Optical Imaging Across Biological Length Scales

From Nanometers to Millimeters

Fall, 2021

HHMI Janelia Research Campus

Course Director:

Teng-Leong Chew (HHMI Janelia)

This 12-day Bootcamp Course, organized by the Advanced Imaging Center, is designed to demonstrate how biological queries and hypotheses steer experimental designs on various microscopy platforms, and across length scales from molecules to small animals.

There is no application fee. Janelia will cover the costs of lodging and food for all participants.


Hands-on practicals with advanced commercial microscopes and emerging imaging technologies available at Janelia's Advanced Imaging Center

Participants will receive didactic instruction and hands-on experience with localization super-resolution microscopy, structured illumination microscopy, STED, image scanning methods for enhanced resolution, expansion microscopy, various light sheet microscopy methods, and label-free nonlinear microscopy. Participatory lab sessions will be conducted with biological samples from single cells to model organisms, on commercial instruments as well as pre-commercial instruments including iPALM, MOSAIC, SCAPE and SiMView. In addition, participants will also learn to use various imaging probes developed at Janelia.

Immersive learning experience in the experimental workflow from project design to quantitative image analysis

This bootcamp course will put a strong emphasis on image processing, quantitative analysis and machine learning using open-source and commercial software. The curriculum will also cover methods for handling big data.


This workshop is designed to provide advanced training in optical microscopy. Applicants must justify the need to learn imaging on multiple modalities. Selection preference will be given to applicants with prior microscopy experience, core facility personnel, and early-career group leaders interested in understanding the full spectrum of optical imaging capabilities.

Teaching faculty members include:

  • Teng-Leong Chew (Janelia)

  • Elizabeth Hillman (Columbia University)

  • Kate McDole (MRC Laboratory of Molecular Biology, UK)

  • Stephan Preibisch (Janelia)

  • Florian Jug (Max Planck Inst. Mol. Cell Biol. & Genetics, Dresden, Germany) 

  • Meredith Price (Bitplane)

  • Stephan Saalfeld (Janelia)

  • Paul Tillberg (Janelia)

  • Members of the Advanced Imaging Center and Light Microscopy Facility (Janelia)

Keynote and plenary speakers include:

  • Ron Vale (Janelia) Keynote Address

  • Eric Betzig (UC-Berkeley)

  • Elizabeth Hillman (Columbia University)

  • Luke Lavis (Janelia)

  • Jennifer Lippincott-Schwartz (Janelia) 

  • Kate McDole (MRC Laboratory of Molecular Biology, UK)

  • Florian Jug (Max Planck Inst. Mol. Cell Biol. & Genetics, Dresden, Germany) 

Instruments involved in the Bootcamp Course include:

  • Lattice light sheet microscope (Betzig, Janelia)

  • Interferometric PALM (Hess, Janelia)

  • SCAPE (Hillman, Columbia Univ.)

  • Z-1 light sheet microscope (Zeiss)

  • Elyra-7 (Zeiss)

  • SiMView light sheet microscope (Keller, Janelia)

  • MOSAIC (Betzig, Janelia)

  • LSM880 AiryScan confocal microscope (Zeiss)

  • Nikon A1R with CSU-W1 SoRa and TIRF 

  • ONI NanoImager

  • STED (Leica)

  • SP8 CARS SRS (Leica)

  • Multimodal SIM (Gustafsson, Janelia)

  • diSPIM (ASI)