# Classify cell type

Garnett\[1] automated cell type classification method should be invoked from a non-normalized raw count matrix data node. It use the specified classifier to generate cell type annotation on the input data

Select a raw count data node, choose **Classification > Classify cell type** task on the pop-up menu

<figure><img src="/files/VA4c267TzkSCkeynhzLT" alt=""><figcaption></figcaption></figure>

If using the **Managed classifiers** tool for the first time, you will be asked to create a new classifier file. Users may select either the **Download Garnett classifier** that matches the species and tissue type with their dataset or the **Import Garnett classifier** that is trained previously.

<figure><img src="/files/gJGAUEC1LBMpSgxXQ5T7" alt=""><figcaption></figcaption></figure>

Next, click the **Create** button to create the classifier file. Once the correct classifier file has been created, select **Finish** to start running the task.

If you would like to classify cell type with the classifier obtained from the same analysis, choose **Project classifiers,** and click on ‘**Select data node**’ to choose the classifier in the analysis. Details on how to train a classifier can be found [here](/icm/analyses/analysis-functionality/task-menu/classification/train-classifier.md). Then click the **Finish** button.

The output data node named **Classify result,** it contains the cell type annotation attributes, "*cell\_type*" is the cell type assignments directly from Garnett model. While "*cluster\_ext\_type*" is the cell type that's determined by expanding cell type assignments to nearby cells using Louvain clustering. Downstream analysis tasks such as normalization and PCA can be performed on the **Classify result** data node.

## References

1. <https://www.nature.com/articles/s41592-019-0535-3>
2. <https://cole-trapnell-lab.github.io/garnett/classifiers/>
3. <https://cole-trapnell-lab.github.io/garnett/docs/#constructing-a-marker-file>


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