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Visium HD plotting tutorial - #93

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Plotting tutorial for Visium HD.

The notebook can be improved in the following way (we can do it in another iteration):

  • the can actually parse the Visium HD data as squares not circles, so we don't have to convert the circles to squares
  • we can rasterize, on the fly, the gene expression data by constructing a lazy SpatialImage object which calls a rasterization function (rasterio, rioxarray or datashader) lazily.

CC @giovp@timtreis

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looks really great @LucaMarconato , LGTM

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Visium HD plotting tutorial by LucaMarconato · Pull Request #93 · scverse/spatialdata-tutorials · GitHub
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Plotting tutorial for Visium HD.
The notebook can be improved in the following way (we can do it in another iteration):
  • the can actually parse the Visium HD data as squares not circles, so we don't have to convert the circles to squares
  • we can rasterize, on the fly, the gene expression data by constructing a lazy SpatialImage object which calls a rasterization function (rasterio, rioxarray or datashader) lazily.
CC @giovp@timtreis
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looks really great @LucaMarconato , LGTM
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Visium HD plotting tutorial by LucaMarconato · Pull Request #93 · scverse/spatialdata-tutorials · GitHub
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Plotting tutorial for Visium HD.
The notebook can be improved in the following way (we can do it in another iteration):
  • the can actually parse the Visium HD data as squares not circles, so we don't have to convert the circles to squares
  • we can rasterize, on the fly, the gene expression data by constructing a lazy SpatialImage object which calls a rasterization function (rasterio, rioxarray or datashader) lazily.
CC @giovp@timtreis
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looks really great @LucaMarconato , LGTM
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Visium HD plotting tutorial by LucaMarconato · Pull Request #93 · scverse/spatialdata-tutorials · GitHub
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Plotting tutorial for Visium HD.
The notebook can be improved in the following way (we can do it in another iteration):
  • the can actually parse the Visium HD data as squares not circles, so we don't have to convert the circles to squares
  • we can rasterize, on the fly, the gene expression data by constructing a lazy SpatialImage object which calls a rasterization function (rasterio, rioxarray or datashader) lazily.
CC @giovp@timtreis
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looks really great @LucaMarconato , LGTM
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, 'i');
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Visium HD plotting tutorial by LucaMarconato · Pull Request #93 · scverse/spatialdata-tutorials · GitHub
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Plotting tutorial for Visium HD.
The notebook can be improved in the following way (we can do it in another iteration):
  • the can actually parse the Visium HD data as squares not circles, so we don't have to convert the circles to squares
  • we can rasterize, on the fly, the gene expression data by constructing a lazy SpatialImage object which calls a rasterization function (rasterio, rioxarray or datashader) lazily.
CC @giovp@timtreis
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looks really great @LucaMarconato , LGTM
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Plotting tutorial for Visium HD.
The notebook can be improved in the following way (we can do it in another iteration):
  • the can actually parse the Visium HD data as squares not circles, so we don't have to convert the circles to squares
  • we can rasterize, on the fly, the gene expression data by constructing a lazy SpatialImage object which calls a rasterization function (rasterio, rioxarray or datashader) lazily.
CC @giovp@timtreis
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looks really great @LucaMarconato , LGTM
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Visium HD plotting tutorial by LucaMarconato · Pull Request #93 · scverse/spatialdata-tutorials · GitHub
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Visium HD plotting tutorial - #93
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Plotting tutorial for Visium HD.
The notebook can be improved in the following way (we can do it in another iteration):
  • the can actually parse the Visium HD data as squares not circles, so we don't have to convert the circles to squares
  • we can rasterize, on the fly, the gene expression data by constructing a lazy SpatialImage object which calls a rasterization function (rasterio, rioxarray or datashader) lazily.
CC @giovp@timtreis
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looks really great @LucaMarconato , LGTM
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, 'i');
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} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
Visium HD plotting tutorial by LucaMarconato · Pull Request #93 · scverse/spatialdata-tutorials · GitHub
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Visium HD plotting tutorial - #93
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Visium HD plotting tutorial#93
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@LucaMarconatoLucaMarconato
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Plotting tutorial for Visium HD.
The notebook can be improved in the following way (we can do it in another iteration):
  • the can actually parse the Visium HD data as squares not circles, so we don't have to convert the circles to squares
  • we can rasterize, on the fly, the gene expression data by constructing a lazy SpatialImage object which calls a rasterization function (rasterio, rioxarray or datashader) lazily.
CC @giovp@timtreis
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looks really great @LucaMarconato , LGTM
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@LucaMarconato@giovp