Comments (4)
hspitzer
commented on June 12, 2024
this might working using rasterio which xarray also supports: http://xarray.pydata.org/en/stable/generated/xarray.open_rasterio.html
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davidsebfischer
commented on June 12, 2024
this is nice! might be better than going via lazy dask arrays like here #54
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hspitzer
commented on June 12, 2024
look at #54 to see an example of using Rasterio to load tif images. Its also possible to specify chunk sizes - which according to the documentation wraps the xarray in a Dask Array. This is not yet tested / timed.
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davidsebfischer
commented on June 12, 2024
i wouldnt bother about timing yet if it works okay ish, we can still improve backend once the front end is fully functional and the code that you proposed looks very lean which is for sure nice-to-have!
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Related Issues (20)
- Spatial network CSR matrix seems not symmetrical HOT 2
- Geographically weighted regression (GWR) for gene-gene correlation
- Do we need to normalization and scaling before calculating spatial autocorrelation?
- Cannot load Visium_FFPE_Mouse_Brain. Error: HTTP Error 403: Forbidden
- Cannot load Visium_FFPE_Mouse_Brain. Error: HTTP Error 403: Forbidden
- Cannot load Visium_FFPE_Mouse_Brain,Visium_FFPE_Human_Normal_Prostate. Error: HTTP Error 403: Forbidden
- Parameters of squidpy.gr.spatial_neighbors() HOT 1
- Comparisons between groups of samples HOT 5
- Memory Consumption Issue in CosMx.
- Any existing effort to port squidpy functionalities to R?
- Analysing 3D data
- Include more options for niche definitions HOT 1
- Allow for spatial perturbation screen analysis HOT 6
- sq.pl.spatial_scatter return_ax = True not working
- error when sq.im.segment HOT 2
- NaN value when importing Visium dataset HOT 9
- EuroPython talk that can give feature insights to SquidPy HOT 2
- Visium analysis with missing highres images
- Issue reading visium data when the GEX file is a matrix
- dated napari tutorial/documentation HOT 1
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