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‎docs/api.md‎

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pp.compute_extracellular_counts
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pp.define_extracellular
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pp.compute_crosstab
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pp.format_adata
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pp.format_adata
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```
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## Tools

‎docs/conf.py‎

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"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
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"scanpy": ("https://scanpy.readthedocs.io/en/stable/", None),
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"numpy": ("https://numpy.org/doc/stable/", None),
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'pandas': ('https://pandas.pydata.org/pandas-docs/stable/', None),
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"spatialdata": ("https://spatialdata.scverse.org/en/stable/",None)
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"pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
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"spatialdata": ("https://spatialdata.scverse.org/en/stable/", None),
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}
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# List of patterns, relative to source directory, that match files and
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nitpick_ignore = [
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# If building the documentation fails because of a missing link that is outside your control,
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# you can add an exception to this list.
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("py:class", "igraph.Graph"),
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("py:class", "igraph.Graph"),
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]

‎docs/notebooks/0_format_Xenium_sdata.ipynb‎

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}
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],
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"source": [
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"path='/media/sergio/Discovair_final/Xenium_Prime_Mouse_Brain_Coronal_FF_outs'\n",
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"sdata=spatialdata_io.xenium(path)"
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"path = \"/media/sergio/Discovair_final/Xenium_Prime_Mouse_Brain_Coronal_FF_outs\"\n",
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"sdata = spatialdata_io.xenium(path)"
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]
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},
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{
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}
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],
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"source": [
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"outpath='/media/sergio/Discovair_final/mousebrain_prime.zarr'\n",
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"outpath = \"/media/sergio/Discovair_final/mousebrain_prime.zarr\"\n",
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"sdata.write(outpath)"
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]
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},
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}
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],
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"source": [
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"xenium_path='/media/sergio/Discovair_final/mousebrain_prime.zarr'\n",
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"xenium_path = \"/media/sergio/Discovair_final/mousebrain_prime.zarr\"\n",
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"sdata = sd.read_zarr(xenium_path)\n",
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"sdata"
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]
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" axes=[\"x\", \"y\"],\n",
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" min_coordinate=[17500, 0],\n",
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" max_coordinate=[35000, 15000],\n",
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" target_coordinate_system='global',\n",
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" target_coordinate_system=\"global\",\n",
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")\n",
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"\n",
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"cropped_sdata"
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}
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],
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"source": [
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"import spatialdata_plot\n",
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"cropped_sdata.pl.render_images(\"morphology_focus\").pl.show( title=\"Morphology image\")"
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"cropped_sdata.pl.render_images(\"morphology_focus\").pl.show(title=\"Morphology image\")"
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]
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},
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{
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}
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],
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"source": [
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"xenium_path_cropped='/media/sergio/Discovair_final/mousebrain_prime_half.zarr'\n",
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"cropped_sdata.write(xenium_path_cropped,overwrite=True)"
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"xenium_path_cropped = \"/media/sergio/Discovair_final/mousebrain_prime_half.zarr\"\n",
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"cropped_sdata.write(xenium_path_cropped, overwrite=True)"
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]
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}
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],

‎notebooks/spatialdata_tutorials/0_format_Xenium_sdata.ipynb‎

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"metadata": {},
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"outputs": [],
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"source": [
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"import spatialdata_io\n",
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"import spatialdata as sd"
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"import spatialdata as sd\n",
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"import spatialdata_io"
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]
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},
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{
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}
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],
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"source": [
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"path='/media/sergio/Discovair_final/Xenium_Prime_Mouse_Brain_Coronal_FF_outs'\n",
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"sdata=spatialdata_io.xenium(path)"
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"path = \"/media/sergio/Discovair_final/Xenium_Prime_Mouse_Brain_Coronal_FF_outs\"\n",
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"sdata = spatialdata_io.xenium(path)"
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]
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},
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{
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}
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],
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"source": [
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"outpath='/media/sergio/Discovair_final/mousebrain_prime.zarr'\n",
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"outpath = \"/media/sergio/Discovair_final/mousebrain_prime.zarr\"\n",
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"sdata.write(outpath)"
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]
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},
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}
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],
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"source": [
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"xenium_path='/media/sergio/Discovair_final/mousebrain_prime.zarr'\n",
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"xenium_path = \"/media/sergio/Discovair_final/mousebrain_prime.zarr\"\n",
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"sdata = sd.read_zarr(xenium_path)\n",
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"sdata"
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]
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" axes=[\"x\", \"y\"],\n",
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" min_coordinate=[17500, 0],\n",
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" max_coordinate=[35000, 15000],\n",
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" target_coordinate_system='global',\n",
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" target_coordinate_system=\"global\",\n",
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")\n",
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"\n",
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"cropped_sdata"
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}
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],
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"source": [
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"import spatialdata_plot\n",
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"cropped_sdata.pl.render_images(\"morphology_focus\").pl.show( title=\"Morphology image\")"
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"cropped_sdata.pl.render_images(\"morphology_focus\").pl.show(title=\"Morphology image\")"
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]
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},
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{
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}
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],
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"source": [
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"xenium_path_cropped='/media/sergio/Discovair_final/mousebrain_prime_half.zarr'\n",
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"cropped_sdata.write(xenium_path_cropped,overwrite=True)"
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"xenium_path_cropped = \"/media/sergio/Discovair_final/mousebrain_prime_half.zarr\"\n",
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"cropped_sdata.write(xenium_path_cropped, overwrite=True)"
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]
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}
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],

