# 8. Calcium Imaging Analysis

The calcium imaging analysis scripts in GAT allow you to:

* Register or align your images if there is a lot of movement or contractions
* Define regions of interest and extract traces normalized to baseline

Example of image alignment

<div><figure><img src="https://460806082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FUMXPxIZOpwi2uL22W18F%2Fuploads%2FTmJ6iZV19LWF4WleX4a5%2Fgcamp_raw_1.gif?alt=media&#x26;token=1f1a5cb3-2cca-4c8e-af33-1b0f157da7a8" alt=""><figcaption><p>Raw data with movement</p></figcaption></figure> <figure><img src="https://460806082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FUMXPxIZOpwi2uL22W18F%2Fuploads%2F0NlC4InWhzEXO5qMd5i3%2Fgcamp_aligned_1.gif?alt=media&#x26;token=0c477423-b3e4-4cba-a76d-a464f68db44d" alt=""><figcaption><p>Aligned data</p></figcaption></figure></div>

{% content-ref url="8.-calcium-imaging-analysis/image-alignment-registration" %}
[image-alignment-registration](https://gut-analysis-toolbox.gitbook.io/docs/8.-calcium-imaging-analysis/image-alignment-registration)
{% endcontent-ref %}

{% content-ref url="8.-calcium-imaging-analysis/extracting-calcium-traces" %}
[extracting-calcium-traces](https://gut-analysis-toolbox.gitbook.io/docs/8.-calcium-imaging-analysis/extracting-calcium-traces)
{% endcontent-ref %}