Integrated Light Microscopy Core

Training and Policies

New User Training

Getting started in the Light Microscopy Facility is quick and easy. To access training, go through the New User Checklist below. Trained users have 24/7 access to the facility and are given permission to schedule their own microscope sessions through our online scheduling software.


  1. Choose a microscope using the descriptions in the Microscopes section of the website. If you’re unsure which microscope is best for your experiment, contact Christine with a brief description of your imaging goals or a link to a published method you are trying to emulate and she will help you decide.
  2. We have created videos for most systems which provide the bulk of training instruction.  To access video training, contact the Technical Director in charge of training on the microscope you want to use and schedule a time to come to either facility in person to create an account on one of our Core data servers with your cNetID and password. This should take <5 minutes.
  3. Once your server account is created, use our server mapping instructions to access the server. Be sure you are on campus or using the VPN.  Find the ~TRAININGvideos folder up at the top and watch the video(s) for the microscope you would like to learn. Some microscopes have videos for specialized tasks you may or may not need.
  4. Read the facility use policies listed below (biosafety, scheduling and data management).
  5. Read our current COVID-19 guidelines.
  6. Set up an account for our online scheduling system. You can use your cNetID and password OR something else.  You will not have permission to book a microscope until after your certification session.
  7. Fill out a copy of the Facility User Record and bring it with you to certification.
  8. Non-UChicago users will also need to supply a standing purchase order number and contact information for their PI and grants administrator / accounts payable contact before certification.
  9. Once you have done steps 3-8 and have a sample to view (or know when you will have a live sample to view), again contact the Technical Director in charge of training to schedule your first in-person imaging session.  We will answer questions that you have about the video training, check that you know the basics of microscope use, and help you troubleshoot. You can then generate data from your sample(s) and practice.
  10. After your certification the Technical Director will use the ISO# you wrote on your Facility User Record to get you after hours card reader access, if necessary.  You may need to update your lab’s COVID Phase 3 Research Resumption Plan (RRP) from Summer 2020 to reflect your Core use in order to get access.



General Use Policies

1.You MUST be trained by a Technical Director (not a lab mate, friend or collaborator) prior to using a piece of equipment. Training is $20 per person plus microscope time and can be done using your own samples. Contact a Technical Director to arrange training.

2. The first person to use a piece of equipment each day turns it on, the last person shuts it down. If there is no Techinical Director present, we ask that if you are not absolutely sure the next person is coming, shut the microscope down and note the time on the logsheet. Better safe than sorry.

3. IF YOU SCHEDULE THE LAST SESSION OF THE DAY, ANY DAY, it is YOUR responsibility to make sure the microscope is not left on for you. This is especially true after hours and on weekends and holidays when Technical Directors are not present. The last person on the schedule is the one who will be charged for microscopes left on. Charges can include fines, all microscope time and repairs for damaged equipment.

4. If you damage a piece of equipment, you may be billed to repair or replace the item. This includes, but is not limited to: leaving oil on objectives, damaging any part of a microscope, flooding microscopes with live preps, spills on keyboards or computers, damage to heaters/CO2 tanks/other auxillary equipment and/or damage resulting from leaving arclamps/lasers/brightfield bulbs on overnight/over the weekend.

Scheduler Policies

1. Only trained users are granted permission to schedule a piece of equipment. Contact a Technical Director to arrange training.

2. Reservations are limited to a maximum of 5 hours per session during business hours (9am – 5pm). Exceptions are made if users agree to work during non-peak hours (evenings, weekends and early mornings). If you need more time, Technical Directors can create longer reservations when necessary. RESERVE WHAT YOU NEED, USE WHAT YOU RESERVE!

3. Each user is limited to a maximum of 15 hours per week per microscope during business hours. Again, exceptions are made if users agree to work during non-peak hours (evenings, weekends and early mornings).

4. The One Hour Rule — if you fail to show for a scheduled reservation within an hour of your scheduled start time, we will cancel your reservation to offer the time to other users and you could be fined (see below).
We understand people run late, but to be fair to other users and avoid fines, PLEASE either contact a Technical Director and/or adjust your reservation on the scheduler!
Missed appointments are fined $40 for each of the first 2 incidents per month, after 2 incidents per month there is a $40 fine plus you will be charged for all of the scheduled time you reserved that month, used or not (see the fines table below). You may lose the ability to reserve via the scheduler if your missed session results in equipment needlessly being left on overnight or over a weekend (yes, we have had this happen). You will need to contact a Technical Director to regain scheduler access.

