By id: openst_skills_index name: OpenST Skills Index description: | Skills for Open-ST spatial transcriptomics data processing, from raw BCL files to spatially-resolved single-cell h5ad objects.
OpenST Skills
Open-ST is an open-source spatial transcriptomics method that captures transcriptome-wide expression at sub-cellular resolution using sequencing-based spatial barcoding on Illumina flow cells.
Available Skills
Computational Analysis Pipeline
Complete end-to-end computational workflow for processing Open-ST data, covering all 6 stages from raw data to analysis-ready objects.
Skill file: openst_computational.md
When to use:
- Processing raw Open-ST BCL/FASTQ files
- Running spacemake for transcriptomic alignment
- Aligning spatial coordinates to tissue images
- Segmenting cells and assigning transcripts
- Reconstructing 3D spatial data from serial sections
- Performing downstream exploratory analysis on Open-ST data
Using Skills
- Read the computational pipeline skill for the full step-by-step workflow
- Follow stages sequentially: Each stage depends on the previous one
- Check system requirements: 128 GB RAM recommended, GPU for segmentation/alignment