Schedule
Day 1 (January 21, 2025)
| Time | Topic | Teacher |
|---|---|---|
| 12:00-13:00 | Arrival and lunch | |
| 13:00-13:15 | Welcome and introduction | Ahmed Mahfouz (LUMC, NL) |
| 13:15-14:00 | Overview of SRT technologies | Lars Borm (KU Leuven/VIB, BE) |
| 14:00-14:45 | Imaging-based SRT data preprocessing | Helena Crowell (CNAG, ES) |
| 14:45-15:15 | Break | |
| 15:15-16:00 | Practical 0: SRT data formats | George Gavrilidis (CERTH, GR) |
| 16:00-17:00 | Practical 1a: Imaging-based SRT data preprocessing | Rasool Saghaleyni (NBIS/SciLifeLab, SE) |
Day 2 (January 22, 2025)
| Time | Topic | Teacher |
|---|---|---|
| 09:00-09:45 | Cell segmentation free analysis of SRT data | Naveed Ishaque (BIH, DE) |
| 09:45-10:45 | Practical 1b: Cell segmentation free analysis of SRT data & Practical 1c: Cell Segmentation | Rasool Saghaleyni (NBIS/SciLifeLab, SE) |
| 10:45-11:15 | Break | |
| 11:15-12:00 | Sequence-based SRT data preprocessing | Ahmed Mahfouz (LUMC, NL) |
| 12:00-13:30 | Lunch | |
| 13:30-14:30 | Practical 2: (Sequence-based data analysis)[day_2/practical_2/workdir/p_2_QC_Sequence_based_Visium_.ipynb] | George Gavrilidis (CERTH, GR) |
| 14:30-15:15 | SRT data integration | Ahmed Mahfouz (LUMC, NL) |
| 15:15-15:45 | Break | |
| 15:45-16:45 | Practical 3: SRT data integration | Benedetta Manzato (LUMC, NL) |
Day 3 (January 23, 2025)
| Time | Topic | Teacher |
|---|---|---|
| 09:00-09:45 | Graph representations & Niche reconstruction | Anna Schaar (Helmholtz Munich, DE) |
| 09:45-10:30 | Spatial domain identification | Marco Varrone (UNIL, CH) |
| 10:30-11:00 | Break | |
| 11:00-12:30 | Practical 4: Niche reconstruction & domain identification | Francesca Drummer (Helmholtz Munich, DE) & Marco Varrone (UNIL, CH) |
| 12:30-14:00 | Lunch | |
| 14:00-14:45 | Spatial statistics | Mark Robinson (Uni Zurich, CH) |
| 14:45-15:45 | Practical 5: Spatial statistics Part A & Part B | Mark Robinson (Uni Zurich, CH) |
| 15:45-16:15 | Break | |
| 16:15-17:00 | Guest lecture: Advanced Spatial Biology with AI | Maria Brbic (EPFL) |
Day 4 (January 24, 2025)
| Time | Topic | Teacher |
|---|---|---|
| 09:00-09:45 | Cell-cell communication | Yvan Saeys (U Ghent/VIB, BE) |
| 09:45-10:45 | Practical 6: Cell-cell communication | Francesca Drummer (Helmholtz Munich, DE) |
| 10:45-11:15 | Break | |
| 11:15-11:45 | Free practical time / Work on assignment | |
| 11:45-12:00 | Wrap-up | |
| 12:00-13:00 | Lunch and departure |