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This guide explains how to use our GUI-based tool in MATLAB, which uses manual input to visualize fluorescent tracks from brain slices in a precise and flexible manner. This can be done by following the following steps:
- Requirements
- Pre-processing histology images
- Navigating in the reference atlas
- Registering slices to the atlas
- Selecting regions of interest
- Visualize & analyze brain regions traversed by an electrode
- Visualize & analyze other types of regions of interest such as labelled cells
