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Tong LI1
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Euro-BioImaging1
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Tong LI1
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Work-in-progress
PaSTa is a nextflow-based end-to-end image analysis pipeline for decoding image-based spatial transcriptomics data. It performs imaging cycle registration, cell segmentation and transcripts peak decoding. It is currently supports analysis of three types of ST technology:
- in-situ sequencing-like encoding
- MERFISH-like encoding
- RNAScope-like labelling
Prerequisites:
- Nextflow. Installation guide: https://www.nextflow.io/docs/latest/getstarted.html
- Docker or Singularity. Installation guide: ...
