UCSD School of Medicine Microscopy Core

Core Access is Closed Due to COVID-19

We are offering imaging services at this time by core staff only. Please contact Jennifer Santini (jsantini@ucsd.edu) for details and approval. Covid-19 research is a priority. 

Currently the Core is supporting sample drop-off/pick-up services only. This works well for Slide Scanner and Electron Microscopy Services. Projects involving other microscopes e.g., confocal, have also been conducted successfully. During a remote session users can work independently via Team Viewer after staff assist in loading a specimen and defining areas. Staff may also perform imaging with user guidance via Team Viewer.

 Campus Phase ORANGE - June 1, 2020

Phase Orange can Be reversed by UCSD at any time

Access for only UCSD laboratories at this time

Assisted imaging is still available to Non-UCSD laboratories

Re-opening date for physical access by users: June 1, 2020   With the goal to support important research work by our users while minimizing the risk of community spread of SARS-CoV-2, the Core will implement the following rules when we re-open for physical access by users:

  1. Facility will be open from 9 AM to 5 PM, Monday - Friday only.

  2. A user should not come if he/she feels sick or has symptoms of cough, etc. (Symptom check before entering)

  3. Users must wear a user-furnished mask while in the core (core will NOT provide masks for users).

  4. Users must wash hands with soap and water (available at the core) before and after use of equipment.

  5. Only 1 person allowed per room at any given time.

  6. A user may only enter the core when it is near or at the start time of his/her pre-scheduled session.

  7. Users must alert staff upon completing work so the area can be thoroughly disinfected by the staff.

  8. Regarding gloves: Users are allowed to use their own clean gloves when handling microscope. Please note that under normal circumstance, gloves are not recommended for microscopy because they make it harder to detect – thus contribute to the spreading of - oil, mountain media etc. But we understand if some users may feel more comfortable wearing gloves. Just exercise caution on oil/media spreading. Washing hands is best.

  9. Scope availability: Each scope is available only on specific days of the week to limit the total number of users in the core at any given time (see schedule below).

  10. For overnight runs, contact staff for assistance with drop-off (including sample loading) or pick-up.

  11. COVID-19 researchers may email staff for priority sign up past the 1-week sign up period.

  12. These rules will continue to evolve to reflect actual user traffic and campus COVID-19 status and guidelines (e.g. infection levels, testing). For more information on campus COVID-19 procedures, visit UCSD Research Ramp Up Guidance

Booking of Microscopes:
You may book only 7 days in advance. If you are doing COVID-19 research, you may request to book further out than 7 days by emailing Jennifer Santini. Since we are running on a limited schedule during the ORANGE Phase of opening, we request that you follow rules for booking so we can maximize productivity.

1. Time slots will be a minimum of 2 hours, beginning at 9AM. If you book starting at 10AM you will be shifted to 9AM by staff to maximize productivity

2. You may book up to two time slots per day only

3. You may not book more than 4 time slots per week

4. You must leave the core at 5PM

5. If you are running an overnight timelapse experiment, you may schedule through core staff. You may manipulate the experiment remotely via team viewer. 

6. No after hours use of equipment through remote access is available at this time with fixed samples, as we can not change slides or turn off the system remotely. 

If you see that your time slot was moved or changed by staff, this is to ensure proper booking and productivity and you are to abide by the time on the schedule. Please double check your booking before you attend. Security badge access is required for entrance into the core and the building. 


Alternating Days for Scope availability (will be reflected in iLab online scheduler):

Mon/Wed/Fri                   Zeiss 880 Airyscan Confocal

                                        SP8 confocal with Lightning Deconvolution

                                        Olympus FV1000 Confocal

                                        Nanozoomer Slide Scanner

                                        DeltaVision Deconvolution

Tuesday                         Keyence

                                        SP8 STED Confocal with Lightning and Falcon FLIM

                                        Imaris and Volocity Software Workstations 

                                        (Software also available remotely through Team Viewer)

                                        Perkin Elmer Spinning Disk Confocal

                                        MVX10 Macroview Stereo Microscope

                                        Zeiss Lightsheet Z.1

Thursday                        Keyence

                                        SP8 STED Confocal with Lightning and Falcon FLIM

                                        Leica SP5 Confocal and Multiphoton

                                        DeltaVision OMX (SIM, TIRF and Widefield)

                                        Zeiss Lightsheet Z.1

                                        Zeiss Upright Widefield with Apotome (with approval)


Training sessions will NOT be provided during PHASE ORANGE, as a 6 foot distance cannot be maintained. Assisted sessions (remotely) may be scheduled with staff if you have not been authorized to use an instrument independently.

Contact: Jennifer Santini (jsantini@health.ucsd.edu)


The Core serves the needs of laboratories across the campus and the local research community. Our cutting-edge instruments push the limits of resolution, speed and sensitivity. We offer resources that range from electron microscopy ultrastructure resolution to whole organism / live animal imaging. The Core strives to promote interdisciplinary, collaborative research among local researchers. Experienced staff are available to assist with everything from sample preparation to imaging and analysis. All instruments are wholly owned by the Core, providing stable resources to support long-term research efforts.

  • Serving the UCSD research community since 2003
  • Open to all UCSD labs and surrounding institutions
  • Designated a Leica Center of Excellence in 2019
  • State-of-the-art instruments owned by the Core
  • 15 light microscopes and 1 electron microscope
  • Software for 3D and 4D analysis
  • Multiple microscope brands represented for best solutions
  • Supported by highly experienced staff
  • No. 1 NINDS P30 center in # of publications supported 

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