diff --git a/docs/tutorials/md/spatial_biology_scimap.md b/docs/tutorials/md/spatial_biology_scimap.md index 0c0022df..bdc5abd8 100644 --- a/docs/tutorials/md/spatial_biology_scimap.md +++ b/docs/tutorials/md/spatial_biology_scimap.md @@ -10,40 +10,35 @@ This series is designed to equip researchers, data scientists, and enthusiasts w ## Set up -[Install Scimap](../md/install_scimap.md) +๐Ÿค– [Install Scimap](../md/install_scimap.md) ๐Ÿ“ฅ [Download demo data](../md/demo_data_scimap.md) -๐Ÿ“ Prepare demo data for analysis +๐Ÿ“ [Prepare demo data for analysis](../md/anndata_scimap.md) ## Cell Phenotyping - ๐Ÿคน๐Ÿผโ€โ™‚๏ธ Phenotype cells by unsupervised clustering - ๐Ÿ‘ฝ Phenotype cells using a hierarchical probabilistic model - ๐Ÿ™Œ Add Regions of Interest (ROIs) for exploration - ๐Ÿคฉ Explore the composition of defined cell types between samples and ROIs +๐Ÿคน๐Ÿผโ€โ™‚๏ธ [Phenotype cells by unsupervised clustering](../md/clustering_scimap.md) +๐Ÿ‘ฝ [Phenotype cells using a hierarchical probabilistic model](../md/scimap_phenotyping.md) +๐Ÿ™Œ [Add Regions of Interest (ROIs) for exploration](../md/add_rois_scimap.md) +๐Ÿคฉ [Explore the composition of defined cell types between samples and ROIs](../md/cell_proportion_scimap.md) ## Spatial Analysis - ๐Ÿ“ Calculate and visualize distances between cell types - ๐Ÿค Cell-cell interaction/ co-occurance analysis - โš–๏ธ Compare proximity scores between samples - ๐Ÿ”ญ Search for spatial patterns +๐Ÿ“ [Calculate and visualize distances between cell types](../md/spatial_analysis_scimap.md) +๐Ÿค [Cell-cell interaction/ co-occurrence analysis](../md/cell_interaction_scimap.md) +โš–๏ธ [Compare proximity scores between samples](../md/proximity_scimap.md) +๐Ÿ”ญ [Search for spatial patterns](../md/spatial_search_scimap.md) ## Cellular Neighbourhoods - ๐ŸŒณ Compute neighborhoods using cell-type or cluster information (includes LDA method) - ๐Ÿš€ Compute neighborhoods using expression data +๐ŸŒณ [Compute neighborhoods using cell-type or cluster information (includes LDA method)](../md/spatial_lda_scimap.md) +๐Ÿš€ [Compute neighborhoods using expression data](../md/spatial_lag_scimap.md) ## Export and Helper Functions - โฌ‡๏ธ Export analysis results to `.csv` - ๐Ÿ‘ฉโ€๐ŸŽจ Animate with scimap - ๐Ÿ‘‘ Merge objects, Classify cells etc.. +โฌ‡๏ธ [Export analysis results to `.csv`](../md/export_scimap.md) +๐Ÿ‘ฉโ€๐ŸŽจ [Animate with scimap](../md/animate_scimap.md) +๐Ÿ‘‘ [Merge objects, Classify cells etc..](../md/scimap_helper_functions.md) ## Videos - ๐ŸŽฅ Video tutorials - - -```python - -``` +๐ŸŽฅ [Video tutorials](../md/scimap_video.md)