Webinars and Online Tutorials

  • Policies

    1. Training requirement: You only have access to equipment you have been trained on by a member of the MicRoN staff and currently have access to in your PMS account.

    2. Acknowledgement agreement: The MicRoN is supported by Harvard University through a TnT grant. To help us with grant renewal, we ask users to please acknowledge the "Microscopy Resources on the North Quad (MicRoN) core at Harvard Medical School" in any publications or public presentations that contain data acquired or analyzed in the MicRoN core.

    3. Record microscopy usage: You must log onto and sign out any MicRoN microscope computers using your PPMS credentials.

    4. Booking and using the microscopes: Please, do not let another person use the time you have book under your name. Cancel your remaining session and ask other users to book the microscope. Please, never share your eCommons/PPMS credentials with other users.

    5. MicRoN users are not authorized to train or allow others to use a microscope in the MicRoN core. Please, do not allow anyone to use the microscopes if they haven’t been trained by the MicRoN staff.

    6. Reservation limitations: The reservation limitations for each microscope are described at the top of the microscope's PPMS online scheduling page. If you are in dire need for more time, please contact the MicRoN manager (paula_monterollopis@hms.harvard.edu).

    7. Cancellation Policy: You must cancel your session as soon as you know you don't need it. Cancelling less than 24h in advance results in the charge of 50% of the fee, unless the session is booked by another user. No-show sessions result in billing 100% of the fee.  

    8. Report problems: Please if you notice that a microscope is not working appropriately or if you are not sure how to use the equipment, please report it to the MicRoN staff. If you break a slide/coverslip/dish, or drip a liquid/solution onto any part of the imaging system, or in any other way may have caused damage, you must report the problem immediately. You will not be in trouble if you report an issue/possible damage, only if you fail to do so.

    9. Please, do not change the equipment: Do not remove objectives, filter cubes, or any microscope part you are not authorized to. Same for installing software, or reconfiguring settings in the acquisition software.

    10. Data Managment: Please note, microscope computers are not long-term data storage devices. Please back up your data into your server/hard-drive as soon as possible.

  • Information for your grant or fellowship

    Grants and fellowships that require a description of the core and its services: Please use the information below.

    "MicRoN is a light microscopy core at Harvard Medical School, supporting more 150 groups in the Longwood Medical area. The core currently supports a wide range of disciplines, including bacterial cell biology, neurobiology, gene therapy development, limb regeneration, immune cell function, cancer immunotherapy, and the development of new tools and genetic models to investigate human disease, aging, and tissue architecture.

    MicRoN is equipped with state-of-the-art instrumentation to support most microscopy modalities and imaging needs:

    • Widefield (4x Nikon Ti or Ti2 inverted microscopes outfitted with a live cell imaging environmental enclosure)
    • TIRF: Nikon Ti with notorized TIRF arm and
    • Spinning disk: 2x Yokogawa CSU-1 scan units on a Nikon Ti or Ti2 inverted stand with a full incubator enclosure. One of the spinning disks is outfitted with a Digital Mirror Device (DMD), for optogenetics.
    • Single point scanning confocal and multiphoton: Zeiss LSM780, Zeiss LSM 980 + AiryScan2 (outfitted with live cell imaging enclosure), Olympus FV3000, Leica Stellaris 8 DIVE FALCON upright (confocal and multiphoton; outfitted with live cell imaging enclosure).
    • FLIM (Fluorescence Lifetime Imaging Microscopy; confocal or multiphoton mode): Leica Stellaris 8 DIVE FALCON upright (confocal and multiphoton)
    • Super-resolution: N-SIM-TIRF structure illumination (2D-, 3D-, TIRF-SIM; outfitted with live cell imaging enclosure) and LSM980 +Airyscan2 (confocal; described above).
    • Slide-scanner: 9-slide widefield (brightfield, color and fluorescence) Nikon Ti inverted microscope.
    • High-Content: InCell 6000 + robotic arm (coming soon).

    The instruments described above, support FRAP (LSM980), long term live cell imaging (in both widefield, confocal and multiphoton modes, all widefields, spinning disk confocals, Zeiss LSM980, Leica Stellaris 8 DIVE), multiplexing imaging (Leica Stellaris 8 DIVE and Zeiss LSM980), and imaging of optically cleared samples (with refractive index matching, dipping lenses; Leica Stellaris 8 DIVE confocal and multiphoton). 

    The core offers tailored one-on-one trainings and support for our trainees, including experimental design, image optimization and data analysis. The dedicated PhD-level core staff assists and collaborates with our trainees in the development or implementation of new technologies facilitating their adoption and in creating custom image acquisition and analysis pipelines to improve imaging workflows and outcome. Finally, the core is committed to helping trainees build quantitative microscopy skills that are critical for a career in life sciences, focusing on rigor and reproducibility"

    Letters of support and assistance with the new NIH policy in Data Management and Sharing: Please contact MicRoN Director Paula Montero Llopis paula_monterollopis@hms.harvard. edu


  • Webinars and Online Tutorials

  • Software

  • MicRoN Big Dipper Image Analysis Work Station

    The MicRoN core is pleased to offer our users image analysis capabilities on a workstation built to handle large datasets. Included in our software portfolio are standard programs such as FIJI, MATLAB, R, CellProfiler, Python, icy, etc. Additionally, we have a full license for arivis Vision4D, a powerful commercial analysis program capable of multi-dimensional data analysis, visualization, and animation with image sets in the terabyte file size.


    To familiarize users with Vision4D we offer a 2-hour tutorial for $50 that will cover the following topics:

    • Data import and image visualization/navigation
    • Finding and viewing image metadata
    • Stitching multi-xy datasets
    • 4D viewing and high-resolution image rendering/video animation
    • An overview of the analysis capabilities and building of a template analysis pipeline for your dataset


    As part of this 2-hour tutorial users must provide a data set to work with for building template analysis pipelines. The template pipeline is not a comprehensive solution for your analysis but should provide a sufficient starting workflow to build on for image analysis.


    MicRoN staff is available to help you troubleshoot your analysis workflow, but currently we do not have the capability to create custom analysis. The core has access to remote support for more in-depth help from the Vision4D software team.


    The workstation is equipped with the following specifications:

    • Intel Xeon Platinum 8260 CPU – 24 cores at 2.4GHz
    • 196GB RAM
    • NVIDIA GeForce GTX 2080 Ti Graphics Card
    • 2TB NVMe hard drive for use during analysis
    • 12TB HDD for short term data storage
    • 38” monitor for high-res visualization
    • 10Gbit ethernet connection for fast server connections*


    *The analysis workstation is not meant for long term storage of data. Please be sure you have a backup copy of your data stored somewhere else. MicRoN is not responsible for loss of data due to hard drive failure. The workstation is equipped with direct server connections, including OMERO, for easy transfer of data.


    We currently have remote access capabilities for the workstation across all software programs. If this is something you would like to use, please let us know so we can get you set up.

  • Nanocourse Lectures

  • Microscopy Information and Education

  • Fluorophores and Fluorescent Proteins

  • Protocols and Sample Preparation

  • Recent Research and Publications


  • Harvard Training Portal