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Issues in the Management of a Core Imaging Facility

The most important aspect of a multi-user core facility is that the data generated are accurate and useful for the goals of the researchers.

by Judy Trogadis
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A successful core facility relies on a combination of knowledgeable staff that understand technological advances, have the ability to educate and inform users, and have a workable system of offering a service.1

Over the last few years, new innovations in specimen labeling, coupled with an increased sensitivity of detection leading to molecular imaging and analysis, has resulted in an increased interest in microscopy and to a proliferation of imaging facilities. The arrival of a user with their precious sample is often the culmination of many hours of research, for example, optimizing immunostaining protocols, transfecting cells with fluorescent tags, or anticipating changes in live cell behavior following treatment with a compound of interest. A novice will need advice on how best to capture useful, relevant data and tell a story with pictures to ensure the message is clearly understood. There is always more than a single way of doing things and in microscopy, as in art, creativity is rewarded. An effective manager of such a facility must be available to facilitate the optimal use of its resources.2

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Equipment and maintenance

Walking into a typical imaging facility, a visitor will find some basic pieces of equipment, each connected to a computer and image capture device, as in the partial list shown in Table 1. In an institution where microscopy is a priority and ample funding is available, additional equipment will include duplicate systems and fully accessorized high-end models that can add to the cost. One can also find some highly specialized systems that carry out limited functions at exceptionally complex and accurate levels.

A collection of such equipment requires maintenance, and thus, the operational costs of an imaging facility are considerable. The major expense is the maintenance contract on the larger systems. The risk is too high to operate without such support, since the repair cost of a single major breakdown can exceed the cost of a yearly service contract. Several cost-saving models exist;3 some institutions arrange group service contracts from a single provider. However, in our facility, our complex and highly specialized instruments have never qualified for this type of group arrangement.

A capable manager can carry out several preventative measures to extend the life of the equipment or repair some breakdowns. Long-term benefits can result from being present at the time of installation of new equipment to observe and ask the company representative basic questions, such as how do you gain access to replacement parts and how do you achieve optimum optical alignment? While the scanning parts of microscopes are too complex for routine maintenance by the facility manager, the microscopes themselves, the condensers, and lenses have to be cleaned and light sources require regular alignment. Users are encouraged to report problems as soon as they are apparent, before they escalate into a major breakdown.

In the age of digital imaging, all equipment comes with its own software, each with a different level of complexity. Some will collect images very easily but may not do extensive image analysis; others only carry out post-collection processing and quantification. In a typical imaging facility, there should be at least one dedicated image processing computer workstation that has several software packages installed. Many data collection systems have an offline version of their software package and this is a practical solution to avoid tying up the microscope with lengthy analysis. It is not within the scope of this article to evaluate various commercial software products, except to mention that it is difficult to find a single software package that contains all the functionalities required to carry out novel image analysis.

A manager should be familiar with the software programs offered in their facility and be able to recommend one to answer a specific question. There are a few recognized software programs, such as Adobe Photoshop; however, a user must be cautious in using it because any image processing prior to subsequent quantification will irreversibly alter the content of the data. Free software is available on the internet and can be sufficient to carry out many tasks. For example, Irfanview ( is an excellent browser to quickly scan directories to find a particular image and will convert formats. ImageJ (, software developed at the NIH on a Java platform, has resulted in scientists worldwide posting new plugins for different analyses that are available for download.

Generally, service contracts do not cover the computer; therefore, users should organize their data properly, store images at an appropriate location on the computer, and remove files at regular intervals. Since surprisingly large amounts of data can be collected within a relatively short period of time, it is not unreasonable to specify a maximum storage space for each user on the hard drive and a time limit (e.g., 60 days), before data is removed from a shared computer. The most common backup medium is on a CD, preferably in duplicate, or on DVD, also in duplicate, although more complex systems exist. A USB key is unreliable as a storage device but can be used to move data from one computer to another. In institutions where the network has been configured to allow the transfer of large amounts of data between computers, microscope users should include this step as part of their logoff procedure.

Rules and regulations

All imaging facilities should have established rules of operation clearly implemented, as expected within any shared facility. The equipment is expensive, the operational learning curve can be steep, and since there are many settings on any microscope to obtain an image, once users learn to get optimal data from properly (and optimally) operating equipment, they should not expect less.

