Empty color values in images after polygon_query from Xenium data

Hi,

I have multiple samples in the same FOV in Xenium data. I am trying to subset each sample with polygon_query.

cropped = polygon_query(
    sdata=sdata,
    polygons=polygon,
    target_coordinate_system="global",
    images=True, 
)

Then I plot the image

cropped.pl.render_images('morphology_mip').pl.show(), but no data show up in the plot.

Here is the data from cropped.images. The c is just 0.

Can you please point out what's the problem there?
Thank you!!

Bo

Hi, I think this could be due to a bug of polygon_query() that we fixed in the spaitaldata package here: scverse/spatialdata#422.

Can you please try the latest main? Unfortunately we haven't made a release for it yet.

Please notice that you may need to also use the latest main from spatialdata-io.

Hi, thanks for reply!

I created a new Conda environment and reinstalled it from git
pip install git+https://github.com/scverse/spatialdata

croppedRegion = polygon_query( spadata, polygon, target_coordinate_system="global", shapes = True, points = True, images = True, labels = True )

But it looks the shapes and points are not included

I see they're deprecated from polygon_query. Can you please let me know how to get them back?

Then I tried to plot the image
croppedRegion.pl.render_images('morphology_mip').pl.show()

but got a ValueError

However, the imagecodecs has already been installed.

Thanks so much for your help!

Conda environment:
aiobotocore 2.5.4 pypi_0 pypi
aiohttp 3.9.3 pypi_0 pypi
aioitertools 0.11.0 pypi_0 pypi
aiosignal 1.3.1 pypi_0 pypi
anndata 0.10.5.post1 pyhd8ed1ab_0 conda-forge
annotated-types 0.6.0 pypi_0 pypi
aom 3.8.1 h078ce10_0 conda-forge
appnope 0.1.4 pyhd8ed1ab_0 conda-forge
arpack 3.8.0 nompi_ha3438d0_101 conda-forge
array-api-compat 1.5 pyhd8ed1ab_0 conda-forge
asciitree 0.3.3 pypi_0 pypi
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
async-timeout 4.0.3 pypi_0 pypi
attrs 23.2.0 pypi_0 pypi
botocore 1.31.17 pypi_0 pypi
brotli 1.1.0 hb547adb_1 conda-forge
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cached_property 1.5.2 pyha770c72_1 conda-forge
cairo 1.18.0 hd1e100b_0 conda-forge
certifi 2024.2.2 py310hca03da5_0
charset-normalizer 3.3.2 pypi_0 pypi
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pyproj 3.6.1 pypi_0 pypi
python 3.10.13 h2469fbe_1_cpython conda-forge
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python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
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snappy 1.1.10 h313beb8_1
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Both spatialdata-io and spatialdata-plot are latest from main. Thanks!

Thanks for the update. Answering point by point.

Here is the data from cropped.images. The c is just 0.

This is actually correct, because the initial image has one channel, so there is only c=0 as valid coordinate.

cropped.pl.render_images('morphology_mip').pl.show(), but no data show up in the plot.

Below I will suggest a way to make the plot being shown. After this, can you please check if the plot is empty also with the new installation? If spatialdata-plot doesn't work, you can also use napari-spatialdata, but still after following the recommendation explained below (save to Zarr and reload the data).

I see they're deprecated from polygon_query. Can you please let me know how to get them back?

The new APIs doesn't require to have points=True, shapes=True as they are considered by default. If you want to exclude them you can subset the SpatialData object (this can be done conveniently with the new subset() API); but here you want to include them so it should work.

But it looks the shapes and points are not included

This is unexpected. Can you please share some code/data to reproduce? We used queries to crop Xenium data multiple times and we didn't have problems. A reproducible example would help understand what is happening please.

Then I tried to plot the image
croppedRegion.pl.render_images('morphology_mip').pl.show()

but got a ValueError

The problem may be due to using the raw data with Dask. Please try to save the data with sdata.write() and then reload it with spatialdta.read_zarr().

We will make the info that data should be saved to Zarr and reloaded to take advantage of the performant and general storage format, more visible in the tutorial.

Thanks so much for clarification!
I used the data from 10x website Xenium Output Bundle.

I selected a region (circled). The coordinates are coordinates.csv

For installation,
pip install git+https://github.com/scverse/spatialdata
pip install git+https://github.com/scverse/spatialdata-io.git@main
pip install git+https://github.com/scverse/spatialdata-plot.git@main

For polygon-query

selected_region = pd.read_csv('/path/to/coordinates.csv',skiprows=[0,1])
_X = selected_region['X']
_Y = selected_region['Y']
coords = [(x,y) for x, y in zip(_X, _Y)]

from shapely.geometry import MultiPolygon, Polygon
polygon = Polygon(coords)

croppedRegion = polygon_query(
       spdata_test,
       polygon,
       target_coordinate_system="global",
   )

Looks points and shapes are still not included.

