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)
| 09:00-09:15 |
Welcome and course introduction |
Jennifer Fransson (NBIS, SE) |
| 09:15-10:00 |
Lecture: Overview of SRT technologies |
Åsa Björklund (NBIS, SE) |
| 10:00-10:15 |
Break |
|
| 10:15-11:00 |
Lecture: Cell segmentation and Data Formats |
Christophe Avenel, Jonas Windhager (NBIS, SE) |
| 11:00-11:10 |
Intro to practicals |
Aditya Singh (NBIS, SE) |
| 11:10-11:45 |
Practical 0: SRT data formats |
Jonas Windhager (NBIS, SE) |
| 11:45-12:45 |
Lunch |
|
| 12:45-14:15 |
Practical 1: Cell segmentation |
Suganya Sivagurunathan (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) |
| 17:30- |
Course Dinner |
|
Day 2 (October 7, 2026)
| 09:00-09:45 |
Lecture: 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 |
Lecture: 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 |
Lecture: 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)
| 09:00-09:45 |
Lecture: 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 |
Lecture: Spatial statistics |
Peiying Cai (UZH/SIB, CH) |
| 12:00-13:00 |
Lunch |
|
| 13:00-14:30 |
Practical 7: Spatial statistics Part A & Part B |
Peiying Cai (UZH/SIB, CH), Jennifer Fransson (NBIS, SE) |
| 14:30-14:45 |
Break |
|
| 14:45-15:30 |
Lecture: Domain identification and niche reconstruction |
|
| 15:30-16:15 |
Practical 8: Domain identification and niche reconstruction |
Benedetta Manzato (LUMC, NL), Emma Vonk (LUMC, NL) |
| 16:15-17:00 |
Guest lecture: From tissue biogeographies to spatial interactomes |
Stefania Giacomello, SciLifeLab / KTH |