workshop-spatial

This repository contains materials and lectures for the joint NBIS and BIIF spatial omics course.

Course content

• Hands-on experience with ST (Visium), ISS, scRNAseq data analysis
• Fluorescence-based image formats, standards and quality control
• Image alignment, registration and ISS decoding
• Nuclei-based and segmentation-free cell identification
• Data imputation using ISS and single cell datasets
• Analysis of Spatial Transcriptomics dataset
• Cell-type deconvolution (ST and single cell)
• Cell-cell and ligand-receptor interaction analysis
• Mapping of multiple spatial data to a common reference
• High-resolution projection of gene expression to H&E images
• Interactive visualisation of spatial omics data

PRELIMINARY Schedule

See https://uppsala.instructure.com/courses/58516/pages/schedule

ENTRY REQUIREMENTS:

Application form:

• Basic knowledge in Python
• Be able to use your own computer with a web camera
• Desirable: Previous experience with single cell RNA-seq analysis is an advantage.
• If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.

STAFF:

Course leaders:

• Christophe Avenel
• Paulo Czarnewski

Lecturers and content creators:

• Lars Borm
• Carolina Wählby
• Giovanni Palla
• Naveed Ishaque
• Anna Shaar
• David Fischer
• Hanna Spitzer
• Sergio Sallas
• Åsa Björklund
• Sebastian Tiesmeyer
• Ludvig Bergenstråle
• Eduard Chelebian
• Axel Andersson

Contributing Institutions:

• Helmholtz-Munich, DE
• Uppsala University
• Stockholm University
• BIH Charité, DE
• NBIS, SE
• ELIXIR-SE, ELIXIR-DE
• EMBO