Speakers
Stanislaw Makarchuk
(Sanger Institute)
Tong Li
(Sanger Institute)
Description
Unlock spatial transcriptomics with our open-source pipeline, generating single-cell datasets from microscopy images. Our modular pipeline streamlines workflows by integrating image registration, segmentation, RNA peak-calling, spot-decoding and visualization steps. With our flexible framework, customize your workflow to meet project requirements. Seamlessly process data using Nextflow, ideal for cloud-based processing. Join us at the workshop to explore how you can apply our whole pipeline for spatial transcriptomics analysis or any pipeline's module for general image analysis tasks within your research project.
| Target audience | Beginner developers, Intermediate developers, Advanced developers |
|---|---|
| Keywords | spatial transcriptomics, ISS, in-situ sequencing, registration, decoding, visualisation, nextflow, modular, pipeline, workflow, merfish, FAIR, whole slide, scalable, portable, reusable, peak calling, spot detection, ome-zarr, ome-ngff, GPU, segmentation, cellpose, vitessce, webatlas |
