Parnassus Advanced Light Microscopy

To request training and access, please complete the following:
 

• Create an iLab account and have your PI/Lab Manager assign a speedtype.
• Fill out the PALM User Request Form and tell us a little about your imaging project so we can work with you to choose the appropriate microscope.
• If you plan to take fluorescent images, please take the online Laser Safety Course. Using other support instruments do not require laser safety training.
• Respond to the follow-up email from PALM to discuss microscope options.
• Coordinate with PALM staff for training.

Any questions? Contact us at [email protected]

A detailed description of all PALM instruments and other UCSF microscopy resources: Microscopy @ UCSF.

Confocal microscopy enables high-resolution optical sectioning of fluorescent specimens by rejecting out-of-focus light, producing high-contrast images and enabling three-dimensional reconstruction.

Laser-scanning confocal microscopy is generally best suited for fixed specimens, providing the highest degree of optical sectioning and image contrast. PALM provides access to several Leica laser-scanning confocal systems (Leica SP8 and Leica Stellaris), offering flexibility in specimen size, objective selection, and imaging wavelengths.

Spinning disk confocal microscopy is optimized for live-cell imaging. Our Nikon CSU-W1/SoRa system supports seven excitation wavelengths covering all commonly used fluorescent proteins and features environmental control (temperature and CO₂) for long-term live-cell imaging, as well as a DMD-based spatial illuminator for photoactivation experiments.

New users receive individualized training to become independent instrument users. After certification, microscope time can be reserved through our online booking system and is billed at the applicable hourly recharge rate.

Mitochondria in a live cell imaged by SoRa spinning disk confocal microscopy.

Multiphoton microscopy uses pulsed near-infrared laser light to excite fluorophores deep within biological tissues. Because near-infrared light penetrates further into tissue and reduces out-of-focus excitation, multiphoton microscopy enables imaging at greater depths with reduced photobleaching and phototoxicity. It is particularly well suited for intravital imaging and other applications requiring deep tissue imaging.

PALM provides access to an older Nikon A1R multiphoton microscope for intravital applications. Researchers interested in multiphoton microscopy are encouraged to contact us to discuss experimental design, instrument capabilities, and project feasibility. We are also preparing to identify means for a new multiphoton system - please reach out to us if you are interested.

Light sheet microscopy encompasses a family of imaging techniques in which the excitation and detection light paths are separated. By illuminating only the focal plane, light sheet microscopes enable very rapid three-dimensional imaging while minimizing photobleaching and phototoxicity. Different implementations are optimized for different specimen types and experimental applications. PALM currently provides access to two complementary light sheet systems.

The LifeCanvas SmartSPIM is designed for imaging optically cleared tissues and whole organs at low magnification (3.6× and 9×). The system supports imaging in up to three fluorescence channels and enables rapid acquisition of large specimen volumes. To lower the barrier to tissue clearing, PALM also provides access to a SmartBatch automated tissue clearing and immunostaining system.

PALM also offers a home-built oblique plane, single-objective light sheet microscope (OPM/SOLS) optimized for high-resolution volumetric imaging of cells, organoids, and other specimens in three-dimensional environments. Using a 40× water immersion objective, the system captures fast 3D datasets without physically scanning the sample, making it well suited for long-term live-cell imaging.

Chromosome segregation by OPM/SOLS light sheet microscopy.

Multiplex immunofluorescence enables simultaneous visualization of dozens of protein markers within a single formalin-fixed, paraffin-embedded (FFPE) tissue section, preserving the spatial relationships between different cell types and tissue structures. This approach is particularly valuable for studies of the tumor microenvironment, tissue architecture, and cellular heterogeneity.

PALM offers multiplex immunofluorescence as a full-service workflow using the Leica CellDIVE platform. This system performs iterative cycles of antibody staining, imaging, and fluorescent dye quenching, allowing sequential detection of dozens of markers on the same tissue section. The service is operated by PALM staff, with recharge based on the number of tissue slides and antibody markers included in the experiment. 

