Center for Biologic Imaging: Policies and Procedures

By using our facility, you agree to all of the policies and procedures below.  Expand the sections by clicking the heading. 


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.

New User Access:

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 (Donna Stolz or Claudette St. Croix) in the center directly.   Contact information can be found on our contact page.  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.

How to Plan Experiments with CBI Staff:

Several experimental modalities are generally performed very closely with CBI faculty and staff, and need to be planned appropriately

All EM experiments should be planned directly with Donna Stolz (

All live cell experiments should be planned directly with Greg Gibson (

All live animal or whole tissue experiments should be planned with Claudette St. Croix (

-  Furthermore, each of our faculty have their own specific research interests so if you know, or are already working with one of our faculty continue to do so and they will efficiently work through the design process. If you are not sure who to get in touch with please contact Simon Watkins (

-  Please do not turn up at the CBI with specimens without prior interaction with faculty and staff. Your specimens will probably not be accepted.

-  Please do not ask staff to accept specimens without prior planning with CBI faculty.

Levels of User Access:

-  Initially usage for all users is restricted to standard working hours during the week. This is simply to ensure that if you have difficulties using a piece of equipment there will be someone around to solve the problem. Please do not attempt to reserve or use equipment outside these hours unless you have either received specific permission from the CBI faculty or have after hours access.

-  Users who have satisfied the faculty and staff of their competence may request after hours access. This is at two levels, after hours Monday to Friday� and 24/7�. While we recognize that some instrumentation is heavily booked and after hours access is an attractive solution to users, you must be able to demonstrate true competence before asking for after hours access.

-  Image processing access is at any time during the working day.


ALL training on ALL instruments MUST BE PERFORMED BY CBI STAFF.  This is a simple but absolutely mandatory rule

NO training should be provided by colleagues, if you are found using instruments which you have not been trained on, we will be forced to remove user privileges for a month and until you have been appropriately trained by CBI staff.

-  All training requests for staff, students and post-doctoral fellows must be made by the PI of the lab to the light lab manager (Mark Ross or EM lab manager (Jonathan Franks -, for multiphoton training contact Greg gibson ( Training slots are limited to one half day a week for each instrument platform (Fluoviews, A1, 90i, Provis), you may have to wait for a week or so to be trained. We will only train individuals who have actual projects ongoing, for light microscopy this means labelled sections or cells, for EM this means fixed specimens ready for processing. We will not train individuals who do not have active projects with the CBI.  

-  Training sessions for image processing can be done at any time by staff/students/post-docs directly with Kevin Alber ( in the computer lab

Reserving the Scopes:

The reservation system is entirely computerized. We need to make sure that all users employ the computer sign up system for all reservations.

ALL reservations should be made through the CBI website.

-  Booking amount is as follows: For most LM scopes, users may book no more than 3 x 3 hour sessions/week on any class of microscope, unless there is time available on the day of use. For EM scopes, users may book no more than 2 x 4 hour sessions per week. For the Nikon multiphoton, during weekdays users may reserve 1 day per week 1 month in advance, you can reserve a second day 2 weeks in advance, you can reserve a third day 1 week in advance, and remaining open days can be used on the day as needed. Weekends can be booked without restriction as needed.

- 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 is 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 its available just sign up for it.

-  If you have reserved a piece of equipment and cannot use your time you must cancel your time, if you fail to do so 3 times you will lose user privileges for a month.

-  If you have reserved a piece of equipment and are 15 minutes late, another user is allowed to use your time.

-  Please arrange your experiments such that you can finish your imaging session at the appropriate time, and such that the next user does not have to wait.

-  If a user is running late due to travel time (shuttles from remote sites such as Hillman, Children's, 2nd Avenue sites, etc), a courtesy call would be appreciated to reserve the remaining time. 412-648-9796 (Light lab), 412-648-8865 (EM lab).

-  Users may not schedule time more than one month in advance.

-  Under no conditions can users book more than one instrument at any one time. Not only does this limit use by other users it also means that instrument supervision is insufficient.

CBI Scheduler Help - Changes in the CBI reservations policy:

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.

