STOmics Software

Analysis tools	System requirements	Main function	Input files
SAW	64-bit Centos/RedHat 78/64 bit Ubuntu 20.04	Data filtering, image registration, obtaining of spatial gene expression matrices, and basic secondary analysis.	References: A reference genome is a comprehensive database of DNA sequences that represents the genomic information of a species. These are available online at databases like Ensembl, UCSC, and NCBI, or you have the option to create your own reference. For microorganism analysis, download index files from Kraken2. Stereo-seq Chip Mask: Stereo-seq chip mask file lists CID (Coordinate ID) sequences for spatial mapping of biological molecules. How to get Mask? Sequencing FASTQ Files: FASTQ files store sequencing data with CID and MID (molecular ID) sequences for spatial identification and molecule quantification. They are generated using DNBSEQ sequencing platforms within your lab or by your DNBSEQ sequencing providers. Images: Microscopic images of tissue sections mounted on Stereo-seq Chips, stained with either nucleus staining or H&E staining, are used to capture tissue morphological information.
StereoMap	64-bit Windows 10 & 11	Performing visualization and interactive operation on datasets, microscope image quality control, and manual processing step by step.

ImageStudio

*ImageStudio has been integrated into StereoMap (≥4.0). ImageStudio is a STOmics image processing software, mainly involving image quality assessment and image manual adjustment modules (image stitching, tissue segmentation, and cell segmentation). The image quality assessment mainly scores the images captured by the microscope in terms of image sharpness and image track lines. The manual image adjustment module is mainly for scenarios that cannot be satisfied by analysts.

ImageStudio software ImageStudio operation manual >

SAW

Stereo-seq Analysis Workflow (SAW) is now released as a self-contained TAR file. The software suite is a set of pipelines bundled to position sequenced reads to their spatial location on the tissue section, quantify spatial feature expression, and visually present spatial expression distribution. SAW processes the data from the Stereo-seq sequencing platform, combined with microscope images, to generate spatial feature expression matrices.

SAW software SAW older version SAW operation manual>

StereoMap

StereoMap is a high-definition visual desktop software to view the results of Stereo-seq data analysis. The software is designed to visualize STOmics' SpatioTemporal omics technologies and products and allows further exploration of SpatioTemporal omics data through a variety of tools provided within the software. The GEF matrix, image RPI and IPR data, and clustering results output from the SAW process can all be displayed in StereoMap.

StereoMap software StereoMap old version StereoMap operation manual>

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