OpenST Skills Index

The Open-ST pipeline processes raw BCL and FASTQ data through an end-to-end workflow to generate spatially resolved h5ad objects. It executes barcode preprocessing, transcriptomic alignment, coordinate registration, segmentation, and reconstruction to deliver analysis-ready spatial data.

The Open-ST computational pipeline consists of six stages: barcode preprocessing, transcriptomic alignment, coordinate registration, segmentation, reconstruction, and downstream analysis. These stages transform raw sequencing outputs into spatially resolved single-cell expression objects.

Yes, the Open-ST pipeline specifies technical requirements, dependencies, and configurations to support reproducible spatial transcriptomics workflows. These specifications ensure consistent transformation of raw BCL or FASTQ data into spatially resolved h5ad objects across different experiments.

Yes, you can convert raw BCL files directly to spatially resolved h5ad objects using this end-to-end pipeline. The workflow applies barcode preprocessing and transcriptomic alignment to the raw BCL input, ultimately producing an analyzable single-cell expression object with spatial coordinates.

The best way to handle coordinate registration and segmentation in Open-ST experiments is to follow the unified end-to-end computational analysis pipeline. It systematically maps these processing steps within the broader workflow to ensure accurate spatial reconstruction and downstream analysis.