I tried to save it to zarr,
croppedRegion.write('/path/to/cropped_region.zarr')

but I got a ValueError.

Thanks so much of your help!!

Bo

@quentinblampey

Thank you for the additional details. I have tried visualizing the data using napari and I get this (the polygon is the one in red):

The reason why the polygon is off (and thus doesn't overlap any shape) is that the polygon coordinates that are saved using Xenium Explorer are in a different coordinate system. The fix is very easy, and is implemented in this function:

spatialdata-io/src/spatialdata_io/readers/xenium.py

Line 329 in 829519d

    
           def xenium_explorer_selection(path: str | Path, pixel_size: float = 0.2125) -> Polygon:

.
The function is not very visible, apologies for that; @quentinblampey and I curated a new tutorial for Xenium data that uses this function and shows additional use cases. I'll add a link of the tutorial to the docs.

The rechunking behavior is instead a bug; a quick fix is to use this code after the query operation:

from spatialdata._utils import multiscale_spatial_image_from_data_tree
from dask.array.core import Array as DaskArray
from multiscale_spatial_image import MultiscaleSpatialImage


def rechunk(msi: MultiscaleSpatialImage) -> DaskArray:
    for scale in msi.keys():
        msi[scale]["image"].data = msi[scale]["image"].data.rechunk()


rechunk(query_result["morphology_focus"])
rechunk(query_result["morphology_mip"])

I will open a PR for that.

This is very helpful. Thanks a lot!

I assume this should work. My current notebook kernel died and I tried to reinstall spatial data-io,
pip install git+https://github.com/scverse/spatialdata-io.git@main, but encountered an error

NotImplementedError

NotImplementedError Traceback (most recent call last) Cell In[4], [line 1](vscode-notebook-cell:?execution_count=4&line=1) ----> [1](vscode-notebook-cell:?execution_count=4&line=1) spdata_test = spatialdata_io.xenium('[/Users/bzhao2/Downloads/Xenium_V1_hPancreas_Cancer_Add_on_FFPE_outs](https://file+.vscode-resource.vscode-cdn.net/Users/bzhao2/Downloads/Xenium_V1_hPancreas_Cancer_Add_on_FFPE_outs)') [2](vscode-notebook-cell:?execution_count=4&line=2) polygon = spatialdata_io.xenium_explorer_selection("[/Users/bzhao2/Downloads/selected_region/coordinates.csv](https://file+.vscode-resource.vscode-cdn.net/Users/bzhao2/Downloads/selected_region/coordinates.csv)") [4](vscode-notebook-cell:?execution_count=4&line=4) query_sdata = sdata_test.query.polygon(polygon, target_coordinate_system="global")

File ~/miniconda3/envs/single-cell/lib/python3.10/site-packages/spatialdata_io/_utils.py:46, in deprecation_alias..deprecation_decorator..wrapper(*args, **kwargs)
44 class_name = f.qualname
45 rename_kwargs(f.name, kwargs, aliases, class_name)
---> 46 return f(*args, **kwargs)

File ~/miniconda3/envs/single-cell/lib/python3.10/site-packages/spatialdata_io/readers/xenium.py:132, in xenium(path, n_jobs, cells_as_circles, nucleus_boundaries, transcripts, morphology_mip, morphology_focus, imread_kwargs, image_models_kwargs)
130 points = {}
131 if transcripts:
--> 132 points["transcripts"] = _get_points(path, specs)
134 images = {}
135 if morphology_mip:

File ~/miniconda3/envs/single-cell/lib/python3.10/site-packages/spatialdata_io/readers/xenium.py:189, in _get_points(path, specs)
184 table["feature_name"] = table["feature_name"].apply(
185 lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x), meta=("feature_name", "object")
186 )
188 transform = Scale([1.0 / specs["pixel_size"], 1.0 / specs["pixel_size"]], axes=("x", "y"))
--> 189 points = PointsModel.parse(
190 table,
191 coordinates={"x": XeniumKeys.TRANSCRIPTS_X, "y": XeniumKeys.TRANSCRIPTS_Y, "z": XeniumKeys.TRANSCRIPTS_Z},
192 feature_key=XeniumKeys.FEATURE_NAME,
193 instance_key=XeniumKeys.CELL_ID,
194 transformations={"global": transform},
195 )
196 return points

File ~/miniconda3/envs/single-cell/lib/python3.10/functools.py:926, in singledispatchmethod.get.._method(*args, **kwargs)
924 def _method(*args, **kwargs):
925 method = self.dispatcher.dispatch(args[0].class)
--> 926 return method.get(obj, cls)(*args, **kwargs)

File ~/miniconda3/envs/single-cell/lib/python3.10/site-packages/spatialdata/models/models.py:507, in PointsModel.parse(cls, data, **kwargs)
469 @singledispatchmethod
470 @classmethod
471 def parse(cls, data: Any, **kwargs: Any) -> DaskDataFrame:
472 """
473 Validate (or parse) points data.
474
(...)
505 :class:dask.dataframe.core.DataFrame
506 """
--> 507 raise NotImplementedError()

NotImplementedError:

The versions are
spatialdata-io 0.0.15
spatialdata-io 0.0.10.dev164+g829519d
dask 2024.3.0

I created a new Conda environment, but the errors persists. It seems the author of dask just released this new version 2024.3.0 yesterday. I am not sure if this causes the error, as the installation worked well several days before.

