Skip to content

Commit d4b9c8c

Browse files
Update README.md with: solutions to common problems
1 parent c0792b0 commit d4b9c8c

1 file changed

Lines changed: 12 additions & 0 deletions

File tree

README.md

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -85,6 +85,18 @@ Technologies that can be read into `SpatialData` objects using third-party libra
8585

8686
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.
8787

88+
## Solutions to common problems
89+
### Problem: I cannot visualize the data, everything is slow
90+
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.
91+
```python
92+
from spatialdata_io import xenium
93+
from spatialdata import read_zarr
94+
95+
sdata = xenium('raw_data')
96+
sdata.write('data.zarr')
97+
sdata = read_zarr('sdata.zarr')
98+
```
99+
88100
## Citation
89101

90102
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

0 commit comments

Comments
 (0)