‎notebooks/spatialdata_tutorials/1_run_segmentation_free.ipynb‎

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"metadata": {},
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"outputs": [],
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"source": [
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"import spatialdata_io\n",
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"import spatialdata as sd\n",
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"import pandas as pd\n",
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"import spatialdata_plot\n",
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"import sys\n",
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"\n",
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"import spatialdata as sd\n",
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"\n",
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"sys.path.append(\"../../src\")\n",
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"import troutpy "
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"import troutpy"
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]
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},
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{
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}
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],
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"source": [
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"xenium_path_cropped='/media/sergio/Discovair_final/mousebrain_prime_crop.zarr'\n",
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"sdata= sd.read_zarr(xenium_path_cropped)"
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"xenium_path_cropped = \"/media/sergio/Discovair_final/mousebrain_prime_crop.zarr\"\n",
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"sdata = sd.read_zarr(xenium_path_cropped)"
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]
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},
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{
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}
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],
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"source": [
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"#define points2regions_params\n",
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"points2regions_params={'num_clusters':100, 'pixel_width':0.4, 'pixel_smoothing':3.5}\n",
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"#run_segmentation_free\n",
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"troutpy.tl.segmentation_free_clustering(sdata, params=points2regions_params, \n",
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" x='x', y='y', feature_name='feature_name', transcript_id='transcript_id')"
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"# define points2regions_params\n",
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"points2regions_params = {\"num_clusters\": 100, \"pixel_width\": 0.4, \"pixel_smoothing\": 3.5}\n",
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"# run_segmentation_free\n",
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"troutpy.tl.segmentation_free_clustering(\n",
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" sdata, params=points2regions_params, x=\"x\", y=\"y\", feature_name=\"feature_name\", transcript_id=\"transcript_id\"\n",
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")"
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]
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},
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{
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}
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],
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"source": [
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"troutpy.pp.define_extracellular(sdata, method='segmentation_free',min_prop_of_extracellular=0.8) "
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"troutpy.pp.define_extracellular(sdata, method=\"segmentation_free\", min_prop_of_extracellular=0.8)"
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]
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},
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{
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}
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],
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"source": [
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"len(sdata.points['transcripts']['extracellular'].compute())"
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"len(sdata.points[\"transcripts\"][\"extracellular\"].compute())"
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]
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},
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{
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],
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"source": [
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"import numpy as np\n",
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"np.sum(sdata.points['transcripts']['extracellular'].compute())"
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"\n",
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"np.sum(sdata.points[\"transcripts\"][\"extracellular\"].compute())"
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]
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},
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{
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}
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],
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"source": [
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"xenium_path_cropped='/media/sergio/Discovair_final/mousebrain_prime_crop_points2regions.zarr'\n",
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"sdata.write(xenium_path_cropped,overwrite=True)"
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"xenium_path_cropped = \"/media/sergio/Discovair_final/mousebrain_prime_crop_points2regions.zarr\"\n",
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"sdata.write(xenium_path_cropped, overwrite=True)"
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]
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},
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{
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"outputs": [],
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"source": [
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"### work a bit into better functions for plotting here\n",
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"plot_data=sdata.points['transcripts'][['segmentation_free_clusters','overlaps_cell','overlaps_nucleus']].compute()\n",
188-
"troutpy.pl.plot_crosstab(plot_data,xvar='segmentation_free_clusters',yvar='overlaps_cell',normalize=True,axis=1,kind='bar',figsize=(20,7),stacked=True,cmap='coolwarm',sortby=True)\n",
189-
"troutpy.pl.plot_crosstab(plot_data,xvar='segmentation_free_clusters',yvar='overlaps_nucleus',normalize=True,axis=1,kind='bar',figsize=(20,7),stacked=True,cmap='coolwarm',sortby=1)\n",
188+
"plot_data = sdata.points[\"transcripts\"][[\"segmentation_free_clusters\", \"overlaps_cell\", \"overlaps_nucleus\"]].compute()\n",
189+
"troutpy.pl.plot_crosstab(\n",
190+
" plot_data,\n",
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" xvar=\"segmentation_free_clusters\",\n",
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" yvar=\"overlaps_cell\",\n",
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" normalize=True,\n",
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" axis=1,\n",
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" kind=\"bar\",\n",
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" figsize=(20, 7),\n",
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" stacked=True,\n",
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" cmap=\"coolwarm\",\n",
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" sortby=True,\n",
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")\n",
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"troutpy.pl.plot_crosstab(\n",
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" plot_data,\n",
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" xvar=\"segmentation_free_clusters\",\n",
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" yvar=\"overlaps_nucleus\",\n",
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" normalize=True,\n",
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" axis=1,\n",
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" kind=\"bar\",\n",
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" figsize=(20, 7),\n",
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" stacked=True,\n",
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" cmap=\"coolwarm\",\n",
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" sortby=1,\n",
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")\n",
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"\n",
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"\n",
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"input_data=sdata.points['transcripts'][['missegmentation_associated']].compute()\n",
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"troutpy.pl.pie_of_positive(input_data,groupby='missegmentation_associated',save=True)"
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"input_data = sdata.points[\"transcripts\"][[\"missegmentation_associated\"]].compute()\n",
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"troutpy.pl.pie_of_positive(input_data, groupby=\"missegmentation_associated\", save=True)"
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]
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}
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],

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