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. Read the facility use policies listed below (general use, scheduling, temporary data storage and biosafety).  Failure to follow these polices can result in data loss, fines, additional cost to your lab or loss of facility use.  You are responsible for adhering to these policies whether you read them or not, so please take the time and if you have questions or concerns let us know.

2. Submit the online Facility User Record, filling in as much as possible for your current imaging experiment. If you know which microscope you would like to use, you can add it in the Additional Comments section and continue to Step 2. If you’re unsure which microscope to use or you have questions, please email Christine and she will use the information on your sheet plus any additional information you can provide to help you choose a system. 

3. We have created training videos for most systems. These provide an overview of each microscope’s features and can be used for initial training and review.  Videos are hosted on the OSRF FTP server.  If your lab uses the FTP core server for other core facilities (flow, sequencing, etc) then your lab has already been assigned a lab id and password. Click here for server access instructions. If your lab does not have OSRF FTP login credentials, please contact the microscopy core to generate a lab id and password. Find the ~TRAININGvideos folder up at the top of the server file and watch the video(s) for the microscope you would like to learn. Some microscopes have videos for specialized features.  If you’re not planning to use those features, you can skip those sections.

4. Complete the EHSA laser safety training course (LSR -001 Class 3b and Class 4 Laser Safety Training, requires cNetID login).  You’ll receive an email which says you completed the course. Please forward this email to Christine to show your completion (no SOP or Initial laser User Form necessary).

5. Set up an account for our online scheduling system. You can use your cNetID and password OR something else. Note you will not have permission to book a microscope until after your in-person certification session (Step 7).

6. 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 their in-person certification session.

7. Once you have done steps 1-5/6 and have a sample to view (or know when you will have a live sample to view), schedule an in-person imaging and certification session by contacting the Technical Director in charge of training on the microscope you would like to learn. Click here to choose the equipment and find the corresponding Technical Director. We will answer questions that you have about the video training, check that you know the basics of microscope use, and help you troubleshoot your sample prep and imaging setup. If you let us know when booking the training that you would like additional time, you can use that time to generate additional data from your sample(s) and practice.

8. After your certification, Core staff will give you permission to book future sessions through the scheduler, and if you need after hours access, email a photo of the back of your University ID to your training facilitator.



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 $40 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 Technical 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. Follow the New User Checklist above for all the steps necessary to be trained and begin working in the Core.

2. Reservations are limited to a maximum of 5 hours per session during peak use hours (Monday – Friday 9am – 5pm). Exceptions are made if users agree to work during non-peak hours (early mornings, evenings, weekends and University holidays). If you need more time, such as for a long term time lapse experiment, Technical Directors can create longer reservations when necessary.

3. Each user is limited to a maximum of 15 hours per week per microscope during business hours (Monday – Friday 9am – 5pm). Again, exceptions are made if users agree to work during non-peak hours. Technical Directors can create more reservations when necessary.

4. Beginning April 4, 2022 — we will charge by the time that you book on the scheduler (plus any use running beyond your booking). When you schedule, you are buying a block of time to use, or not use, as you see fit. Missed appointments (no shows) will be charged for time booked minus the amount of time used by someone else, if any. Sessions canceled more than 24 hours in advance of the session start time will not be charged, sessions canceled LESS THAN 24 hours in advance of the session start time will cost the full canceled time minus the amount of time used by someone else, if any. The “one free last-minute cancel per month” rule is now abolished.

5. The last user of the day is responsible for making sure the microscope is turned off at the end of their session. If you forget to shut down the system, or if your missed appointment or last minute cancellation results in the microscope being left on overnight or over a weekend / holiday, you may be subject to charges for wasted arclamp hours and/or damages to equipment.  You may also lose your ability to reserve your own microscope time on the scheduler and need to contact a Technical Director to schedule future sessions.   

Please book what you need and use what you book. We encourage you to make use of the scheduler’s reminder feature and calendar functions.

A change is necessary because the current policy has proven to be ineffective in curbing reservation of more time than is used. Less than half of scheduled time on high-end systems is being used. This limits the microscope plans by other users, limits maintenance, harms requests for new equipment grants, and wastes the microscope system lifetime. GOAL: DON’T RESERVE MORE THAN YOU WILL ACTUALLY USE. Share the resource!

Data Storage (Server) Policies

1. The data generated on any of our instruments is transferred automatically to the OSRF server. Access to the server is available through the online portal. 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. Save files to the “USER DATA – OSRF SERVER UPLOAD” folder. There is a shortcut to this folder located on the desktop of every microscope computer. Data stored in any other location will not be uploaded. 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.

3. It is the responsibility of each user to properly safeguard the data. The server and acquisition computers are not designed as safe storage space. Please take some time to make sure that you have collected every piece of data from the OSRF server. Data files transferred to the server will remain there for an unspecified period of time. The Technical Director will make a public announcement on the website, the Booked scheduler and by email if we ever have to delete data. The function of the Microscopy Facility server is to facilitate transfer of the data. We offer no guaranty for the safety of the data stored on it. Data preservation is ultimately the responsibility of the user.

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.