PALM continues to expand and optimize its validated CellDIVE antibody library. Our current panel is focused on immuno-oncology applications, and additional antibodies can be validated and incorporated into customized panels as part of the service. We also have instructions on how to prepare FFPE slides for CellDIVE experiments.

Immune cells in liver tissue imaged by CellDIVE multiplex immunofluorescence.

For thin fluorescent specimens, widefield microscopy can provide excellent image quality with much faster acquisition than confocal microscopy. PALM provides access to a Keyence all-in-one microscope for rapid transmitted-light and fluorescence imaging, as well as a Leica THUNDER system that uses computational clearing to improve image contrast and reduce out-of-focus background. Together, these can provide fast and flexible options for routine imaging of fixed and live specimens.

PALM provides access to an Alvéole PRIMO UV-micropatterning system for generating extracellular matrix and other protein micropatterns on glass coverslips with micrometer-scale resolution. The system can also be used for UV exposure of photoresist on silicon wafers to fabricate molds for PDMS-based microfluidic devices.

We also have a Formlabs Form 3 resin 3D printer for rapid prototyping and fabrication of small custom components. These are specialized services, so please contact PALM directly to discuss your project and determine whether our capabilities are suitable for your application.

Fluorescent fibronectin micropatterns.

PALM provides three dedicated image analysis workstations with a variety of software packages, including Imaris and Nikon NIS-Elements, for visualization, processing, and quantitative analysis of microscopy data. These workstations are available for reservation on iLab. PALM staff are also available for consultation on image analysis workflows, from selecting appropriate approaches to developing quantitative analysis strategies for specific experiments.

Please contact us to discuss your image analysis needs or to schedule a consultation.

• Training and certification. All users must be trained and certified by PALM staff before independently operating any instrument. Training by other users is not permitted.
• Reservations. Microscopes can be reserved on iLab up to two weeks in advance; analysis workstations and tissue slicers up to 3 weeks in advance. Please book only the time you reasonably expect to use and cancel reservations you no longer need as early as possible. See cancellation policy below. If your project requires scheduling further in advance, please contact PALM and we will work with you to accommodate your needs whenever possible.
• Cancellation policy. Reservations for microscopes may be cancelled through iLab up to 48 hours before the scheduled start time; analysis workstations and tissue slicers up to 4 hours before start time. If you need to cancel within 48 hours because of an unexpected emergency or other exceptional circumstance, please contact PALM as soon as possible. Late cancellations will be reviewed on a case-by-case basis. Samples not being ready, cells failing to grow, or finishing an experiment earlier than anticipated are generally not considered valid reasons for late cancellation.
• Respect shared equipment. Please leave instruments in the same condition you would like to find them. Remove your samples, clean any oil or media spills, dispose of used lens paper and tissues, and leave your workspace tidy before ending your session.
• Report problems immediately. If something is not working properly—or if you accidentally damage an instrument or accessory—please let us know as soon as possible. Equipment problems and accidents happen; reporting them promptly helps us minimize downtime and keep instruments available for everyone.
• Be considerate of other users. Arrive on time for your reservation and leave sufficient time at the end of your session for cleanup so the next user can begin on schedule.
• Protect your data. Users are responsible for backing up their own data. PALM cannot guarantee long-term storage of image data on acquisition computers. Data older than 30 days may be deleted without notice.
• Acknowledgements and publications. If your work uses PALM resources, please acknowledge the facility in any resulting publications using the following statement: "We thank the UCSF Parnassus Advanced Light Microscopy (PALM) CoLab for microscopy resources used in this publication." Please notify PALM as soon as your work is published so we can track publications that have benefited from the facility. Publications using the Nikon CSU-W1/SoRa microscope should also acknowledge NIH Shared Instrumentation Grant S10 OD028611.

Contact us at: [email protected]
Phone: (415) 476-4550

Torsten Wittmann, PhD
PALM CoLab Director
Email: [email protected]

Austin Edwards
Bioinformatics Programmer
Email: [email protected]

Mohammad Naser, PhD
Microscopy Specialist
Email: [email protected]

Nathanie Trisnadi, PhD
Microscopy Specialist
CoLabs Scientific Operations Lead
Email: [email protected]