This repository contains materials and lectures for the joint NBIS and BIIF spatial omics course.
- 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
See https://uppsala.instructure.com/courses/58516/pages/schedule
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.
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