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Open-ST
Open-source spatial transcriptomics
An open-source and cheap method with efficient and sub-cellular whole-transcriptome capture.
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Open-ST
rajewsky-lab/openst
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Introduction
Experimental
Experimental
Getting started
Capture area generation
Tissue processing and RNA quality control
Library preparation
Sequencing of Open-ST library
Computational
Computational
Getting started
Preprocessing capture area library
Preprocessing transcriptomic library
Pairwise alignment
Segmentation and single-cell quantification
3D reconstruction
API
FAQ
Examples
Examples
Getting started
Dataset summary
Adult mouse hippocampus
Adult mouse hippocampus
Introduction
Preprocessing transcriptomic library
Pairwise alignment
Segmentation and single-cell quantification
Exploratory analysis (Jupyter)
E13 mouse head
E13 mouse head
Introduction
Preprocessing transcriptomic library
Pairwise alignment
Segmentation and single-cell quantification
Exploratory analysis (Jupyter)
(3D) Metastatic Lymph Node
(3D) Metastatic Lymph Node
Introduction
Environment setup
Preprocessing sequencing data
Alignment and single-cell quantification
3D reconstruction
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