-  If you are the PI of, or are supported by an actively funded or pending grant which includes the CBI you will be able to book time month in advance of the use date.

-  If you have arranged a direct billing solution with the CBI faculty or administration you will be able to book time 2 weeks in advance of the use date

-  If you are actively collaborating with the CBI to develop a funding program that includes the CBI you will be able to book time one month in advance of the use date.

-  If you are a junior faculty developing your research program you will be able to reserve time 2 weeks in advance of the scheduled appointment.

-  If you have yet to arrange collaborative funding or reimbursement with the CBI you will be able to reserve instrumentation time one week in advance.

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.

Looking After the Equipment and the Center :

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. 

-  If you don't know or are not sure what you are doing please ask CBI staff for help.

-  If you don't know or are not sure what you are doing do not get help from another user.

-  Please do not install anything on CBI computers.

-  Please do not move any equipment in imaging suite, carts, incubators, chambers etc.

-  If the microscope seems to be performing less well than it should please ask CBI staff do not try to fix the problem yourself.

Do Not let people into the imaging suite. If they are supposed to be there they will have an ID that will let them in. You may lose user privileges if you do.

Do Not block the door open. You may lose user privileges if you do.

-  Clean up after yourself, leave the microscope as you would like to find it.

-  Please do not change the room thermostats, ask CBI staff if it feels to warm or too cold.

Getting Enough Time on the Microscopes:

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:

-  Try to be flexible with the instrumentation you use. All the confocals within the CBI are current models. While we recognize the Nikon A1 is by far the most popular instrument, the Fluoviews remain very high quality instruments. Arrange a training session on that microscope

-  Work after hours: as soon as you have achieved after hours usage work outside the normal working day, evenings and early mornings are very quiet.

Computing and Image Processing:

The CBI is equipped with over 250 terabytes of online storage space and most current image analysis packages including Metamorph, NIS Elements, Imaris, Amira, Image Pro, Photoshop and Autoquant's deconvolution package. Its very easy to get image processing wrong, which means you can waste huge amounts of time getting poor data out, or perhaps the wrong data. So please talk to CBI faculty and staff if you are not sure what you are doing.

-  You do not need to sign up for time on the CBI image processing facility workstations, all access is first come first served

-  Please get help from Kevin Alber within the Image processing facility if you do not know how to use the package of interest

-  Please ask the director (Simon Watkins) if you need to design an algorithm to extract quantitative data from image sets (he loves this kind of thing).

-  We routinely backup all fixed cell data sets from the widefield, confocal and electron microscopes. Kevin will help you get this data back if it has been removed from our server.

-  We do not back up live cell data.

-  We encourage you to make copies of your own data and take them with you.

-  Ultimately you should look after your own data, we do our best to look after it for you but we cannot be responsible if it gets lost.

Acknowledgement of Interaction with the CBI:

-  Most investigators will have established solid collaborative interactions with faculty in the CBI, and in common with any collaboration where there is intellectual and experimental contribution to the work performed this is best reflected as co-authorship on subsequent papers. This involvement will be self evident.

-  If the interaction is purely technical (you used resources such as equipment etc) then this is not a collaborative interaction, and does not merit involvement in publications. However, it is important to the center that you acknowledge our funding and the fact that the CBI contributed to the research as provider of instrumentation.

-  If you are not sure of the best way to acknowledge the CBI or its faculty please contact the appropriate CBI faculty or the director to clarify.

Biohazardous Material Rules and Policy:

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, St. Croix or Stolz 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, St. Croix, or Stolz 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: 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, St. Croix, or Stolz 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 (  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, St. Croix or Stolz 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 work stations

d. 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. 


e 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 libidum.

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 Glass Cleaner.

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

-       Blood Borne Pathogen Training (annually)

-       Chemical Hygiene Training (every three years)

-       Instructions for completion of EH&S training may be found here:&nnbsp;


IACUC Training

-       Fundamental of Laboratory Animal Research Training (general session and specific animal session as it pertains to research)

-       For additional information regarding required IACUC training modules contact the Research Conduct and Compliance Office.

Oher University Training

-       Human Subjects Research Module (as it pertains to research)

-       This training module is available through the CME program in HSConnect.