Core research guidelines, including who can use the core, what services we currently provide, and how we can keep you safe.
To gain full access to the facility, ALL users must
- Read this Core Usage Policies document
- Read the BL1 Safety Policies
- Respond to the email sent by core staff acknowledging that you have read both documents
- We will provide door codes once you have acknowledged reading the policies
- Most users do not need to read the BL2 Safety Policies unless directed by core staff
Who can use the Microscopy Core?
MIT and affiliated external users
These include with kerberos and MIT ID Card who work on campus and users affiliated with MIT but are not located in an MIT building (e.g., Whitehead Institute, Broad Institute, Draper Laboratory, Ragon Institute). Examples include graduate students who have an MIT appointment, and Postdoctoral Associates or Technical and Research Staff whose PI has an appointment at MIT.
- May use the core, but must register for iLab. See Core Access.
External Users not affiliated with MIT
These include users not affiliated with MIT and not located in MIT buildings such as users from external academic institutions or companies.
- May use assisted services. Please contact core personnel to check availability and arrange assistance.
- May use a small subset of microscopes independently. Usage is limited to normal business hours. Contact core staff for specifics.
- External for-profit users must have a technical service agreement for KI Core Access.
- May NOT image live human samples such as human-derived cell lines or tissues. ALL BL2 imaging requires an existing MIT Biological Research Registration to amend.
Services Offered
Independent Use of Microscopes
Microscopes are available for independent use but only for users who are currently trained on an instrument. Door codes will only be provided to trained users.
New user training
Please schedule all training via email. Contact core director Jeffrey Kuhn jrkuhn@mit.edu or confocal specialist Jeffrey Wyckoff jwyckoff@mit.edu.
We train with your samples and only when you are able to begin independent imaging soon after training. We do not pre-train weeks or months in advance for experiments planned later.
Assisted Use
We offer guided assisted imaging for all microscopes. User input is vital during assisted imaging. Core personnel will operate equipment and image your prepared samples while you watch in the same room.
Help
Core personnel are usually available during normal business hours for microscopy questions during your imaging session. We may be assisting other users or attending seminars or meetings. If you want to make sure we will be available for your imaging session, contact us ahead of time. If you need extensive help, please arrange it before your imaging session. We are happy to schedule additional training sessions as needed.
User Guidelines
Decontamination
Microscopy is often up-close and personal with multiple users on the same instrument throughout the day. We want to keep up the habit of microscope decontamination through cold and flu season! We have posted simplified decontamination guides guides in each microscope room. Please follow the microscope decontamination procedure after you finish. Decontaminate microscope surfaces, eyepieces, eyepiece pillar, stage, keyboard, mouse, etc as directed in the posted guide.
For example, microscope eyepieces and the eyepiece pillar are possible sources of contamination. Tear ducts are a major cold and flu transmission route. You can catch a cold simply by touching your eye after touching a contaminated surface. Just think what an eyepiece could do. So if you look through the eyepieces, please decontaminate the eyepieces and eyepiece pillar after your session!
Glove Policy
We do not require gloves to use our instruments except for trained BL2 use. It is your choice for BL1. If you choose to use gloves, we require that you use vinyl gloves provided by the core facility. Fresh gloves are available by each sink. Wash hands upon core entry and don a fresh pair of gloves. Change gloves after placing your sample in the imaging chamber and never re-use gloves. If you take them off, get a fresh pair. If you have any allergies or other restrictions, please notify core personnel.
Mask and Eyewear Policy
- We do not require masks.
- We encourage but do not require eyewear for BL1 work.
- Eyewear is mandatory for BL2 work.
Biosafety Levels
The microscopy core defaults to a BL1 imaging facility. BL1 imaging includes fixed samples that are no longer pathogenic. Imaging of unfixed non-primate specimens including mouse cell lines can also be performed under BL1 conditions.
Live or unfixed samples that include ANY human tissue, primary human cells, primate cells, or primate or human cell lines require BL2-level imaging and a short training session.
Please check with core personnel if you are unsure whether your sample is BL1 or BL2.
