Day 1, Mon (29-Aug-2022)
09.00 - 09:30	Welcome and course introduction	*Paulo Czarnewski & Christophe Avenel*
09:30 - 10:30	Lecture: Spatial Omics Overview	*Lars Borm*
10:30 - 11:00	Coffee Break Lab: 00_precourse.ipynb
11:00 - 12:00	Lecture: Introduction to Image informatics	*Christophe Avenel*
12:00 - 13:00	Lunch
13:00 - 14:00	Lab: 01_ISS_data_loading.ipynb	*Christophe Avenel & Eduard Chelebian*
14:00 - 15:00	Lecture: Image pre-processing	*Christoffer Langseth*
15:00 - 15:30	Coffee Break
15:30 - 16:30	Lab: 02_ISS_decoding.ipynb	*Christophe Avenel & Eduard Chelebian*
16:30 - 17:00	Summary	*Paulo Czarnewski*

Day 2, Tue (30-Aug-2022)
09:00 - 09:30	Lab: 02_ISS_decoding.ipynb	*Christophe Avenel & Eduard Chelebian*
09:30 - 10:30	Lecture: Segmentation-free cell identification	*Naveed Ishaque & Sebastian Tiesmeyer*
10:30 - 11:00	Coffee Break
11:00 - 12:00	Lab: 03_0_segmentation_free_unsupervised.ipynb	*Naveed Ishaque & Sebastian Tiesmeyer*
12:00 - 13:00	Lunch
13:00 - 14:00	Lab: 03_1_segmentation_free_supervised.ipynb	*Naveed Ishaque & Sebastian Tiesmeyer*
14:00 - 15:00	Lecture: Basic QC and data analysis	*Giovanni Palla & Hannah Spitzer*
15:00 - 15:30	Coffee Break
15:30 - 16:30	Lab: 04_single_cell.ipynb	*Giovanni Palla & Hannah Spitzer*
16:30 - 17:00	Summary	*Paulo Czarnewski*

Day 3, Wed (31-Aug-2022)
09:00 - 09:30	Lecture: ISS data analysis	Sergio Salas
09:30 - 10:30	Single cell data : AnnData Lab: 06_ISS_segmentation_and_SC_imputation.ipynb	Sergio Salas
10:30 - 11:00	Coffee Break
11:00 - 12:00	Lecture: Spatial Transcriptomics	Giovanni Palla Hannah Spitzer
12:00 - 13:00	Lunch
13:00 - 15:00	Lab: 07_ST_data_analysis.ipynb Lab: 07a_spatial_adata.ipynb Lab: 07b_spatial_domains.ipynb Lab: 07c_ST_image_analysis.ipynb	Giovanni Palla & Hannah Spitzer
15:00 - 15:30	Lecture: Celltype deconvolution overview	Alma Andersson*
15:30 - 16:00	Coffee Break
16:00 - 16:30	Lecture: Cell-cell communication inference	Anna Schaar & David Fischer
16:30 - 17:00	Summary	Paulo Czarnewski

Day 4, Thu (01-Sep-2022)
09:00 - 10:00	Lab: 08_ST_SC_celltype_deconvolution.ipynb	*Paulo Czarnewski*
10:00 - 10:30	Lab: 09_ST_ISS_communication_inference.ipynb	*Anna Schaar & David Fischer*
10:30 - 11:00	Coffee Break
11:00 - 12:00	Lab: 09_ST_ISS_communication_inference.ipynb	*Anna Schaar & David Fischer*
12:00 - 13:00	Lunch
13:30 - 14:00	Lab: Free exercises
14:00 - 15:00	Lecture: Common Coordinated Frameworks	Alma Andersson*
15:00 - 15:15	Coffee Break
15:30 - 16:30	Data: Spatial_transcriptomics_qc_int_dr_cl.h5ad Annotated: 154441.h5ad 154442.h5ad Lab: 10_ST_ISS_eggplant.ipynb	*Paulo Czarnewski*
16:30 - 17:00	Summary	*Paulo Czarnewski*

Day 5, Fri (02-Sep-2022)
09:00 - 09:30	Lecture: Xfuse	Ludvig Bergenstråle
09:30 - 10:30	Lab: 11_ST_Xfuse.ipynb	Ludvig Bergenstråle & Paulo Czarnewski
10:30 - 11:00	Coffee Break
11:00 - 11:30	Course feedback
11:30 - 12:00	Course Summary

The complete course materials can be downloaded using:

git clone https://github.com/NBISweden/workshop-spatial.git