Guidelines are not merely instructions for using equipment, they also address safety issues. By the time a sample is brought into the imaging facility, it should no longer have the same degree of hazard associated with it as it had during the preparation. In other words, emphasis is now on maintaining a safe environment for others using the shared equipment. Gloves should not be worn when using a computer keyboard or focusing a microscope, contamination should not be a concern for the next user. A microscope stage should not have any residue on it after someone has finished using it, and both slides and outside surfaces of samples should be clean and dry. It is a definite advantage for a manager to be familiar with histochemical techniques to provide advice on different slide preparation procedures.

New users
In our facility, I arrange to meet new users to discuss their project and decide which of the various imaging modalities would best suit their needs. Even for a task as simple as viewing fluorescent images, the possible wavelengths of the fluorescently labeled specimen have to be determined in order to match the available detection systems, filters, lasers, etc. If a study entails live-cell imaging, the person doing the work is given an explanation of the necessary conditions required for keeping cells alive and are shown the additional equipment we have for achieving this goal. This may include a stage/objective heater, gas regulators, an enclosed stage incubator, and humidity control.

After the initial meeting the user fills out a form containing information about their laboratory, grants that support the study, and the anticipated level of usage. If heavy use is expected, a brief description of the project is included to be approved for merit prior to proceeding. The form also includes the specific microscopy experience of all individuals from the same laboratory who would be using the equipment. In this way, all users will be identified and their levels of expertise determined for training sessions. In return, a user is supplied with the rules of operation such as the fee schedule, how booking is done, appointments made or broken, and rules of data handling on shared computers. During the first training session, everyone is given their own password-protected user account on each computer with the lowest level of permission required by the software to operate properly.

Microscopy Listservs Web Site
Confocal microscopy
General microscopy
Image J software
Microscopy education

Web site

Microscopy, Imaging Resources
Microscopy Primer imageformationhome.html
Imaging Technology
Microscopy Resource Center
Useful Microscopy Links
J. Paul Robinson
Microscopy courses Web site
Woods Hole Marine Biological
Cold Spring Harbor
UBC 3D Live Cell Imaging

The amount of training is determined by the complexity of the instrument and a user’s microscope experience. Personally, I prefer individuals or a small group of 2–3 people and instruction with a user’s own preparation will make the session more stimulating and will encourage questions. During the optimization of settings, the important message is underlined that a clear question will determine the magnification, choice of area, and composition of an image. A training session should touch on basic principles of imaging, microscope alignment, and principles of confocal microscopy. If the initial training is thorough and users feel comfortable with the controls, they will feel as if we are working with them on the project and are more likely to ask for help when things are not working as planned. Periodically, we may look through the images together and re-visit their initial project goals.

Final image analysis and possible quantification are also discussed and should be done soon after the beginning of image collection. It is essential to analyze preliminary data because one may find that settings, resolution, and contrast are not adequate and have to be modified before proceeding.

Ultimately, a manager should be assured that a user is comfortable with the equipment, treats it with respect, and will get useful data. Even if they have used similar equipment in the past, manufacturers and models use different procedures, and therefore, all new users should attend at least one instruction session before working independently. It is helpful if a brief set of instructions is displayed at each microscope and should contain essential information such as sequence of turning machine on/off, initialization steps, and folders to open to get started.

A system needs to be in place to schedule time on the various microscope systems. The simplest method is to have a schedule book or calendar at each work station where users can book times, and at the end of a session, hours of use are written into a log book. Although this process can work reasonably well, there are more precise and accurate methods, especially for users who are not located physically within an institution. Web-based calendars are now commonly used and have several advantages. From a user’s point-of-view, they can schedule time from their own work areas, and should a problem arise, can promptly cancel their appointment. Electronic scheduling can instantly provide a manager with the overall level of activity in the facility, and furthermore, most software can produce reports for billing purposes and can be used to identify inexperienced users who may have operated the equipment inappropriately.

Generally, scheduling software has a separate calendar for each piece of equipment and can be configured according to the established rules. Contiguous hours of use can be limited, maximum hours per week per person can be defined, and cancellations at the start time or soon after can be denied. Scheduling software may be written or modified from existing programs by in-house programmers. Several free scheduling programs can be found on-line and standard commercial software used by many imaging facilities is called “Calcium” (

Of course, if equipment is immediately available, people will use it without prior booking and a system is needed to monitor use at each workstation. The simplest system, an honor system where entries are made in a book, is not always the most efficient, and a better method is to install monitoring software. Since this is difficult to find, I use a simple macro that, as it launches the microscope program, records the name of the user, date, and times of both start and end. This solution may be difficult to implement if a single executable program and its location cannot be clearly identified.

