Schedule

Day 1

Time	Topic	Teacher
12:00-13:00	Arrival and lunch
13:00-13:15	Welcome and course intro	Ahmed Mahfouz (LUMC, NL)
13:15-14:00	Overview of technologies	Lars Borm (KU Leuven, VIB, BE)
14:00-14:45	imaging-based spatial data analysis (preprocessing, data structures, cell segmentation, QC and normalization)	Helena Crowell (CNAG, ES)
14:45-15:15	Break
15:15-16:00	Practical 0: Data formats (SpatialData, AnnData,…)	George Gavrilidis
16:00-17:00	Practical 1a: imaging-based data QC and normalization	Rasool Saghaleyni

Day 2

Time	Topic	Teacher
09:00-09:45	imaging-based spatial data analysis (segmentation-free analysis)	Naveed Ishaque (BIH, DE)
09:45-10:45	Practical 1b: imaging-based data segmentation-free analysis + Practical 1c:segmentation (optional)	Rasool Saghaleyni
10:45-11:15	Break
11:15-12:00	sequence-based data analysis (preprocessing, data structures, QC and normalization)	Ahmed Mahfouz (LUMC, NL)
12:00-13:30	Lunch
13:30-14:30	Practical 2: sequence-based data analysis	George Gavrilidis
14:30-15:15	Integration with scRNA-seq/deconvolution/annotation/imputation	Ahmed Mahfouz (LUMC, NL)
15:15-15:45	Break
15:45-16:45	Practical 3: integration with scRNA-seq	Ahmed Mahfouz, Benedetta Manzato (LUMC)

Day 3

Time	Topic	Teacher
09:00-09:45	Graph representations/Niche reconstruction	Anna Schaar (Helmholtz Munich, DE)
09:45-10:30	Spatial domain identification/spatial annotation	Marco Varrone (UNIL, CH)
10:30-11:00	Break
11:00-12:30	Practical 4: Niche reconstruction and domain identification	Francesca Drummer/Marco Varrone
12:30-14:00	Lunch
14:00-14:45	Spatial statistics	Mark Robinson (Uni Zurich, CH)
14:45-15:45	Practical 5: spatial stats	Mark Robinson
15:45-16:15	Break
16:15-17:00	Guest lecture:	Maria Brbic (EPFL)

Day 4

Time	Topic	Teacher
09:00-09:45	cell-cell communication (CCC)	Yvan Saeys (U Ghent, VIB, BE)
09:45-10:45	Practical 6: CCC	Francesca Drummer
10:45-11:15	Break
11:15-11:45	Free practical time (finish stuff) / work on assignment
11:45-12:00	Wrap-up (how)
12:00-13:00	Lunch and departure