New easier intro notebooks

[LucaMarconato]

We have received feedback that our intro notebooks "Use SpatialData with your data":

1. I. Use SpatialData with your data: the SpatialData object
2. II. Use SpatialData with your data: SpatialElements and tables are too tech heavy.

We should consider moving them to a section of notebooks targeting methods developers and make a slimmer version of them (maybe a single intro notebook?) using a biological dataset.

Any of the 5 datasets described here: https://github.com/scverse/spatialdata/issues/700#issuecomment-2326790050 could be used.

[ckmah]

After some discussion, this might be better addressed by restructuring the tutorials and the intro notebooks will help facilitate this. We can break this down into several issues as proposed below:

Organize tutorials for easier usage

• Problem: Currently, many tutorials require in-depth technical knowledge specific to SpatialData and related file formats.

• Audience: people with compbio/bioinformatics background trying to do spatial analysis with downstream packages depending on SpatialData (similar to relationship between AnnData and Scanpy)

• Goal: rewrite the part 1/part 2 tutorials so it is easier for users to get started.

Tutorial subsections

Basic

• 748 Getting Started: Most basic/common tasks using a single biological dataset (or subset). Explain SpatialData and SpatialElements, querying, basic reading/writing, plotting with spatialdata-plot.

  • Link out to “Technology Focus” notebooks for specific reading and visualization examples.
  • Link out to “Part 1” notebook for Zarr, OME-NGFF, partial write element now moved under Advanced.
  • Link to "Part 2" for advanced creation and annotation of SpatialElements.

• 751

Technology Focus

• current technology focus notebooks listed under “Visualization”

Advanced

• most of current tutorial notebooks 😅