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 | 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 | 2:00 | Exercise: setup and data structure | Deepak Tanwar, Julien Roux | Setup, Exercise 1 | |
| block 4 | 2:00 | 3:30 | Quality control and normalization (sequencing-based) | Deepak Tanwar | link | Exercise 2 |
| break | 3:30 | 4:00 | Coffee break | |||
| block 4 | 4:00 | 5:00 | Quality control (image-based) | Ivan Berest | link | Exercise 3 |
Day 2
| block | start | end | topic | instructors | presentation | exercise |
|---|---|---|---|---|---|---|
| recap | 9:00 | 9:15 | Recap from day 1 | Joana Carlevaro-Fita | ||
| block 1 | 9:15 | 10:15 | Normalization and scaling | Deepak Tanwar | link | Exercise 4 |
| break | 10:15 | 10:45 | Coffee break | |||
| block 2 | 10:45 | 11:30 | Lecture: feature selection, dimensionality reduction | Joana Carlevaro-Fita | link | |
| block 2 | 11:30 | 12:30 | Exercise: feature selection, dimensionality reduction | Joana Carlevaro-Fita, Julien Roux | Exercise 5 | |
| break | 12:30 | 13:30 | Lunch | |||
| block 3 | 1:30 | 2:00 | Lecture: clustering | Joana Carlevaro-Fita | link | |
| block 3 | 2:00 | 2:45 | Exercise: clustering and visualization | Joana Carlevaro-Fita, Julien Roux | Exercise 6 | |
| break | 2:45 | 3:15 | Coffee break | |||
| block 4 | 3:15 | 3:45 | Lecture: annotation | Ivan Berest | link | |
| block 4 | 3:45 | 4:45 | Exercise: annotation | Ivan Berest, Julien Roux | Exercise 7 |
Day 3
| block | start | end | topic | instructors | presentation | exercise |
|---|---|---|---|---|---|---|
| recap | 9:00 | 9:15 | Recap from day 2 | Joana Carlevaro-Fita | ||
| block 1 | 9:15 | 10:15 | Spatial statistics | Mark Robinson | link | |
| break | 10:15 | 10:45 | Coffee break | |||
| block 2 | 10:45 | 12:30 | Co-localization analysis | Martin Emons | link | Exercise 8 |
| break | 12:30 | 13:30 | Lunch | |||
| block 3 | 1:30 | 3:00 | SVG and DSP for spatial data | Peiying Cai | link | Exercise 9, Exercise 10 |
| break | 3:00 | 3:30 | Coffee break | |||
| post-course | 4:45 | 5:00 | Post-course information | Deepak Tanwar | link |