Larner College of Medicine

Guidance

The MIC is here to facilitate investigators in their research endeavors. We offer training and expertise for using the microscopes and workstations in the facility. Initial training (1hr) is free. As a multiuser facility, we ask that all users follow these guidelines.

Policies

General Policies
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  • Most of the facility's equipment is accessible after regular workday hours.
  • The CBSR space is a restricted research space on campus. The facility is only accessible through a card swipe system, researchers interested in gaining access should email MIC@med.uvm.edu, be prepared to explain your need for access allowing several days for processing and activation.
  • Users require an iLab account to access the facility for online scheduling, trainings and service requests.
  • All equipment has a 15-minute rule which is as follows: If you are signed up to use a piece of equipment and do not show up for the first 15 minutes of your time, another user may take your time slot. If you know you cannot make your appointment, please delete your time from the online schedule or call 656-0813 to cancel and we will free up your time for another user.
  • For those people who would like assistance using any instruments, please contact the facility personnel prior to signing up so that we can coordinate scheduling and have someone available to help you.

Safety Policies
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Please see the bulletin board in the hallway outside of the imaging rooms for lab safety procedures. Note: As per UVM Risk Management guidelines food and drink are not allowed in the facility.

Hard Drives and Your Data
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The hard drives must remain free for optimal use. Therefore, we ask that all images be saved to an external media during collection or transferred at the end of each session and deleted from the hard drive. If you have questions about how to do this, contact a staff person to help you. The hard drive (C drive) is checked weekly and any images left on this drive are deleted without notice.

Working Alone/After Hours Policy
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Due to increasing safety standards, the Microscopy Imaging & Cytometry core does not allow tissue processing, incubations or work with chemicals to be done after 4:30pm weekdays. The main lab and the cutting room (ultramicrotomes, paraffin microtome and cryostats) will be closed during these hours. The imaging and cytometry rooms are the only ones available after hours and on weekends. 

We strongly encourage users doing imaging after hours to take safety precautions. Safety precautions for anyone working alone should be:

  • Always notify someone if you are working alone.
  • Keep a laboratory phone (911 for UVM police services) or cell phone on you at all times with the UVM police services number (802-656-3473).
  • Contact MIC staff
  • Please see the bulletin board in the hallway outside of the imaging rooms for lab safety procedures. Note: As per UVM Risk Management guidelines food and drink are not allowed in the facility.

Core Training
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The Microscopy Imaging & Cytometry Core is designed to facilitate investigators in their research endeavors. We will offer training and expertise for using the microscopes and workstations in the facility. Initial training (1hr) is free. As a multiuser facility, we ask that all users follow these guidelines. If you have equipment questions, please ask the facility staff for assistance.

Microscopy Imaging & Cytometry Core Facility Acknowledgement

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General Acknowledgment:
Imaging and/or Cytometry work was performed at Microscopy Imaging and Cytometry at the University of Vermont (RRID# SCR_018821). If you used specific instruments or equipment that was purchased with grant funding the corresponding sentence should be added. Find that instrument or equipment citation language under Instruments - Microscopy Imaging & Cytometry 

Manipulation of Digital Images

Manipulation of Digital Images

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UVM's Microscopy Imaging Core's 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. Nonlinear adjustments (e.g., changes to gamma settings) must be disclosed in the figure legend.”

It is our policy in the Microscopy Imaging Core (MIC) to encourage clients to optimize their cell/tissue processing and image capture parameters initially so that post-image capture manipulation is 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, so that any manipulations are saved to a “copy” of the image. Journals may request to see the original raw, unaltered image.  If you have any questions regarding this policy, please contact a member of the MIC staff. 

Background

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The issue of the manipulation of digital images came to the forefront due to several highly-publicized cases. Two members of the MIC attended a workshop on the ethical manipulation of digital images held at a meeting of the New England Society for Microscopy (May, 2006). The outcome of that meeting was that there really is no strong universal consensus on how this issue should be handled. The Microscopy Society of America has since issued a policy on this issue. We in the MIC have considered this issue in depth and how it may impact our clients. Based upon these considerations, we adopted a modified statement from the Journal of Cell Biology as the MIC Policy on the Manipulation of Digital Images.

Reference Information

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Information describing issues related to digital image manipulation can be found in the following references:

Rigor and Reproducibility

Rigor and Reproducibility Statement

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The Microscopy Imaging Center is committed to performing rigorous and reproducible research as outlined by the eight points below.

Eight steps to Rigorous and Reproducible Experiments in Biomolecular Research:

  1. If using a core facility, consult with the core staff in the planning stage. Consult with a statistician if you need help developing a Power Analysis to assure that your results will be adequately powered.
  2. Design your experiment with sufficient controls (rigor) and replicates (reproducibility).
  3. Assure that ALL of your reagents (antibodies, cell lines, mice) are fully validated (see below).
  4. Have a clear and detailed protocol (SOP) and data analysis plan. Assure that the protocol is strictly followed or that any deviation is well documented.
  5. Assure that the staff or students performing the experiment are well trained and understand each step and the importance of performing them precisely.
  6. Use only well-maintained instrumentation, preferably maintained and operated in a core facility with expert staff (see #1 above).
  7. Document all steps, reagents, equipment and data analysis methods used in the experiment. Assure that the both the documentation and the data itself are properly stored in a safe data management repository.
  8. Acknowledge all grants that support the core, the core (by name), and core staff in publications.