Spatial Transcriptomics & Tissue Mapping — Hands-on

Gain expertise in spatial transcriptomics and tissue mapping—QC, registration, deconvolution, spatial statistics, and integrated multi-omics reporting.

Spatial Transcriptomics & Tissue Mapping

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Session Index

Session 1 — Data QC, Imaging & Preprocessing Session 2 — Registration, Deconvolution & Integration Session 3 — Spatial Stats, Neighborhoods & Pathways Session 4 — Mini Capstone: Spatial Pipeline

Session 1

Fee: Rs 6300

Data QC, Imaging & Preprocessing

Slides, spots/beads, barcodes & metadata; H&E basics

Theory

FASTQ & image QC, background & artifact checks

FastQC MultiQC OpenSlide scikit-image

Tissue detection, segmentation & nuclei/cell masks

Cellpose ilastik QuPath

Session 2

Fee: Rs 8400

Registration, Deconvolution & Integration

Read mapping & spot-calling; image-to-spot registration

Space Ranger Loupe Browser Visium

Cell-type deconvolution & scRNA integration to spots

tangram cell2location stereoscope

Downstream analysis in Seurat/Scanpy & ST toolkits

Seurat Scanpy STUtility

Session 3

Fee: Rs 11200

Spatial Stats, Neighborhoods & Pathways

Spatial autocorrelation, domains & neighborhood graphs

Squidpy Giotto Moran’s I/Geary’s C

Differential spatial expression & ligand–receptor views

SpatialDE CellPhoneDB NicheNet

Pathway overlays & tissue microenvironment mapping

GSEA/ORA KEGG/Reactome

Session 4

Fee: Rs 14000

Mini Capstone: Spatial Pipeline

Design a Visium-style end-to-end spatial workflow with provenance

Theory

Automate QC→register→deconvolve→analyze→report with dashboards

Snakemake Conda/Mamba Quarto/JupyterLab

Export figures/tables & submission-ready metadata (GEO/ArrayExpress)

pandas plotly Seurat/Scanpy

PDF

Spatial Transcriptomics & Tissue Mapping Training | Visium, Deconvolution & Spatial Stats

Spatial Transcriptomics & Tissue Mapping — Hands-on