This page contains advice compiled from several CT lab managers, technicians, and operators that have either set up their lab from scratch or took on managing a CT facility created by someone else. Every lab is unique which often results in unique policies, so we are providing this advice to hopefully inspire optimal solutions for your specific situation.
It is recommended to consult directly with an experienced lab manager to receive personalized advice for your circumstances. An experienced lab manager can help highlight challenges particular to your lab and provide ideas for how best to address them.
Additional advice can be found in Slack groups including nocturngroup.slack.com and ctforum.slack.com
- Roles in the Lab User/client, operator, and data analyst
- Training New Operators
- Prepping a Prep Lab Useful lab supplies for sample mounting
- Usage and Scan Data Client expectations and data management
- Maintenance Future-proofing facilities and maintenance contracts
- Administration Billing and acknowledgments
- Contributors
Roles in the Lab
User/Client: Requests a scan to be performed, provides the sample; provides funding (if necessary)
Operator: sets up the sample, acquires and exports data
Data analyst: processes acquired data, creates segmentations and/or required measurements as needed
A user is the person who commissions the scan. An operator is trained to run the machine. A user and an operator can be the same person and can perform any combination of the above roles. Some typical examples of users include professors, curators, students. Some examples of operators include technicians, lab managers, trained and authorized students.
A postdoc trained on the CT scanner can provide the sample, acquire the data, and then analyze it. At the other extreme, a faculty member could provide a sample to a core facility, have it scanned by a technician, and have it processed by a separate data analyst. Often, either the user or the operator is also the data analyst.
Training New Operators
Generally, CT lab staff provide training on operation of the CT scanner. Typically, users selected for training have at least completed their undergraduate degree and are either employees or grad students of the scanning institution. Some labs have an open policy for training. For instance, anyone who wants to use the scanner can get training. Other labs have stricter eligibility requirements such as a high sample size. Other information to consider about the prospective user’s project: are they scanning for a dissertation? Will they be using the scanner for a long enough period of time to develop competency? Work hours as a lab manager is a limited resource, so choosing between training a new user who only uses the machine once or twice with minimal knowledge and experience or doing the scans yourself and knowing they will be high quality will be important.
After-hours access (outside 9am-5pm, M-F) is another thing that trained users may be interested in. Different institutions have different policies, so you’ll have to figure out what works for you. Some places will allow users to scan outside of working hours with no restrictions. Others prefer users do not scan at off hours out of concern for safety when lab staff are sleeping and unreachable. Being able to operate the scanner unsupervised is a commonly used criterion, because it is more difficult for lab staff to assist when they are away from the facility. Knowing which users are using the scanner when would help you know when to be reachable. As the CT lab manager, you’re responsible for users’ safety (and the machine’s) when using the space, so you’ll have to figure out which kinds of policies you’re most comfortable with.
Prepping a Prep Lab
In addition to space for the CT scanner, acquisition and reconstruction computers, you’ll likely need additional counter space for preparing and mounting specimens for scanning. If you want to offer staining as part of your lab’s services, you’ll also need access to a fume hood.
Keep track of the density of the objects you’re scanning. High-density packing materials might be a problem with the specimen when scanning.
See: Useful lab supplies for sample mounting
If you are interested, able, and allowed to offer additional specimen prep like contrast staining, there are additional considerations. If a specimen comes from the museum, the user would need permission from the museum to do the staining. And you or the user would likely need to inform the museum on the state of the specimen when returning it. Museums may prefer to store previously stained specimens in separate jars to avoid contamination with other specimens. Keep in mind, you’ll have to have supplies and time for destaining the specimen if the user or museum requires it. You could also offer only a single “trial” staining to determine if contrast staining even works with the kind of specimens the client is interested in. Maybe the client continues to fund and do the staining or will pay you for future staining work. As mentioned earlier, providing staining will also require access to a fume hood.
Work with a safety officer at your institution to make sure the chemicals are stored safely and you know how to use the chemicals in a way that does not put you or others at risk.
Considerations:
- Are iodine and other chemicals stored in the CT lab or not?
- Do you have time and the resources to deal with it?
- Who’s paying for chemicals and prep time?
