# Introduction

## What is SAW[\[1\]](#references)?

STOmics transcriptomic technology, developed by STOmics Tech, integrates equipment and kits to enable high-throughput transcriptomic sequencing. This technology allows for achieving high temporal resolution at both tissue and cellular dimensions.

The Stereo-seq chip has the advantage of capturing time-varying information about feature expression at tissue and cellular dimensions. This capability aids in better comprehending temporal changes and molecular regulatory networks in organisms. The technique allows researchers to evaluate feature expression patterns at various time points and investigate the dynamic process of transcriptional control.

<figure><img src="/files/kALLMGm7SLCevQOXiuGD" alt=""><figcaption><p>Stereo-seq workflow</p></figcaption></figure>

Specifically designed for Stereo-seq sequencing data, SAW is a spatiotemporal bioinformatics software suite. It supports the space-time dimension by restoring the Coordinate ID (CID) and expression level of each Molecular ID (MID) in the sample tissue. Extract high-density and significant biological information from massive datasets.

Now SAW allows analysts to map the transcriptome in formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples, for more exploratory research regarding normal development, disease pathology, and clinical translation.

## Pipelines

SAW provides the following pipelines for analyzing Stereo-seq data:

* [**SAW count**](/saw-user-manual-v8.2/analysis/pipelines/count.md) is a central component of the software suite, compatible with most Stereo-seq FF,  Stereo-seq FFPE and Stereo-CITE FF 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.
* [**SAW realign**](/saw-user-manual-v8.2/analysis/pipelines.md) is a complementary pipeline designed to accept the manually processed image `.tar.gz` file, to restart the analysis with adjusted images. When the image quality control (QC) result is unsuccessful or the output results of the automatic workflow are not perfect enough, `SAW realign` would be very helpful.
* Other [**complementary pipelines** ](/saw-user-manual-v8.2/analysis/pipelines.md)serve for analysis preparation, secondary analysis, and file format conversions.

## **Microscope imaging**

SAW makes use of a microscope image as a morphology reference for visualizing the feature expression matrix. Image types, including fluorescence and H\&E-stained images, are available in SAW analysis. For detailed guidelines, refer to [microscope images](/saw-user-manual-v8.2/analysis/inputs/images.md).

## **Automatic aligning of image and matrix**

The majority of the time, SAW count will automatically fulfill the registration between a microscope image and a feature expression matrix. In cases where automatic registration is unsuccessful or the image QC result is unsuccessful, manual processing and adjustment of images can be completed using StereoMap. More information is provided in [the tutorial of `SAW realign`](/saw-user-manual-v8.2/tutorials/with-manually-processed-files.md) .

***

## References

1. Gong, C., Li, S., Wang, L., Zhao, F., Fang, S., Yuan, D., Zhao, Z., He, Q., Li, M., Liu, W., Li, Z., Xie, H., Liao, S., Chen, A., Zhang, Y., Li, Y., & Xu, X. (2024). SAW: An efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics. *Gigabyte.* <https://doi.org/10.46471/gigabyte.111>


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