I downgraded dask to 2024.2.1, and import spatialdata_io, but another error emerged,

ValueError

NotImplementedError Traceback (most recent call last)
Cell In[4], line 1
----> 1 spdata_test = spatialdata_io.xenium('/Users/bzhao2/Downloads/Xenium_V1_hPancreas_Cancer_Add_on_FFPE_outs')
2 polygon = spatialdata_io.xenium_explorer_selection("/Users/bzhao2/Downloads/selected_region/coordinates.csv")
4 query_sdata = sdata_test.query.polygon(polygon, target_coordinate_system="global")

File ~/miniconda3/envs/single-cell/lib/python3.10/site-packages/spatialdata_io/_utils.py:46, in deprecation_alias..deprecation_decorator..wrapper(*args, **kwargs)
44 class_name = f.qualname
45 rename_kwargs(f.name, kwargs, aliases, class_name)
---> 46 return f(*args, **kwargs)

File ~/miniconda3/envs/single-cell/lib/python3.10/site-packages/spatialdata_io/readers/xenium.py:132, in xenium(path, n_jobs, cells_as_circles, nucleus_boundaries, transcripts, morphology_mip, morphology_focus, imread_kwargs, image_models_kwargs)
130 points = {}
131 if transcripts:
--> 132 points["transcripts"] = _get_points(path, specs)
134 images = {}
135 if morphology_mip:

File ~/miniconda3/envs/single-cell/lib/python3.10/site-packages/spatialdata_io/readers/xenium.py:189, in _get_points(path, specs)
184 table["feature_name"] = table["feature_name"].apply(
185 lambda x: x.decode("utf-8") if isinstance(x, bytes) else str(x), meta=("feature_name", "object")
186 )
188 transform = Scale([1.0 / specs["pixel_size"], 1.0 / specs["pixel_size"]], axes=("x", "y"))
--> 189 points = PointsModel.parse(
190 table,
191 coordinates={"x": XeniumKeys.TRANSCRIPTS_X, "y": XeniumKeys.TRANSCRIPTS_Y, "z": XeniumKeys.TRANSCRIPTS_Z},
192 feature_key=XeniumKeys.FEATURE_NAME,
193 instance_key=XeniumKeys.CELL_ID,
194 transformations={"global": transform},
195 )
196 return points

File ~/miniconda3/envs/single-cell/lib/python3.10/functools.py:926, in singledispatchmethod.get.._method(*args, **kwargs)
924 def _method(*args, **kwargs):
925 method = self.dispatcher.dispatch(args[0].class)
--> 926 return method.get(obj, cls)(*args, **kwargs)

File ~/miniconda3/envs/single-cell/lib/python3.10/site-packages/spatialdata/models/models.py:507, in PointsModel.parse(cls, data, **kwargs)
469 @singledispatchmethod
470 @classmethod
471 def parse(cls, data: Any, **kwargs: Any) -> DaskDataFrame:
472 """
473 Validate (or parse) points data.
474
(...)
505 :class:dask.dataframe.core.DataFrame
506 """
--> 507 raise NotImplementedError()

NotImplementedError:

Thanks so much for your help!

Exactly, Dask now uses dask_expr as a backend for Dask DataFrames; we haven't updated the repository to use that (as you observed is a very recent change).

Anyway I am a bit surprised that you get the second error after a downgrade. Can you please set a breakpoint/put a print(type(table)) in xenium.py right before calling PointsModel.parse()?

You should get a dask.dataframe.core.DataFrame, but in your case you are getting a different type.

Thanks for your prompt response.
I made spatialdata-io working by installing dask 2024.2.1 first. Looks the cropped image is square not a circle, but this is very great. Thank you so much for your help!

@Bo-UT

Hi @Bo-UT, we are soon pushing a new release of SpatialData in which for now we have constrained the version of dask being used until we have adjusted the code base to work with the new dask-expr

Great to hear that it worked!

Looks the cropped image is square not a circle,
Yes this is the intended behavior; a discussion around this (a bit technical) is in this comment: scverse/spatialdata#151 (comment).

Anyway when the rasterize() APIs will be implemented for vector data, we could add a helper function to compute a raster mask from the polygon so that one can then use this mask to set to 0 the pixels outside the queried region.

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Empty color values in images after polygon_query from Xenium data #117

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Empty color values in images after polygon_query from Xenium data #117

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LucaMarconato commented on Mar 8, 2024

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