- Are you doing the staining or are users allowed to do the staining?
Usage and Scan Data
Collecting usage data about scans is helpful for reporting to higher-ups, as this may help with grant writing or continuing funding and support for the CT lab. The ability to present the demographics of the user base and the specimens that are being scanned shows the importance of the facility. Museum collections often want to know how their specimens are being used for research, including if they have been stained or scanned, so being able to send a summary of the specimen list would be good in case users forget to report these details back to the museum. Collecting scan parameters and related metadata helps track the performance of the machine and may be helpful for troubleshooting with CT technicians. Collecting data such as the user/client, specimen number, specimen description, basic scan parameters, and source of funding is useful. Scan parameters vary from scanner to scanner, so become familiar with the terms for your machine, but resolution, voltage, current, timing, filters, number of projections, and scan duration are fairly common parameters. A binder or spreadsheet for users to enter the information would work. You could also grab metadata files and record the relevant data all in one place.
User or Client Expectations
Clients may expect beautiful scans for everything, but it is important to communicate that the results may not look as pretty as they had hoped.
PC: Daryl Coldren.
In general, keep in mind that you are the expert on your machine and CT scanning. If your client is asking for something unusual or demanding certain things that are not possible with your machine, you have to make that clear. Be honest in communication.
It is better for clients to overestimate scan time for quotes or grant applications than underestimate. It is not always possible to tell if their specimen(s) will be difficult or not.
Sometimes clients have submitted a grant or scheduled visitors to come and scan without communicating with the scanning facility to see if the machine is free. Encourage professors, curators, students, etc. to reach out to you first to determine if the machine is going to be available for their use at that time, so there is no worry about a visitor coming for no reason or a grant expiring without using the money. And sometimes your scanner might not actually be the machine that would work best for their specimens, so verifying and communicating ahead of time will save a lot of headaches later.
Since soft skills like customer service really come in handy when dealing with clients, here’s some discussion that may be helpful if you do not necessarily have a customer service background:
21 Key Customer Service Skills (and How to Develop Them)
Understand your Institution’s data privacy policies and communicate them to your client, making sure that your client understands and will abide by those rules.
Don’t hurt yourself trying to make everyone happy. Learn how to say “no” tactfully.
It may help to create a website with FAQs and establish what information you need from clients. This will also help facilitate communication with clients regarding expectations and might help them understand what may go in grants or what questions they need to ask you to fill out their grants or project applications correctly.
Data Management
Some facilities do not allow users to keep data on their computers and some do, but have a time limit or data cap. This decision rests on how much money exists for supplying storage for a certain amount of time, but also on the lab manager’s time, because it could be extremely labor intensive to sort through and find the oldest files to clear. But generally, data management is the responsibility of the user and it is best to encourage them to take their data when they are done scanning. Institutions may have file storage hosting options available. Discuss with your IT department. There is usually a monthly or yearly fee depending on the amount of extra storage you want, so keep the rate of data acquisition and file size in mind when discussing. If there is no funding for sustaining this, then you can either have a large hard drive on your acquisition computer or buy external expansion drives. Encourage users to not leave data on the computer.
Questions to ask IT about data storage and transfer options
- Is there a transfer limit? Some services, like Box, limit the amount of data transferred in a 24 hour period.
- Can transfer links have an expiration date? Or be date limited?
- If your data storage protocol includes removing data after a set amount of time, how can this be logistically facilitated?
- Can you transfer within and outside your network? Some organizations may block external access. If external access is blocked, is there a possibility of opening an academic network?
- Is there a cost for storing and transferring data from a cloud or server (could be financial or time-based)?
Checkout NoCTURN’s Data Management Sharing Plan (DMSP) for CT data on the Open Science Committee’s Resource Page
Maintenance
Future-proofing
Having a good record of the machine’s maintenance history is useful for keeping up to date with common maintenance items and understanding the frequency of larger or less common maintenance items. This is also helpful information to have when on-site field techs have questions about the machine’s history.
If you change a filament, rotate the target, or recalibrate the machine, those are useful things to write down. For example, if your filament is burning out faster than is expected, there might be a larger issue with the scanner.
