Case Studies

Light sheet microscopy is a very versatile technique. Here we present some case studies that demonstrate how navigate can be used to configure and acquire data from different types of light sheet microscopes. We also provide information on how to use the REST-API to communicate with other software, such as ilastik, for image segmentation and analysis, and how to use the feature container to execute multiscale imaging and smart microscopy.

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Setting Up a Microscope

• Setting up an Axially Swept Light-Sheet Microscope
  • Important points
  • First steps
  • Sequentially adding devices

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Operating a Microscope

• 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

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Using the REST-API

• 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

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Performing Smart Microscopy

• Human-in-the-Loop Multiscale Imaging
• Automatic Multiscale Tiling
• Smart 3D Object Detection