5. The Twelve Hour Rule (starting Oct. 1, 2009) — If a scheduled session is canceled within 12 hours or less of the scheduled start time, you will be charged 50% of the reserved time unless you find someone else to book all or part of the time slot. For example, if you reserve a session for Tuesday 9am – 11am and cancel the reservation BEFORE 9pm Monday night, there will be no charge. If you cancel the reservation AFTER 9pm Monday, you will be charged for 1 hour of microscope usage (50% of the two hour reservation) unless someone fills the session.
We understand that preparations can fail at the last minute, so we will allow ONE FREE same-day cancellation per user, per month with no questions asked.
You may lose the ability to reserve via the scheduler if your last-minute cancellation results in equipment needlessly being left on overnight or over a weekend. You will need to contact a Technical Director to regain scheduler access.
Due to heavy booking and an unprecedented number of no-shows and last-second cancellations, we are forced to implement this new policy. We hope to minimize the time systems sit idle between users, the loss of recharge revenue needed to operate the core, and the forcing of users to work late or on weekends because scheduler appear to be full during business hours.

Data Storage (Server) Policies

1. Data stored on our distribution servers are backed up nightly and will remain on the server for 30 days. Data that are over 30 days old are automatically deleted. It is the user’s responsibility to make a permanent copy of his or her data.

2. Local machine hard drives are for temporary storage ONLY. We do not guarantee the safety of any data stored on local machines. DO NOT SAVE ITEMS TO THE DESKTOP! Use the User_Data folders/disks for temporary file storage and then copy your data to the server as soon as possible (for example, copy files from an overnight timelapse to the server the next morning). Data stored on local workstation hard drives will be moved to the server or deleted (depending on whether or not we can identify who it belongs to) at any time without notice.

Biosafety Policies

All users bringing potentially pathogenic samples to the Core facility must follow these precautions. Failure to do so may result in fines, restrictions and / or banishment from the Microscopy Core Facilities.

1. All users working with Risk Group 2, human pathogens or other potentially biohazardous agents must have a registered IBC Protocol. An IMCF User Request For Use of Potentially Biohazardous Agents form (available here) and any associated Agent Profile Forms must be on file with the Microscopy Core prior to beginning work on any microscope.

2. If you are working with infected whole animals, you must contact the Office of Biological Safety (773-834-2707; and the Microscopy Core Facility prior to imaging any samples.

3. Read and understand the Agent Profile Form for your pathogen(s) and notify a Technical Director of your intention to use potentially pathogenic samples before beginning work in the facility.

4. Post a sign at the microscope indicating a biohazardous agent is being used while working. Consult the Office of Biological Safety for guidance.

5. No eating, drinking or applying cosmetics in the microscope rooms.

6. Sample preparation requirements:

  • The sample should be prepared in your lab, sealed with parafilm, surface decontaminated, and carried to the Microscopy Core Facility in a closed, secondary container (e.g., Tupperware-like container). The sample should be disinfected with the disinfecting agent listed in your lab’s IBC protocol and Agent Profile Form prior to leaving your lab.
  • Upon entering the Microscopy Core Facility, decontaminate the outside of your sample again with 70% ethanol.
  • If the agent you are working with is resistant to ethanol, use the disinfecting wipes (quaternary ammonium compound) provided by the Core Facility and follow with 70% ethanol wipe down.
  • Samples CANNOT not be manipulated in the Facility. This means no pipetting, adding, rinsing, mixing, or even removing the lid of the dish.

7. 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 handling your sample requires gloves, use the One Glove Rule to mitigate contamination of common equipment. Use the plastic film available in the Microscopy Core to cover the keyboard to make cleanup easier.

8. Report any spills, drips, splatters, or any potential contamination of the equipment to a 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. Consult the Office of Biological Safety for guidance (call 773-834-2707).

9. When you are finished with your work, wipe down the microscope, workstation (keyboard and mouse), and other work areas with 70% ethanol. If the agent you are working with is resistant to ethanol, use 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.

10. Carry all of your waste back to your lab for disposal. There is no red bag disposal in the facility.