The scanner manufacturer usually has regularly scheduled maintenance visits depending on the company, anywhere from 1-4 times a year. If there are additional issues, they’ll come out again, of course, but it could take a little while to schedule them. And if the parts have to come from overseas, that could further delay a repair.
Make friends with colleagues who have and use tools in your department or other departments such as: facilities, fabrication, shop, and engineering. This is invaluable for the one time you suddenly need an obscure tool that you don’t have.
Contracts
Be familiar with the duration and contents of your maintenance contract since terms can change. What parts are covered? What parts do you have to pay for out of your facility account? How often do certain parts need replacing? Is it an older machine? As a machine ages, contract parts can lose coverage. Keep an eye on contract prices. You can save money with a multi-year contract since prices tend to go up each year.
If your maintenance contract is covered for a certain number of years, who will fund renewal? You may have to write instrumentation grants or learn to promote yourself with institution donors to continue funding your lab if usage fees do not cover maintenance costs (and salary, if applicable). Tracking maintenance and running costs will be important for grant writing and planning for the future, so make sure you know those things. Contracts may also vary between countries, so if you’re seeking advice from other managers, discuss things with those in the same country to make sure you’re discussing the same options that are available.
Administration
Pricing and Billing
Pricing for scans can depend on a few things. For instance, the funding source of the scanning facility. You may also need to be aware of how the facility is funded and any conditions that must be met (promote entrepreneurship, outreach to marginalized groups, etc.) which may influence how you prioritize clients or set pricing.
Other administrators can also decide based on usage and expenses. Internal clients may not have overhead worked into their rates whereas external clients might have to be scanned at a higher rate to cover the institution’s overhead. If the client is also the operator then scan time and reconstruction time can usually be charged at a lower rate. If you or your staff have to do the scanning, you also have to factor in staff time, which would increase the rate. The scanner may also be free to all users, but that can change depending on how that facility is being funded (e.g., grant funding, internal funding, etc.) If the fee structure is going to change, that will take some planning ahead and communication with future clients interested in scheduling scans after the date the change takes place.
You may be in charge of generating the content of the invoices, so be sure to communicate with your account manager or billing staff to learn what information they will need from you and from the client to send out the bills. You may also be in charge of tracking scans and payments and following up with the client if they have not paid. Sometimes that can be an issue. If your institution or facility has a Laboratory Information Management System (LIMS), that would help streamline the workflow, but keeping your own spreadsheet can be helpful too.
You should also be aware of how your facility accounts work. If your account is a university recharge account, you must spend all the money in that account by the end of the year. Balances cannot carry over.
Acknowledgments and User Agreements
User agreements are essential for many reasons including crediting the technician or manager who created the images and the institution. The agreements are also used to make it clear how the scan data is meant to be used and how it’s not. Therefore, it is important to create clear policies for acknowledgements in publications or company material.
Contributors:
- Alex Waters (ealexwaters@northwestern.edu): Northwestern University, Center for Advanced Molecular Imaging, RRID:SCR_021192
- April Neander (aisch@uchicago.edu): The University of Chicago, PaleoCT Lab, RRID: SCR_024763
- Jaimi Gray (jaimigray@utexas.edu): University of Texas, UTCT
- Jamie Knaub (jknaub2020@fau.edu): FAU Laboratory Schools Berlin Family Bioimaging Lab (formerly FAU High School Owls Imaging Lab), RRID: SCR_023805
- JJ Hill (hilljj@si.edu): Smithsonian Institution National Museum of Natural History, Scientific Imaging at the Micro Computed Tomography Imaging Center (mCTIC), RRID: SCR_025090
- Kelsi Hurdle (khurdle@nyit.edu): NYIT Visualization Center, RRID: SCR_024652
- Morgan Chase: American Museum of Natural History, Microscopy and Imaging Facility (alumna)
- Stephanie L Baumgart (sbaumgart@ufl.edu): University of Florida Herbert Wertheim College of Engineering Research Service Centers, RRID:SCR_025135
- Teresa Porri (tp252@cornell.edu): Cornell BRC Imaging Facility, RRID:SCR_021741