Schedule
Please note: This is a preliminary schedule and will be updated prior to the course. Lecture slides will be made available before or during the course.
Day 1 (October 6, 2026)
| Time | Topic | Teacher |
|---|---|---|
| 09:00-09:15 | Welcome and course introduction | Ahmed Mahfouz (LUMC, NL) |
| 09:15-10:00 | Overview of SRT technologies | Åsa Björklund (NBIS, SE) |
| 10:00-10:15 | Break | |
| 10:15-11:00 | Cell segmentation | Christophe Avenel (NBIS, SE) |
| 11:00-11:45 | Practical 0: SRT data formats | Jonas Windhager (NBIS, SE) |
| 11:45-12:45 | Lunch | |
| 12:45-14:15 | Practical 1: Cell segmentation | Christophe Avenel (NBIS, SE) |
| 14:15-15:00 | Lecture: Imaging-based spatial data analysis (preprocessing, QC and normalization) | Christophe Avenel (NBIS, SE) |
| 15:00-15:15 | Break | |
| 15:15-16:45 | Practical 2: Imaging-based analysis and QC | Åsa Björklund (NBIS, SE) & Stefan Ebmeyer (NBIS, SE) |
Day 2 (October 7, 2026)
| Time | Topic | Teacher |
|---|---|---|
| 09:00-09:45 | Cell segmentation free analysis of SRT data | Naveed Ishaque (BIH, DE) |
| 09:45-11:15 | Practical 3: Cell segmentation free analysis of SRT data | Aditya Singh (NBIS, SE) & Lucie Pfeiferova (CAS, CZ) |
| 11:15-12:00 | Sequence-based data analysis (preprocessing, data structures, QC and normalization) | Åsa Björklund (NBIS, SE) |
| 12:00-13:00 | Lunch | |
| 13:00-14:30 | Practical 4: Sequence-based data analysis | Åsa Björklund (NBIS, SE), Leslie Solorzano (NBIS, SE) |
| 14:30-14:45 | Break | |
| 14:45-15:30 | Spatial and single cell data integration | Ahmed Mahfouz (LUMC, NL) |
| 15:30-17:00 | Practical 5: Spatial and single cell data integration | Benedetta Manzato (LUMC, NL), Emma Vonk (LUMC, NL) |
Day 3 (October 8, 2026)
| Time | Topic | Teacher |
|---|---|---|
| 09:00-09:45 | Multi-slice spatial data integration | Benedetta Manzato (LUMC, NL) |
| 09:45-11:15 | Practical 6: Multi-slice spatial data integration | Benedetta Manzato (LUMC, NL), Emma Vonk (LUMC, NL) |
| 11:15-12:00 | Spatial statistics | |
| 12:00-13:00 | Lunch | |
| 13:00-14:30 | Practical 7: Spatial statistics Part A & Part B | Jennifer Fransson (NBIS, SE) |
| 14:30-14:45 | Break | |
| 14:45-15:30 | Domain identification and niche reconstruction | |
| 15:30-17:00 | Practical 8: Domain identification and niche reconstruction | Benedetta Manzato (LUMC, NL), Emma Vonk (LUMC, NL) |
Day 4 (October 9, 2026)
| Time | Topic | Teacher |
|---|---|---|
| 09:00-09:45 | Guest lecture | |
| 09:45-10:30 | Cell-cell communication | Francesca Drummer (Helmholtz, DE) |
| 10:30-12:00 | Practical 9: Cell-cell communication Part A & Part B | Francesca Drummer (Helmholtz, DE), Leslie Solorzano (NBIS, SE) |
| 12:00-13:00 | Lunch and departure |