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Registering Cleared Tissues


Tutorial Description

Light-sheet fluorescence imaging of cleared tissue provides an accessible yet powerful means for researchers to obtain brain-wide snapshots at sub-cellular resolution. As a rapidly growing technique, tissue clearing has provided us with insights into disease pathology, vascular patterning, and brain region function.

Tissue clearing is often used as an unbiased tool to screen for patterns across all regions of the brain. This necessitates accurate registration across all brain regions. With Light-sheet imaging, labs can generate cellular resolution snapshots in as little as 20min or high magnification snapshots in as little as 2 hours. Therefore, registration techniques must be fast yet accurate.

In this tutorial, we will discuss the theory behind light-sheet fluorescence imaging and tissue clearing. We will then discuss how we can use analysis and registration tools to go from raw image data to regionalized quantification. Along this journey, we will go over common artifacts present in datasets and how these artifacts can affect registration.

The goal of this tutorial is for students to understand how registration fits into the light-sheet imaging workflow, the limits of current registration tools, and how we can begin to generate a next generation of registration tools for light-sheet imaging data.

About the hackathon Light Sheet Dataset.

Duration: 0.5 hours.

Learning Outcomes

  1. Outcome 1. Understanding of the basic theory behind optical clearing and light-sheet imaging.
  2. Outcome 2. Understanding basic analysis and registration workflow for light-sheet data.
  3. Outcome 3. Awareness of the unique advantages and challenges that clearing and light-sheet imaging pose for registration.
  4. Outcome 4. Ability to identify subtle yet significant errors in registration.
  5. Outcome 5. Appreciate how errors in registration can affect significance calls.

Approach and Materials

Background and References