Home
Welcome to the allenCCF wiki!
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 brain regions traversed by an electrode
- Analyze other types of ROIs such as labelled cells
- Find the electrode insertion angle to target brain regions of interest
