New intro guide

datasets/README.md

@@ -48,12 +48,21 @@ Also, here you can find [additional datasets and resources for methods developer
 If you use the datasets please cite the original sources and double-check their license.
 
 [^2]: From https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-intestine
+
 [^3]: Janesick, A. et al. High resolution mapping of the breast cancer tumor microenvironment using integrated single cell, spatial and in situ analysis of FFPE tissue. bioRxiv 2022.10.06.510405 (2022) doi:10.1101/2022.10.06.510405.
+
 [^4]: Schapiro, D. et al. MCMICRO: A scalable, modular image-processing pipeline for multiplexed tissue imaging. Cold Spring Harbor Laboratory 2021.03.15.435473 (2021) doi:10.1101/2021.03.15.435473.
+
 [^5]: Moffitt, J. R. et al. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science 362, (2018).
+
 [^6]: Hartmann, F. J. et al. Single-cell metabolic profiling of human cytotoxic T cells. Nat. Biotechnol. (2020) doi:10.1038/s41587-020-0651-8.
+
 [^7]: Windhager, J., Bodenmiller, B. & Eling, N. An end-to-end workflow for multiplexed image processing and analysis. bioRxiv 2021.11.12.468357 (2021) doi:10.1101/2021.11.12.468357.
+
 [^8]: Eling, N. & Windhager, J. Example imaging mass cytometry raw data. (2022). doi:10.5281/zenodo.5949116.
+
 [^9]: Eling, N. & Windhager, J. steinbock results of IMC example data. (2022). doi:10.5281/zenodo.7412972.
+
 [^10]: Guilliams, Martin, et al. "Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches." Cell 185.2 (2022) doi:10.1016/j.cell2021.12.018
+
 [^11]: Pollaris, Lotte, et al. "SPArrOW: a flexible, interactive and scalable pipeline for spatial transcriptomics analysis." bioRxiv (2024) doi:10.1101/2024.07.04.601829

notebooks.md

@@ -9,6 +9,18 @@ Notebooks tailored to showcase specific functionalities of the SpatialData ecosy
 ```{eval-rst}
 .. grid:: 2 3 3 3
 
+    .. grid-item::
+
+        .. container:: custom-card
+
+            .. image:: notebooks/examples/attachments/elements.png
+                :target: notebooks/examples/intro.html
+
+            .. toctree::
+                :maxdepth: 1
+
+                notebooks/examples/intro.ipynb
+
     .. grid-item::
 
         .. container:: custom-card