Tools

Explore the tools and pipelines available for spatial biology research.

Available Tools

in situ sequencing

• PLP probe design : A portal to design probes for in situ sequencing method.
• NicheCompass Nextflow Pipeline: A powerful pipeline for niche analysis.

Spatial Proteomics

• Signal to noise ratio app
• is-PLA pipeline: A pipeline to detect is-PLA signals and intersect with other selected biomarkers.
• Extracting biomarkers from images in QuPath A script for QuPath to export and save each biomarker in an independent file. Check the demonstration in this video.

Spatial Transcriptomics

• nf-core/spatialvi
  nf-core pipeline to analys Visium data.

General

• TissUUmaps: A browser-based tool for fast visualization and exploration of millions of data points overlaying a tissue sample.
• ScilifeLab Serve: A platform offering machine learning model serving, app hosting, web-based integrated development environments, and other tools to life science researchers.