, however the server space they connect to holds data from all of the groups using the Center, so we ask that you respect each other’s data. Because of this we cannot secure datasets for individuals. The following guidelines should help you plan how you manage data within the Center.

Cryostat training is available now. If you need to be trained, ask your PI to make a request from one of the CBI faculty (Simon Watkins, Claudette St. Croix, Alan Watson or Patricia Loughran).

You must wear metal mesh protective gloves to protect from cuts. You will need to provide these for size, contamination, and cleanliness reasons. (for purchase details see HERE)

The CBI will provide:

You must bring all other materials (Purchasing information for these supplies can be downloaded HERE)

Once you have finished sectioning, you will be expected to clean the cryostat as normal (vacuum out the cryostat, wipe down surfaces, place debris in the biohazard waste and trash in the bin, and leave the room in a condition you would like to find it.)

No reservations can be made for the cryostat(s) that start before 9:00 am or finish after 4:00 pm

Time used on the cryostat must still be reserved VIA the CBI scheduler as normal (Cryostat 2, under the “CBI Main” section of the scheduler)

Normal 3 hour/day maximum and 9 hour/week maximum restrictions still apply.

Center for Biological Imaging Guidelines for Use of Biohazards in Shared Facilities

1.  All groups and laboratories using live animals for microscopy must have an approved IACUC protocol prior to bringing living animals to the CBI. Further no instrument reservations should be made without an approved protocol being on record in CBI logs.   Rooms and microscopes that will be used for live animal work must be approved as animal outside use areas and must be appropriately equipped. It is essential that you consult with Dr. Watkins or St. Croix while preparing to submit your IACUC protocol describing proposed work in the CBI.

2.  All groups and laboratories using recombinant or synthetic nucleic acids for microscopy must have an approved IBC protocol describing the work prior to bringing samples to the CBI.  It is essential that you consult with Dr. Watkins or St. Croix prior to bringing recombinant or synthetic nucleic acid materials into the CBI.

3. All users working with known or potential human pathogens or other potentially biohazardous agents must comply with the University of Pittsburgh's Biosafety Guidelines (EH&S Guideline Number 05-003: https://www.ehs.pitt.edu/assets/docs/biosafety-guidelines.pdf) in addition to all requirements of these CBI-specific shared facility guidelines.

a.  For work associated with an approved IACUC protocol for which an EH&S risk assessment has been generated, a copy of the EH&S approved risk assessment, which describes biological agent-specific risks as well as proper work practices, decontamination methods, and/or specialized personal protective equipment must be provided to Dr. Watkins or St. Croix prior to beginning work.

b.  Work with biological hazards not described in an IACUC protocol must be registered with EH&S via an agent registration workbook(https://www.ehs.pitt.edu/biological/workbook.html).  At the time of EH&S registration user groups shall request generation of an EH&S risk assessment, which describes biological agent-specific risks as well as proper work practices, decontamination methods, and/or specialized personal protective equipment.  A copy of the approved EH&S risk assessment must be provided to Dr. Watkins, St. Croix, or Stoltz prior to beginning work.

4. No eating, drinking or applying cosmetics in the microscope rooms ever.

5. Read and understand the EH&S risk assessment for your pathogen(s) and notify Dr. Watkins or St. Croix of your intention to use potentially pathogenic samples before beginning work in the facility.

6. Biohazard signage must be posted on the microscope room door indicating the biological agent in use and the appropriate biosafety level to be used while working with the agent. The EH&S risk assessment shall indicate the IBC or EH&S approved biosafety level to be used with each specific agent.

7.  Sample preparation requirements:

a. The sample should be prepared in your lab, sealed with parafilm, surface decontaminated with an appropriate EPA-registered disinfectant, and carried to the Microscopy Core Facility in a sealed, secondary container labeled with a biohazard symbol (e.g., Tupperware-like container) in accordance with EH&S Guidelines 03-017, Specimen Transport Between Research Facilities. The secondary container should be disinfected with an appropriate EPA-registered disinfectant prior to leaving your laboratory.

b. Upon entering the Microscopy Core Facility, decontaminate the outside of your sample using the EPA-registered disinfecting wipes (quaternary ammonium compound) provided by the CBI and follow with a 70% ethanol wipe down. These EPA-registered disinfecting wipes are provided at all microscope workstations

c. If you wish to perform experiments on material using the CBI culture facilities it is critical that these experiments are approved by CBI faculty and performed only within designated culture facilities identified within the CBI.  This includes using incubators with labeled shelves, which will be designated by CBI staff.

d. All work with biological agents with the potential to produce aerosols should be carried out inside a biosafety cabinet, and all microscope slides, dishes, etc. will be surface-decontaminated with an appropriate EPA-registered disinfectant (e.g. quaternary ammonium compound wipes or vesphene) prior to removal from the biosafety cabinet and transport to the microscope.

8. No gloves on the keyboards, computer mice, or any common equipment. It is important to note that, because samples are fixed and/or sealed and have been surface decontaminated twice, handling samples with gloves is unnecessary. If you touch common equipment with a gloved hand, you must immediately decontaminate the equipment. Handling common equipment with contaminated gloves places all users of the facility at risk for exposure. If samples require BSL-2 handling practices, either don gloves when required to manipulate sample and remove gloves and sanitize hands prior to touching common equipment or use the One Glove Rule to mitigate contamination of common equipment. Plastic film is available in the Microscopy Core to cover the keyboard to make cleanup easier, and should be used when samples require BSL-2 handling practices.  Hand sanitation dispensers are present in all open lab areas and in the corridors inside the imaging suites; these should be used ad libitum.

9. Report any spills, drips, splatters, or any potential contamination of the equipment to a CBI Technical Director immediately.Post a warning sign that the equipment cannot be used until fully cleaned and decontaminated. The Technical Director will coordinate clean up procedures.EH&S is available for consultation in case of large spills, or in situations where sensitive equipment may need to be decontaminated(412-624-9505).

10. When you are finished with your work, wipe down the microscope, workstation (keyboard and mouse), and other work areas with the disinfecting wipes (quaternary ammonium compound) provided by the Core Facility and follow with 70% ethanol wipe down. Clean the objectives with lens paper and 70% ethanol and follow with Sparkle GlassCleaner.

11. After imaging, cells may be fixed in 2% paraformaldehyde in the designated biosafety cabinet.  The cells may then be stained for other specific proteins as appropriate and imaged again.  Once cells are fixed the samples are no longer biohazardous.  If cells/samples will not be fixed, the cells should be treated with an appropriate EPA-registered disinfectant (e.g. 1 part Clorox bleach to 9 parts liquid sample volume) for an appropriate time (e.g. 20 minutes for Clorox bleach), the liquid removed to the appropriate liquid waste container or disposed via sink and the vessel discarded in the University's biohazard waste stream.

12. Training requirements.  All personnel must complete the following training prior to working in the CBI and as part of their general workplace training within the University

EHS Training

IACUC Training

Other University Training