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schedule.qmd
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---
title: "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](presentations/1_Day1_Technology_overview_LarsBorm_2025.pdf) | Lars Borm (KU Leuven/VIB, BE) |
| 14:00-14:45 | [Imaging-based SRT data preprocessing](presentations/2_Day1_Imagingbased_SRT_preprocessing_HelenaCrowell_2025.pdf) | Helena Crowell (CNAG, ES) |
| 14:45-15:15 | Break | |
| 15:15-16:00 | Practical 0: [SRT data formats](day_1/practical_0/workdir/p0_data_formats_spatialdata.ipynb) | George Gavrilidis (CERTH, GR) |
| 16:00-17:00 | Practical 1a: [Imaging-based SRT data preprocessing](day_1/practical_1/workdir/p1_qc_normalization.ipynb) | Rasool Saghaleyni (NBIS/SciLifeLab, SE)|
: {tbl-colwidths="[25,50,25]"}
## Day 2 (January 22, 2025)
| Time | Topic | Teacher |
|------------- |--------------------------------------------------------------------------------------------------------- |-------------------------- |
| 09:00-09:45 | [Cell segmentation free analysis of SRT data](presentations/3_Day2_segmentation_free_analysis_NaveedIshaque_2025.pdf) | Naveed Ishaque (BIH, DE) |
| 09:45-10:45 | Practical 1b: [Cell segmentation free analysis of SRT data](day_1/practical_1/workdir/p1_segmentation_sainsc.ipynb) & Practical 1c: [Cell Segmentation](day_1/practical_1/workdir/p1_segmentation_cellpose.ipynb) | Rasool Saghaleyni (NBIS/SciLifeLab, SE) |
| 10:45-11:15 | Break | |
| 11:15-12:00 | [Sequence-based SRT data preprocessing](presentations/4_Day2_seq_based_SRT_preprocessing_AhmedMahfouz_2025.pdf) | 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](presentations/5_Day2_SRT_integration_AhmedMahfouz_2025.pdf) | Ahmed Mahfouz (LUMC, NL) |
| 15:15-15:45 | Break | |
| 15:45-16:45 | Practical 3: [SRT data integration](day_2/practical_3/workdir/p1_integration_sc.ipynb) | Benedetta Manzato (LUMC, NL) |
: {tbl-colwidths="[25,50,25]"}
## Day 3 (January 23, 2025)
| Time | Topic | Teacher |
|------------- |------------------------------------------------------------- |------------------------------------ |
| 09:00-09:45 | [Graph representations & Niche reconstruction](presentations/6_Day3_graphs_niches_AnnaSchaar_2025.pdf) | Anna Schaar (Helmholtz Munich, DE) |
| 09:45-10:30 | [Spatial domain identification](presentations/7_Day3_spatial_domains_MarcoVarrone_2025.pdf) | Marco Varrone (UNIL, CH) |
| 10:30-11:00 | Break | |
| 11:00-12:30 | Practical 4: [Niche reconstruction & domain identification](day_3/practical_4/workdir/p4_niche_domain.ipynb) | Francesca Drummer (Helmholtz Munich, DE) & Marco Varrone (UNIL, CH)|
| 12:30-14:00 | Lunch | |
| 14:00-14:45 | [Spatial statistics](presentations/8_Day3_spatial_stats_MarkRobinson_2025.pdf) | Mark Robinson (Uni Zurich, CH) |
| 14:45-15:45 | Practical 5: Spatial statistics [Part A](day_3/practical_5/01-point-pattern-analysis-vignette.qmd) & [Part B](day_3/practical_5/02-lattice-data-analysis-vignette.qmd) | Mark Robinson (Uni Zurich, CH) |
| 15:45-16:15 | Break | |
| 16:15-17:00 | Guest lecture: Advanced Spatial Biology with AI | Maria Brbic (EPFL) |
: {tbl-colwidths="[25,50,25]"}
## Day 4 (January 24, 2025)
| Time | Topic | Teacher |
|------------- |--------------------------------------------------------- |------------------------------- |
| 09:00-09:45 | [Cell-cell communication](presentations/9_Day4_CellCellCommuniation_YvanSaeys_2025.pdf) | Yvan Saeys (U Ghent/VIB, BE) |
| 09:45-10:45 | Practical 6: [Cell-cell communication](day_4/practical_6/workdir/p6_ccc.ipynb) | 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 | |
: {tbl-colwidths="[25,50,25]"}