Course schedule
Note
Apart from the starting time the time schedule is indicative. Because we can not plan a course by the minute, in practice the time points will deviate.
Day 1
| block | start | end | topic | instructors | dataset | presentation | exercise |
|---|---|---|---|---|---|---|---|
| introduction | 9:00 | 9:30 | Introduction to the course | Deepak Tanwar | - | link | |
| block 1 | 9:30 | 10:15 | Introduction to spatial omics | Joana Carlevaro-Fita | - | link | |
| break | 10:15 | 10:45 | Coffee break | - | |||
| block 2 | 10:45 | 11:45 | Segmentation | Ivan Berest | - | link | |
| block 3 | 11:45 | 12:30 | Lecture: pre-processing, and data structure | Deepak Tanwar | - | link | |
| break | 12:30 | 13:30 | Lunch | - | |||
| block 3 | 1:30 | 3:00 | Exercise: setup and data structure | Deepak Tanwar, Julien Roux | Visium HD binned, Xenium, Visium HD segmented | Setup, Exercise 1A, Exercise 1B, Exercise 1C | |
| break | 3:00 | 3:30 | Coffee break | - | |||
| block 4 | 3:30 | 5:00 | Quality control (image-based) | Ivan Berest | Xenium | Exercise 2B |
Day 2
| block | start | end | topic | instructors | dataset | presentation | exercise |
|---|---|---|---|---|---|---|---|
| recap | 9:00 | 9:15 | Recap from day 1 | Joana Carlevaro-Fita | - | link | |
| block 1 | 9:15 | 10:30 | Quality control (sequencing-based) | Deepak Tanwar, Julien Roux | Visium HD | link | Exercise 2A |
| break | 10:30 | 11:00 | Coffee break | - | |||
| block 2 | 11:00 | 12:00 | Normalization and scaling | Deepak Tanwar, Julien Roux | P2 CRC Visium HD and Xenium | link | Exercise 4A, Exercise 4B |
| block 3 | 12:400 | 12:30 | Lecture: feature selection, dimensionality reduction | Joana Carlevaro-Fita | P2 CRC Visium HD | link | |
| break | 12:30 | 1:30 | Lunch | - | |||
| block 3 | 1:30 | 2:30 | Exercise: feature selection, dimensionality reduction | Joana Carlevaro-Fita, Julien Roux | P2 CRC Visium HD | Exercise 5 | |
| block 4 | 2:30 | 3:00 | Lecture: clustering | Joana Carlevaro-Fita | P2 CRC Visium HD | link | |
| break | 3:00 | 3:30 | Coffee break | - | |||
| block 4 | 3:30 | 4:15 | Exercise: clustering and visualization | Joana Carlevaro-Fita, Julien Roux | P2 CRC Visium HD | Exercise 6 | |
| block 5 | 4:15 | 5:15 | Exercise: annotation | Ivan Berest, Julien Roux, Joana Carlevaro-Fita | single-cell reference; dataset to be confirmed | Exercise 7 |
Day 3
| block | start | end | topic | instructors | dataset | presentation | exercise |
|---|---|---|---|---|---|---|---|
| recap | 9:00 | 9:15 | Recap from day 2 | Joana Carlevaro-Fita | - | ||
| block 1 | 9:15 | 10:15 | Spatial statistics | Mark Robinson, Peiying Cai, Martin Emons, Samuel Gunz | Part 1, Part 2 | ||
| break | 10:15 | 10:45 | Coffee break | - | |||
| block 2 | 10:45 | 12:30 | Multi-scale analysis | Martin Emons, Samuel Gunz | P2 CRC Visium HD | Exercise 8 | |
| break | 12:30 | 13:30 | Lunch | - | |||
| block 3 | 1:30 | 3:00 | SVG and DSP for spatial data | Peiying Cai | P1 CRC, P5 CRC, P3 NAT, P5 NAT (Visium HD) | Exercise 9 | |
| break | 3:00 | 3:30 | Coffee break | - | |||
| post-course | 4:45 | 5:00 | Post-course information | Deepak Tanwar | - | link |