Rules of Use: University Imaging Centers
The University Imaging Centers (UIC) is a fee-for-use facility open to investigators and projects of members of the University of Minnesota community as well as external users. All external users are subject to the UIC external rates. An External Sales agreement is required for all users outside the University of Minnesota.
Acknowledgments and Collaborations
The use of the University Imaging Centers resources and its staff should be acknowledged in any presentation or publication of the data.
For the purposes of funding and justification, it is important that if you use the University Imaging Centers services for any aspect of your research, teaching or publication, you acknowledge those services as having been provided by the University Imaging Centers at the University of Minnesota and thanking the appropriate staff.
Collaboration and co-authorship:
In some cases it will become obvious that the staff is contributing more than just technical advice to a project. In these cases it may be appropriate that the investigators include the staff member as a co-author. The distinction would be that the staff member is doing work on the project to an extent that is not usually provided to other clients of the UIC, and that they are helping interpret and give direction to the portion of the study that deals with microscopy. Co-authorship with UIC personnel will not excuse the investigator from cost recovery for supplies or use of the equipment.
Additionally, almost all of the University Imaging Center's instruments were obtained via grants and therefore require proper acknowledgment.
Materials & Methods:
Text descriptions of our instrumentation and services for material and methods sections of manuscripts can be provided.
Send us a copy of your Publication:
Please send a PDF copy of your publication to firstname.lastname@example.org, or a UIC staff member.
Example Scenarios with baseline recommendations:
|Sample Preparation||Fast, routine preparation with standard protocol.||Simple acknowledgment|
|Development of new sample preparation protocols. Optimization of existing protocols for specific samples.||Inclusion of specific facility member on author list|
Training of users to acquire images themselves.
Simple acquisition of raw data.
|Design or re-design of experimental conditions.||Inclusion of specific facility member on author list|
|Image Analysis||Recommendation of analysis software and tools.
Basic data analysis help and advice.
Constructive data analysis and interpretation.
Creation of complex custom image analysis tools.
|Inclusion of specific facility member on author list|
This work was supported by the resources and staff at the University of Minnesota University Imaging Centers (UIC). SCR_020997
- Acknowledgment should always include the UIC Research Resource Identifier (RRID). The UIC RRID is SCR_020997
- Remember to acknowledge specific staff when appropriate.
- If you have any questions on how or if you should acknowledge the UIC please contact UIC staff.
A variety of microscopy techniques are used by researchers in the life and biomedical sciences. As these techniques become more powerful and more complex, it is vital that scientific articles containing images obtained with advanced microscopes include full details about how each image was obtained. To explore the reporting of such details we examined 240 original research articles published in eight journals. We found that the quality of reporting was poor, with some articles containing no information about how images were obtained, and many articles lacking important basic details. Efforts by researchers, funding agencies, journals, equipment manufacturers and staff at shared imaging facilities are required to improve the reporting of experiments that rely on microscopy techniques.
Rigor and Reproducibility
The University Imaging Centers (UIC) are committed to providing researchers with tools to ensure their research is rigorous and reproducible.
What are rigor and reproducibility?
Rigor means following procedures that will increase the likelihood of obtaining an accurate representation of the phenomenon under study.
Reproducibility means recording and communicating those procedures such that they can be replicated accurately.
If your experiments are performed rigorously and reproducibly, other researchers should be able to replicate your procedures, have a high likelihood of obtaining similar results on similar samples, and have those results be an accurate representation of the phenomenon being studied.
Rigor requires you pay attention to:
- The reagents and protocols used to prepare your samples. UIC staff follow best practices in sample preparation, and can provide the exact protocols that were followed for inclusion in methods sections of papers.
- The condition of the instruments used to take images and analyze images. UIC staff performs regular maintenance on all of our instruments and covers our most complex systems with comprehensive service contracts. These actions contribute to a stable of reliable instruments that can be used by trained researchers with confidence. If UIC staff detects problems with any instrument or software, we communicate the problem to any users that might have been affected, as well as workarounds, and timelines for complete resolution.
- The controls included in your experiments. When requested UIC staff will provide general recommendations for controls in light-microscopy sample preparation.
