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Update README.md with: solutions to common problems
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LucaMarconato authored Jan 4, 2025
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Expand Up @@ -85,6 +85,18 @@ Technologies that can be read into `SpatialData` objects using third-party libra

This library is community maintained and is not officially endorsed by the aforementioned spatial technology companies. As such, we cannot offer any warranty of the correctness of the representation. Furthermore, we cannot ensure the correctness of the readers for every data version as the technologies evolve and update their formats. If you find a bug or notice a misrepresentation of the data please report it via our [Bug Tracking System](https://github.com/scverse/spatialdata-io/issues?q=sort%3Aupdated-desc+is%3Aissue+is%3Aopen) so that it can be addressed either by the maintainers of this library or by the community.

## Solutions to common problems
### Problem: I cannot visualize the data, everything is slow
Solution: after parsing the data with `spatialdata-io` readers, you need to write it to Zarr and read it again. Otherwise the performance advantage given by the SpatialData Zarr format will not available.
```python
from spatialdata_io import xenium
from spatialdata import read_zarr

sdata = xenium('raw_data')
sdata.write('data.zarr')
sdata = read_zarr('sdata.zarr')
```

## Citation

Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x
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