User fees
Operational costs of an imaging facility are high and administrators encourage cost recovery in the form of user fees. Useful discussions on this topic can be found in the Archives of the Confocal Listserv (see Table 2). Since complete cost recovery is not possible primarily because of steep maintenance contracts, the debate continues on how much revenue should user fees generate. Fees for using equipment are inevitable in most institutions; however, they should not be at a level that discriminates against those with modest funding.

It must be appreciated, however, that core facilities containing technologically complex equipment require long range plans and financial support to remain competitive, to develop new techniques, to upgrade the instrumentation to the highest performance, and to invest in education. A scientist cannot fully explore novel methods that require time to validate if the results will be based on cost rather than on outcome.4

Fees are often posted on facility web sites and are given to new users. The initial training fee, which may include a microscope tutorial, is higher than the unassisted hourly rate, and those from other institutions and/or non-academic users could also pay more. A database can keep track of users, their supervisors, grant information, hours of use, and can generate bills at regular intervals.

A manager's continuing education

Many managers of imaging facilities are hired not because of their managerial training and abilities but because of their scientific background and expertise in the field of microscopy. However, to be effective in that position, a technically trained person also requires interpersonal communications skills while focusing on people, the users of the facility. Our role is further extended by helping researchers answer their biological, genetic, and biochemical questions using some form of optical microscopy and some novel techniques. The field of imaging is constantly changing and we should remain up-to-date with current techniques to make the scientists competitive in writing papers, getting grants, etc. There are several easy ways to achieve this.

It is simple to subscribe electronically to the TOCs (Tables of Contents) of a few journals and skim through the titles for new articles on imaging. It is also easy to subscribe to some listservs and listen to interesting discussions from the scientific community as well as vendors and to participate in the threads. Their archives are easily searchable for topics. Additionally, there are some excellent microscopy tutorial web sites. The most useful ones are listed in Table 2.

I file potentially useful emails from the listservs into different folders on my computer for use in the future. Thus, when asked a question, I may not know the answer immediately, but have built a resource to look for answers. Staying knowledgeable attracts users and makes our work more interesting.

External resources

An imaging facility’s operation can be greatly enhanced by resources from other departments within an institution. Due to the nature of our work, an electronics or biomedical engineering department can provide a service. Unfortunately, they are often reluctant advisors because at times they do not understand the problems, they may fear warranty issues, or they are just too busy to make an open-ended service call. Nevertheless, they can help troubleshoot connections, provide generic parts, fuses, cables, tools, and help build some electronic devices, such as monitoring systems. At times they actually welcome the challenge of non-routine questions.

An Information Technology (IT) department is also an essential adjunct to an imaging facility. Internet access, transfer of files to remote sites, and advice on operating systems should all be within their capabilities even though most departments will not support the complex imaging software used in many facilities. IT staff generally do not view imaging workstations as friends because in many institutions, especially in hospitals where confidentiality issues and internet hacking are large concerns, computers may be absorbed into a limited-access environment where users lose administrative rights that result in software not operating properly. This can become a heated issue and has to be resolved at each institution.

The public relations department can be an ally by promoting the establishment and maintenance of a website. Some of the topics could include the history of the facility, naming any benefactor, description, and photos of the equipment, instructional documents, an image gallery, the scheduling software, forms for new users, fee schedule, etc. This public display is very beneficial, raising the profile of a facility, even of the institution. The visually pleasing nature of microscopy can create an eye-catching design very easily.

Finally, most core imaging facilities are under the supervision of a scientist or a committee with members who represent both scientists and administration. This upper level of management fulfills a useful function, such as a periodic review of policies, approval of long-term studies that anticipate extensive utilization of the facility’s resources, and act as general scientific advisors for ongoing projects.

  1. DeMaggio, S. “Running and setting up a microscope core facility.” Meth. Cell Biology 70 (2002): 475–485.
  2. Allen, K. “The three E’s in a cytometry core facility: Education, education, education.” XXII Intl. Soc. For Analytical Cytology International Congress, Abstracts; Cytometry 59A (2004): 157.
  3. Collins, LW. “Managing Laboratory Maintenance.” American Laboratory, February (2006): 20–23.
  4. Angeletti, RH, Bonewald, LF, DeJongh, K, Niece, R, Rush, J, Stults, J. “Research Technologies: Fulfilling the promise.” FASEB J. 13 (1999): 595–601.