- The way in which you decide which parts of your sample to study. This can involve decisions on which parts of samples to prepare (for example, how to section a piece of tissue, which sections to stain) and where in those samples to take images. UIC staff provide suggestions for how to make sampling decisions, as well as resources for further reading.
- The way in which a microscope is set up for imaging. UIC provides individual, detailed training with each researcher’s samples to ensure they know how to properly set up imaging conditions.
Reproducibility requires you to pay attention to:
- Documenting parameters used for image acquisition and saving data in proper formats. UIC provides advice on how to accurately record those parameters, as well as which formats are appropriate when saving data during our individual training sessions.
- Documenting procedures used for imaging and image analysis. UIC can provide advice on what constitutes a proper record of those procedures.
- Properly writing methods sections. UIC staff is available to consult on writing methods sections for papers and can provide detailed information on light-sources, filter sets, detectors, and other hardware components for proper description in methods sections.
While the University Imaging Centers can guarantee work directly undertaken by its staff is done to the highest standards, it is the responsibility of the individual researcher to ensure they follow our recommendations to ensure the rigor and reproducibility of their research.
Please note that the NIH now requires rigor and reproducibility to be addressed explicitly in many grant applications. More information can be found here.
How do I get started?
The first step towards using UIC resources is to create your iLab account. This account will be used to reserve time as well as log into your reserved session on UIC instruments after being trained.
After creating your iLab account the next step is to submit a training request.
UIC staff will reach out to discuss the project and details of the experiment and work with you to select an appropriate microscopic modality. In this way, everyone is fully aware of the strengths and weaknesses in the experimental design, and the UIC personnel can provide maximum methodological and instrumental support throughout the project. If necessary to increase the sophistication of experiments, formal collaboration between the UIC and the PI's laboratory is possible. We will provide 1 hour of introductory experimental consulting at no charge. Further training or technical support may carry additional fees.
- Equipment and technical time rates are available here.
- Time on equipment must be reserved in advance and usage logged in iLab. If you need to modify your appointment, contact staff as soon as possible. Appointments not canceled 12 hours in advance may be subject to a minimum of one-hour fee and up to the full reservation if not utilized.
Using UIC Facilities
- No modifications to the instruments are permitted without prior approval from the managing staff. Use of equipment off-site is restricted and subject to pre-approval.
- Food and beverages are prohibited in most of the facilities. Biosafety including blood, radioactivity and biohazard risks are also not allowed without written permission. Only non-hazardous chemicals required by experiment are authorized.
- Users shall provide their own specialized equipment, supplies, and reagents (dyes, sample holders media, etc.). Microscope slides and No. 1.5 coverslips are available.
- Users are not to adjust acquisition / imaging software parameters that would impact other users. Many instruments allow users to save user specific settings. Contact staff if default software adjustments need to be made.
- Users are responsible for thoroughly cleaning the equipment used after each session, including workbench, glassware, and computer workstations.
- Optical microscope users - Oil immersion objectives must be gently wiped clean with optical lens paper only. You will be held responsible if you contaminate dry objectives with oil. UIC will gladly show you proper methods of objective cleaning.
- Users are responsible for disposing of wastes in the appropriate waste containers.
- Actual usage time (including warm-up/start-up) for each instrument MUST be recorded online. Failure to do so can result in loss of access to the UIC. It is the users responsibility to provide accurate billing information.
- The UIC provides only limited and temporary data storage space. Please move your data from our computers / servers immediately. We recommend bringing your own removable storage device or transferring through the network. Then copy your data to an automatically backed up computer.
- Users must report instrument problems/damages to the staff immediately.
- When in doubt about proper operation and cleaning of the equipment, the user is responsible for contacting staff. Failure to do so may result in the user being held accountable for consequential damages, up to the full value of the damage.
- Users are not permitted to train others in the operation of instruments. All training must be performed by UIC staff.
- Users should acknowledge the University Imaging Centers in published presentations whenever possible.
Time Use Policy
Time between the hours of 8:00 am to 5:00 pm Monday to Friday is deemed "prime time" and subject to the following restrictions:
- Use of certain instruments may be limited to 5 consecutive "prime time" hours per user per day, and must either finish no later than 1:00 pm or start no earlier than 12:00 pm. Day-long reservations may be granted based on experimental grounds to accommodate, in particular, live cell or live animal imaging. UMN research that requires imaging for greater then 4 continuous hours qualifies for an extended usage discount. External users do not qualify for the extended usage discount.
