Offline Software

Analysis tools	System requirements	Main function
ImageStudio	64 bit Windows10	Image quality assessment, image stitching, tissue segmentation, and cell segmentation
SAW	64 bit Centos/RedHat 78/64 bit Ubuntu 20.04	Data filtering, image registration, and obtaining of spatial single-cell gene expression matrices
StereoMap	64 bit Windows10	Data visiualization and interactive display

ImageStudio

ImageStudio is a SpatioTemporal omics offline 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 and is used to determine whether they are suitable for downstream data analysis. The manual image adjustment module is mainly for scenarios that cannot be satisfied by

ImageStudio software ImageStudio operation manual

SAW

The Stereo-seq Analysis Workflow (SAW) integrates several Stereo-seq spatial group gene expression analysis tools that can be used to reduce and visualize the spatial expression information of sequencing data on microarrays. Spatial expression matrices are obtained that can be used for downstream analysis

SAW software > 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 operation manual

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