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13/06/2025

Community Tool Recommendations for Cell Segmentation in Stereo-seq Data

We present benchmark results comparing eight cell segmentation tools across four typical staining conditions (DAPI, ssDNA, H&E, and mIF). Our data-driven recommendations provide researchers with guidance for selecting optimal segmentation algorithms based on specific experimental conditions.

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Stereo-seq Image Processing: Troubleshooting Common Analysis Challenges
19/05/2025

Stereo-seq Image Processing: Troubleshooting Common Analysis Challenges

Building on our previous blog "Stereo-seq Image Processing: Essential Steps and Their Key Points ", which detailed core image processing steps, this blog now explore practical solutions to common analysis challenges using StereoMap's tools and third-party software integration.

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12/05/2025

Stereo-seq Image Processing: Mastering Essential Steps and Their Key Points

This blog distills the webinar (Stereo-seq image analysis)’s key concepts and explains the fundamentals behind these processing stages. Our goal is to provide you with the essential knowledge for Stereo-seq image analysis and to assist in troubleshooting any related issues you may encounter.

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A Practical Guide to SAW Output Files for Stereo-seq
27/03/2025

A Practical Guide to SAW Output Files for Stereo-seq

In this blog, we will introduce the key output files generated by SAW, explain their generation process, and outline the methods for utilizing or converting them for advanced analysis.

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Spateo: A breakthrough computational framework enabling 3D holograms with exquisite spatial molecular details for any species
25/02/2025

Spateo: A breakthrough computational framework enabling 3D holograms with exquisite spatial molecular details for any species

An international team of scientists from leading research institutes worldwide collaborated to conduct pioneering research in building a 3D spatiotemporal modeling framework—Spateo (https://github.com/aristoteleo/spateo-release). Their accomplishment was published as a featured article in Cell, titled “Spatiotemporal modeling of molecular holograms”.

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CellBin: The Core Image Processing Pipeline in SAW for Generating Single-cell Gene Expression Data for Stereo-seq
24/01/2025

CellBin: The Core Image Processing Pipeline in SAW for Generating Single-cell Gene Expression Data for Stereo-seq

CellBin, an image processing pipeline embedded in SAW (Stereo-seq Analysis Workflow), the primary bioinformatics software for Stereo-seq data analysis, plays a crucial role. The pipeline includes several image processing algorithms tailored for various Stereo-seq applications, such as a unique nuclei segmentation algorithm that adapts to different sample staining methods.

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Mouse brain single-cell clustering result (cellbin)
21/01/2025

STOmics Stereo-seq Technology: The ‘True’ Single-cell Resolution Spatial Multi-omics Platform for Scientific Discovery

Stereo-seq is a sequencing-based spatial multi-omics platform that is not limited by pre-designed probes or panels and can capture the whole transcriptome for scientific discovery.

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Stereo-seq workflow: next generation of drug development and clinical application
14/01/2025

Stereo-seq Empowers Translational Research and Drug Development

STOmics provides the world's leading spatial multi-omics product set, which enables unbiased discoveries at both the protein and transcriptome levels within the same tissue section at single-cell resolution. This capability addresses biological questions across scientific and translational research.

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