Merge branch 'master' of https://github.com/labsyspharm/scimap

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)  
+🤖 [Install Scimap](../md/install_scimap.md)  
 📥 [Download demo data](../md/demo_data_scimap.md)  
-📁 Prepare demo data for analysis  
+📁 [Prepare demo data for analysis](../md/anndata_scimap.md)  
 
 ## Cell Phenotyping
 
-    🤹🏼‍♂️ Phenotype cells by unsupervised clustering
-    👽 Phenotype cells using a hierarchical probabilistic model
-    🙌 Add Regions of Interest (ROIs) for exploration
-    🤩 Explore the composition of defined cell types between samples and ROIs
+🤹🏼‍♂️ [Phenotype cells by unsupervised clustering](../md/clustering_scimap.md)  
+👽 [Phenotype cells using a hierarchical probabilistic model](../md/scimap_phenotyping.md)  
+🙌 [Add Regions of Interest (ROIs) for exploration](../md/add_rois_scimap.md)  
+🤩 [Explore the composition of defined cell types between samples and ROIs](../md/cell_proportion_scimap.md)  
 
 ## Spatial Analysis
 
-    📍 Calculate and visualize distances between cell types
-    🤏 Cell-cell interaction/ co-occurance analysis
-    ⚖️ Compare proximity scores between samples
-    🔭 Search for spatial patterns
+📍 [Calculate and visualize distances between cell types](../md/spatial_analysis_scimap.md)  
+🤏 [Cell-cell interaction/ co-occurrence analysis](../md/cell_interaction_scimap.md)  
+⚖️ [Compare proximity scores between samples](../md/proximity_scimap.md)  
+🔭 [Search for spatial patterns](../md/spatial_search_scimap.md)  
 
 ## Cellular Neighbourhoods
 
-    🌳 Compute neighborhoods using cell-type or cluster information (includes LDA method)
-    🚀 Compute neighborhoods using expression data
+🌳 [Compute neighborhoods using cell-type or cluster information (includes LDA method)](../md/spatial_lda_scimap.md)  
+🚀 [Compute neighborhoods using expression data](../md/spatial_lag_scimap.md)  
 
 ## Export and Helper Functions
 
-    ⬇️ Export analysis results to `.csv`
-    👩‍🎨 Animate with scimap
-    👑 Merge objects, Classify cells etc..
+⬇️ [Export analysis results to `.csv`](../md/export_scimap.md)  
+👩‍🎨 [Animate with scimap](../md/animate_scimap.md)  
+👑 [Merge objects, Classify cells etc..](../md/scimap_helper_functions.md)  
 
 ## Videos
 
-    🎥 Video tutorials
-
-
-```python
-
-```
+🎥 [Video tutorials](../md/scimap_video.md)