Case Studies

Light sheet microscopy is a very versatile technique. Here we present some case studies that demonstrate how navigate can be used to acquire data from different types of light sheet microscopes. These include:

• An Axially Swept Light-Sheet Microscope that scans the beam in both the laser propagation (Y) and detection (Z) directions synchronously with a piezo mounted objective. Tiling in X, Y, and Z is provided by a motorized stage.

• A Digitally Scanned, Axially Swept Light-Sheet Microscope that scans the beam laterally (X) with galvanometric mirrors to create a virtual sheet of light, and axially (Y) with an electronically tunable lens. The sample is moved in the detection direction (Z) to acquire a stack. Tiling in X, Y, and Z is provided by a motorized stage.

• An Axially Swept Light-Sheet Microscope that scans the beam in the laser propagation direction (Y), but acquires a stack by moving the sample in the detection direction (Z. Tiling in X, Y, and Z is provided by a motorized stage.

• An Axially Swept Light-Sheet Microscope that is configured in an upright, di-SPIM-like, geometry. The beam is scanned in the laser propagation direction (Y), but the sample is scanned at a constant velocity in a direction that is 45 degrees to the detection and laser propagation directions (X). Acquiring data in this format permits imaging of thinner (e.g., ~2 mm) specimens with very large lateral extents without the overhead associated with stepping and settling the sample stage. Tiling in X, Y, and Z is provided by a motorized stage.

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• Setting up an Axially Swept Light-Sheet Microscope
  • Important points
  • First steps
  • Sequentially adding devices
• Imaging on a mesoSPIM BT
  • Setting the beam parameters
  • Loading and finding the sample
  • Imaging a z-stack
  • Tiling a sample larger than the field of view
• Imaging on the CT-ASLM-V1 and CT-ASLM-V2
  • Setting up the chamber
  • Sample loading and finding the samples
  • Imaging a Z-Stack with Stelzer mode
  • Imaging a Z-Stack with ASLM mode
  • Tiling a sample larger than the field of view
• Imaging on an Upright ASLM
  • Imaging a Z-Stack using Constant Velocity Acquisition Mode
  • Imaging a Z-Stack using two-axis scanning
• Analyzing Images via REST-API
  • Install navigate-ilastik server
  • Run navigate-ilastik-server
  • Set REST-API configuration
  • Load and set ilastik project
  • Use ilastik feature