LucaMarconato

New docs section: how to integrate `spatialdata` in your tool

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Aim: adding a page in the docs to help methods developers that want to use SpatialData in their tools. The page could cover the following, showing how SpatialData could be...

Annotating coordinate systems

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Just a random note on this: I agree that having SpatialData - level attributes would be super helpful. Beyond that, I think it would be great to be able to...

New easier intro notebooks

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We have received feedback that our intro notebooks "Use SpatialData with your data": 1. [I. Use SpatialData with your data: the SpatialData object](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/models1.html) 2. [II. Use SpatialData with your data:...

Benchmark spatial partitioning in dask geopandas

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Spatial partitioning with Dask geopandas is described here: https://dask-geopandas.readthedocs.io/en/stable/guide/spatial-partitioning.html

Benchmarks performance on HPC

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CC @melonora @berombau Working with Zarr files on a HPC may create problems due to Zarr v2. One of the challenges for the hackathon will be to setup a set...

Faster version `aggregate()` method available

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While extending SOPA for Visium HD data, @quentinblampey encountered a performance bottleneck with `aggregate()` that he could improve using pure `geopandas` code. Since we use `geopandas` internally, this could be...

Parallelize `aggregate()`

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`aggregate()` is not exploiting dask partitions and parallelization; using it may improve performance. We could make some experiments/benchmarks.

Make a biological transformation notebook

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The [transformation notebook](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/transformations.html) is centered on showing how the API works and not in telling a biological story (for instance it uses a raccoon image image instead of a biological...

It would be convenient to know the data extent, or the extent of some elements, and being able to query and save a smaller object without having to open Python.

Related to https://github.com/scverse/spatialdata-io/issues/231 and https://github.com/scverse/spatialdata-io/pull/72. We could enable a way to merge/edit spatialdata stored objects in a modular way without having to use Python code. ## a possible example The...