# count

## SAW count

`SAW count` is the central component of the software suite, compatible with most Stereo-seq FF and Stereo-seq FFPE datasets. The inputs consist of a chip mask, FASTQ files, a reference and a microscope image. So that the pipeline counts gene expression reads to generate expression matrices and analysis results from the Stereo-seq chip.

According to the STOmics product lines, parameter usage varies lightly. Before performing an analysis on `SAW count`, pay attention to the information regarding your assay kit version. Choose the appropriate one.

## Stereo-seq T FF

*\*T stands for Chip T*

{% tabs %}
{% tab title="V1.2" %}
[**Count for Stereo-seq T FF V1.2 Spatial Gene Expression**](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.1/analysis/pipelines/count/stereo-seq-t-ff)
{% endtab %}

{% tab title="V1.3" %}
[**Count for Stereo-seq T FF V1.3 Spatial Gene Expression**](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.1/analysis/pipelines/count/stereo-seq-t-ff)
{% endtab %}
{% endtabs %}

## Stereo-seq N FFPE

*\*N stands for Chip N*

{% tabs %}
{% tab title="V1.0" %}
[**Count for Stereo-seq N FFPE V1.0 Spatial Gene Expression**](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.1/analysis/pipelines/count/stereo-seq-n-ffpe-v1.0)
{% endtab %}
{% endtabs %}

## Stereo-CITE T FF

*\*T stands for Chip T*

{% tabs %}
{% tab title="V1.0" %}
[**Count for Stereo-CITE T FF V1.0 Spatial Gene and Protein Expression**](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.1/analysis/pipelines/count/stereo-cite-t-ff)
{% endtab %}

{% tab title="V1.1" %}
[**Count for Stereo-CITE T FF V1.1 Spatial Gene and Protein Expression**](https://stereotoolss-organization.gitbook.io/saw-user-manual-v8.1/analysis/pipelines/count/stereo-cite-t-ff)
{% endtab %}
{% endtabs %}