4 items tagged with 'spatial'.
Stable
Type: Nextflow
Creators: Marek Cmero, Pradeep Rajasekhar, WEHI SODA Hub Technical Team, Ishrat Zaman, Raymond Yip
Submitter: Marek Cmero
Graphical and Interactive Spatial Proteomics Image Analysis Workflow
Open in Codespaces
Click the link above to open the workflow in GitHub Codespaces.
A demonstration video for this workflow is available at https://youtu.be/vHjdCAZQhfE
For more information on how to use Bwb, click this LINK.
Pre-print: ...
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: ...
Tests 
