Schedule
Day 1, Mon (29-Aug-2022) |
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| 09.00 - 09:30 | Welcome and course introduction Download Welcome and course introduction | Paulo Czarnewski & Christophe Avenel |
| 09:30 - 10:30 | Lecture: Spatial Omics Overview Download Spatial Omics Overview | Lars Borm |
| 10:30 - 11:00 | Coffee Break Lab: 00_precourse.ipynb Links to an external site. |
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| 11:00 - 12:00 | Lecture: Introduction to Image informatics Download Introduction to Image informatics | Christophe Avenel |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 14:00 | Lab: 01_ISS_data_loading.ipynb Links to an external site. | Christophe Avenel & Eduard Chelebian |
| 14:00 - 15:00 | Lecture: Image pre-processing Download Image pre-processing | Christoffer Langseth |
| 15:00 - 15:30 | Coffee Break | |
| 15:30 - 16:30 | Lab: 02_ISS_decoding.ipynb Links to an external site. | Christophe Avenel & Eduard Chelebian |
| 16:30 - 17:00 | Summary | Paulo Czarnewski |
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| 09:00 - 09:30 | Lab: 02_ISS_decoding.ipynb Links to an external site. | Christophe Avenel & Eduard Chelebian |
| 09:30 - 10:30 | Lecture: Segmentation-free cell identification Download Segmentation-free cell identification | Naveed Ishaque & Sebastian Tiesmeyer |
| 10:30 - 11:00 | Coffee Break | |
| 11:00 - 12:00 | Lab: 03_0_segmentation_free_unsupervised.ipynb
Links to an external site. |
Naveed Ishaque & Sebastian Tiesmeyer |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 14:00 | Lab: 03_1_segmentation_free_supervised.ipynb Links to an external site. | Naveed Ishaque & Sebastian Tiesmeyer |
| 14:00 - 15:00 | Lecture: Basic QC and data analysis Download Basic QC and data analysis | Giovanni Palla & Hannah Spitzer |
| 15:00 - 15:30 | Coffee Break | |
| 15:30 - 16:30 | Lab: 04_single_cell.ipynb Links to an external site. | Giovanni Palla & Hannah Spitzer |
| 16:30 - 17:00 | Summary | Paulo Czarnewski |
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| 09:00 - 09:30 | Lecture: ISS data analysis Download ISS data analysis | Sergio Salas |
| 09:30 - 10:30 | Single cell data : AnnData
Download AnnData Lab: 06_ISS_segmentation_and_SC_imputation.ipynb Links to an external site. |
Sergio Salas |
| 10:30 - 11:00 | Coffee Break | |
| 11:00 - 12:00 | Lecture: Spatial Transcriptomics Download Spatial Transcriptomics | Giovanni Palla Hannah Spitzer |
| 12:00 - 13:00 | Lunch | |
| 13:00 - 15:00 | Lab: 07_ST_data_analysis.ipynb
Links to an external site. Lab: 07a_spatial_adata.ipynb Links to an external site. Lab: 07b_spatial_domains.ipynb Links to an external site. Lab: 07c_ST_image_analysis.ipynb Links to an external site. |
Giovanni Palla & Hannah Spitzer |
| 15:00 - 15:30 | Lecture: Celltype deconvolution overview Download Celltype deconvolution overview | Alma Andersson* |
| 15:30 - 16:00 | Coffee Break | |
| 16:00 - 16:30 | Lecture: Cell-cell communication inference Download Cell-cell communication inference | Anna Schaar & David Fischer |
| 16:30 - 17:00 | Summary | Paulo Czarnewski |
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| 09:00 - 10:00 | Lab: 08_ST_SC_celltype_deconvolution.ipynb Links to an external site. | Paulo Czarnewski |
| 10:00 - 10:30 | Lab: 09_ST_ISS_communication_inference.ipynb Links to an external site. | Anna Schaar & David Fischer |
| 10:30 - 11:00 | Coffee Break | |
| 11:00 - 12:00 | Lab: 09_ST_ISS_communication_inference.ipynb Links to an external site. | Anna Schaar & David Fischer |
| 12:00 - 13:00 | Lunch | |
| 13:30 - 14:00 | Lab: Free exercises | |
| 14:00 - 15:00 | Lecture: Common Coordinated Frameworks Download Common Coordinated Frameworks | Alma Andersson* |
| 15:00 - 15:15 | Coffee Break | |
| 15:30 - 16:30 | Data: Spatial_transcriptomics_qc_int_dr_cl.h5ad
Download Spatial_transcriptomics_qc_int_dr_cl.h5ad Annotated: 154441.h5ad Download 154441.h5ad 154442.h5ad Download 154442.h5ad Lab: 10_ST_ISS_eggplant.ipynb Links to an external site. |
Paulo Czarnewski |
| 16:30 - 17:00 | Summary | Paulo Czarnewski |
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| 09:00 - 09:30 | Lecture: Xfuse Download Xfuse | Ludvig Bergenstråle |
| 09:30 - 10:30 | Lab: 11_ST_Xfuse.ipynb Links to an external site. | Ludvig Bergenstråle & Paulo Czarnewski |
| 10:30 - 11:00 | Coffee Break | |
| 11:00 - 11:30 | Course feedback Links to an external site. | |
| 11:30 - 12:00 | Course Summary | |
The complete course materials can be downloaded using:
git clone https://github.com/NBISweden/workshop-spatial.git