Biosafety Signs
BL2 imaging is indicated by a temporary sign on the microscope door or fume hood. Pay attention to BL2 signs! Do not enter a BL2 room with until you have had our core-specific BL2 training.
Wet-lab area
We have a small wet-lab area in room 280 for BL1 sample manipulation. You must label ALL bottles and centrifuge tubes containing liquid. Unlabeled abandoned tubes, even water, must be identified through EHS before we can dispose of them. We have a separate designated area for BL2 sample manipulation. BL2 users must go through separate training.
Scheduling and Billing
Scheduling for independent use
In order to prevent scheduling conflicts, please reserve instrument time in advance through iLab. Try to schedule accurately. Don't schedule lengthy sessions unless you are confident that your samples are good! We realize that experimental conditions change during imaging, but please add a new iLab reservation if you need extra time. This policy both informs others remotely and reminds you check the instrument schedule for updates.
Please book time carefully! We charge for the maximum of your scheduled time or your used time.
Walk-up use
We also allow walk-up instrument use. If a scope is not reserved on iLab and nobody else is using it, you may make an instant reservation. We ask that you reserve your anticipated instrument time on iLab right after logging on to the computer. This will mitigate conflicts with other potential walk-up users. Making a formal iLab reservation also provides us proper billing information.
Cancellations
Cancellations must be made at least four hours before your reservation starts (the lockout period). Reserved instrument time that is missed or cancelled within the lockout period will still be billed. If you need to cancel within the lockout period, please contact us and we will do our best to find an alternative user who can take your reservation.
Scheduling for assisted use or training
Assisted use or instrument training should be scheduled directly with core personnel through email.
Core Access and Usage Limits
Building access
External building 76 access is normally available via your MIT ID card. External users without MIT IDs may be granted weekly TIM ticket access by core personnel. TIM ticket access point is the middle door along Main street.
Internal building 76 access (elevators and stairwells) must be requested through core staff. Note that elevators and doors are unlocked during normal business hours. Please ask us for after-hours and weekend internal access if you do not have it. Core staff may elect to sponsor external users for MIT ID cards.
Core Door Codes
You must acknowledge that you have read this guide before we give you the door codes. Do NOT share door codes or we will change them.
Occupancy Limits
There are no occupancy limits.
Microscope rooms may now have multiple users at once. Some rooms now contain two instruments. Please be courteous and aware of other microscope facility users in your room, especially for turning on and off the lights.
Data Storage and Analysis
Exporting Images
Backup to the server is part of your imaging time: Users should back up their data at the close of each imaging session. Move data files to your own storage space on the shared network file store such as the Luria data cluster, or the OMERO image server within seven (7) days. Facility personnel will assist with recommendations for data back-up and access. Core personnel will purge data periodically from each microscope when the need arises. We encourage you to use your own lab's storage service.
No Hard Drives or USB drives!
Do NOT plug your own hard drive, USB stick, or any other device directly into a microscope computer. Instead, use secure network storage for all operations. Consult with core personnel if you have any specific data issues. We will work with you to find a safe solution.
Workstations
Please check iLab for workstation availability. There are a number of free and open-source image analysis applications such as Fiji. The core will be evaluating new remote analysis packages. Please contact core personnel for alternate imaging software.
ACKNOWLEDGE THE CORE
The cores at the KI are partially funded by a grant P30-CA14051 from the National Cancer Institute. Just like your lab, continued support depends on the number of publications we contribute to and the number of grants we support.
If you publish data taken on our microscopes, please acknowledge the microscopy core in publications and talks. See these instructions on the SBC website when writing acknowledgements.
Tell us when your publication is accepted so we can collect metrics for the next round of grant renewal.
If you receive a new grant and listed our core as a key resource, please tell us about that too! It counts for continued funding.
Finally, core staff members are scientists too! If we helped you develop a new method or experiment, helped you write a method section, or were instrumental in collecting data with you, please consider adding authorship. We know that authorship issues can be tricky to navigate, but core staff citations count toward core grant funding.