Offline Software

Analysis tools	System requirements	Main function
ImageStudio	64-bit Windows 10	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, obtaining of spatial gene expression matrices, and basic secondary analysis.
StereoMap	64-bit Windows 10 & 11	Performing microscope image quality control, visualization and interactive operation on datasets, 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 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 StereoMap operation manual>

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