- Use of a given instrument greater than 15 hours per laboratory per week may require prior approval of UIC management.
- Reservations outside "Prime Time" and during weekend and official holidays can be made only by previously trained users that have key card access. Please consult with staff well in advance to confirm eligibility.
- Reservations must be made under the trained user's name who will be using UIC instrumentation. "Sharing" reservations is not permitted. If a different trained user from the same lab plans to utilize the instrument during the reserved time they must have a new reservation made under their name.
This policy will be implemented by monitoring the reservation calendar. Reservations made in conflict with this policy and without first consulting with UIC staff may be cancelled without notice.
Microscopes are available to trained users 24/7 with the following limits:
- You will be billed for the maximum time between reserved time and actual logged time.
- If your usage time exceeds your reservation, you will be billed for the additional usage.
- Should your reservation exceed your usage time, charges still apply for the time you've blocked off on the calendar.
User data is the users' responsibility. User files left locally on UIC systems are not backed up and will be deleted as needed. The UIC provides data transfer space on our servers so that users of the facility have a method to move files from our equipment to other computers or off-line storage devices as per your data management plan. The purpose of the space is not for storage of your data. Please remove your files as soon as possible so that others can use the space. Files left on our server for over three months will be automatically deleted. We recommend using Google Drive to backup data as needed. If you need assistance please contact UIC staff.
Manipulation of Digital Images
The issue of the manipulation of digital images has come to the forefront recently due to several publicized cases. The Microscopy Society of America has issued a policy on this issue (see Reference #2 below). We in the Imaging Center have considered the issue in depth and how it may impact our clients. Based upon these considerations, we have adopted a modified statement from the Journal of Cell Biology as the Imaging Center Policy on the Manipulation of Digital Images:
"No specific feature within an image may be enhanced, obscured, moved, removed, or introduced. The grouping of images from different fields of view or exposures must be made explicit by the arrangement of the figure (e.g., using dividing lines) and in the text of the figure legend. Adjustments of brightness, contrast, or color balance are acceptable if they are applied to the whole image (and to corresponding control images as well), as long as they do not obscure or eliminate any information present in the original. All adjustments, especially nonlinear adjustments, (e.g., changes to gamma settings) must be disclosed in the figure legend or materials and methods."
It is our policy in the Imaging Center to encourage clients to optimize their cell/tissue processing and image capture parameters initiially so that post-image capture manipulation becomes unnecessary. It is also good policy to relate any image manipulation performed in the figure legend, even if deemed to be minor. However, remember that the "raw" image must be maintained and saved, so that any manipulations are done to a "copy" of the image. Journals may request to see the original raw, unaltered image (see #7 below). A good discussion describing issues related to digital image manipulations can be found in the following references.
• Rosser M, and Yamada KM (2004) What's in a picture? The temptation of image manipulation. J Cell Biol 166:11-15.
• Mackenzie JM, Burke MG, Carvalho T and Eades A (2006) Ethics and digital imaging. Microsc Today, pp. 40-41 (January 2006).
• Editorial (2006) A picture worth a thousand words (of explanation). Nat Methods 3:237.(link is external)
• Rosser M (2006) How to guard against image fraud. The Scientist, pp.24-25 (March 2006).
• Hayden JE (2000) The ethics of digital manipulation in scientific images. J Biocommun 27:11-19.
• Couzin J (2006) Don't pretty up that picture just yet. Science 314:1866-1868
• Photoshop: Friend or Fraud? A JBC Editorial (2007).
The services and systems offered are available to researchers within the University of Minnesota system and affiliated institutions, as well as some off-campus entities with NIH funding, for their basic research projects or as part of basic research collaborations with other academic institutions or nonprofit organizations. Involvement or funding from for-profit (commercial) organizations is available on a contractual basis. The UIC reserves the right to refuse service to any entity or project that may present a biological or health hazard, introduce potential pathogens, or otherwise pose a risk to staff or contamination to the facility.