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‎notebooks/developers_resources/storage_format/_latest_run_notebook.ipynb‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -929,4 +929,4 @@
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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}

‎notebooks/examples/visium_hd_mouse_brain.ipynb‎

Lines changed: 50 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -31,11 +31,11 @@
3131
"import spatialdata as sdata\n",
3232
"import spatialdata_io as sdio\n",
3333
"import matplotlib.pyplot as plt\n",
34-
"import spatialdata_plot\n",
3534
"import os\n",
3635
"import tempfile\n",
3736
"import subprocess\n",
3837
"import scanpy as sc\n",
38+
"\n",
3939
"print(f\"spatialdata_io=={sdio.__version__}\")\n",
4040
"print(f\"spatialdata=={sdata.__version__}\")"
4141
]
@@ -67,7 +67,6 @@
6767
"metadata": {},
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"outputs": [],
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"source": [
70-
"\n",
7170
"print(f\"Downloading files to: {tmp_dir}\")\n",
7271
"\n",
7372
"# List of files to download\n",
@@ -81,7 +80,7 @@
8180
" \"https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Mouse_Brain/Visium_HD_3prime_Mouse_Brain_molecule_info.h5\",\n",
8281
" \"https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Mouse_Brain/Visium_HD_3prime_Mouse_Brain_segmented_outputs.tar.gz\",\n",
8382
" \"https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Mouse_Brain/Visium_HD_3prime_Mouse_Brain_spatial.tar.gz\",\n",
84-
" \"https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Mouse_Brain/Visium_HD_3prime_Mouse_Brain_web_summary.html\"\n",
83+
" \"https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_3prime_Mouse_Brain/Visium_HD_3prime_Mouse_Brain_web_summary.html\",\n",
8584
"]\n",
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"\n",
8786
"# Download files\n",
@@ -96,7 +95,7 @@
9695
" tar_path = os.path.join(tmp_dir, fname)\n",
9796
" subprocess.run([\"tar\", \"-xzf\", tar_path, \"-C\", tmp_dir], check=True)\n",
9897
"\n",
99-
"print(\"Download and unpack complete.\")\n"
98+
"print(\"Download and unpack complete.\")"
10099
]
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},
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{
@@ -156,12 +155,13 @@
156155
}
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],
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"source": [
159-
"visium_hd_mouse_brain = sdio.visium_hd(tmp_dir,\n",
160-
" load_segmentations_only=True,\n",
161-
" # needed for centroids but otherwise don't have to load nuclei\n",
162-
" # Will increase load time as matrix is calculated from the 2um binned data\n",
163-
" load_nucleus_segmentations=True,\n",
164-
" )"
158+
"visium_hd_mouse_brain = sdio.visium_hd(\n",
159+
" tmp_dir,\n",
160+
" load_segmentations_only=True,\n",
161+
" # needed for centroids but otherwise don't have to load nuclei\n",
162+
" # Will increase load time as matrix is calculated from the 2um binned data\n",
163+
" load_nucleus_segmentations=True,\n",
164+
")"
165165
]
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},
167167
{
@@ -240,7 +240,7 @@
240240
}
241241
],
242242
"source": [
243-
"visium_hd_mouse_brain.pl.render_images().pl.show()\n"
243+
"visium_hd_mouse_brain.pl.render_images().pl.show()"
244244
]
245245
},
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{
@@ -342,7 +342,7 @@
342342
"gene_name = \"Hpca\"\n",
343343
"(\n",
344344
" visium_hd_mouse_brain.pl.render_images(\"Visium_HD_3prime_Mouse_Brain_lowres_image\")\n",
345-
" .pl.render_shapes(\"Visium_HD_3prime_Mouse_Brain_cell_segmentations\", color = gene_name)\n",
345+
" .pl.render_shapes(\"Visium_HD_3prime_Mouse_Brain_cell_segmentations\", color=gene_name)\n",
346346
" .pl.show(coordinate_systems=\"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
347347
")"
348348
]
@@ -409,8 +409,12 @@
409409
],
410410
"source": [
411411
"# Add mitochondrial gene calculation for QC\n",
412-
"visium_hd_mouse_brain.tables[\"cell_segmentations\"].var[\"mt\"] = visium_hd_mouse_brain.tables[\"cell_segmentations\"].var_names.str.startswith((\"MT-\", \"mt-\"))\n",
413-
"sc.pp.calculate_qc_metrics(visium_hd_mouse_brain.tables[\"cell_segmentations\"], qc_vars=['mt'], inplace=True, percent_top=None)\n",
412+
"visium_hd_mouse_brain.tables[\"cell_segmentations\"].var[\"mt\"] = visium_hd_mouse_brain.tables[\n",
413+
" \"cell_segmentations\"\n",
414+
"].var_names.str.startswith((\"MT-\", \"mt-\"))\n",
415+
"sc.pp.calculate_qc_metrics(\n",
416+
" visium_hd_mouse_brain.tables[\"cell_segmentations\"], qc_vars=[\"mt\"], inplace=True, percent_top=None\n",
417+
")\n",
414418
"\n",
415419
"fig, axes = plt.subplots(2, 2, figsize=(12, 10))\n",
416420
"\n",
@@ -420,7 +424,7 @@
420424
" stripplot=False,\n",
421425
" inner=\"box\",\n",
422426
" ax=axes[0, 0],\n",
423-
" show=False\n",
427+
" show=False,\n",
424428
")\n",
425429
"axes[0, 0].set_title(\"Total UMI\")\n",
426430
"\n",
@@ -430,7 +434,7 @@
430434
" stripplot=False,\n",
431435
" inner=\"box\",\n",
432436
" ax=axes[0, 1],\n",
433-
" show=False\n",
437+
" show=False,\n",
434438
")\n",
435439
"axes[0, 1].set_title(\"Total Genes\")\n",
436440
"\n",
@@ -440,16 +444,16 @@
440444
" stripplot=False,\n",
441445
" inner=\"box\",\n",
442446
" ax=axes[1, 0],\n",
443-
" show=False\n",
447+
" show=False,\n",
444448
")\n",
445449
"axes[1, 0].set_title(\"Mitochondrial Genes\")\n",
446450
"\n",
447451
"# Hide the unused subplot\n",
448-
"axes[1, 1].axis('off')\n",
452+
"axes[1, 1].axis(\"off\")\n",
449453
"\n",
450454
"plt.tight_layout()\n",
451455
"plt.show()\n",
452-
"plt.close('all')"
456+
"plt.close(\"all\")"
453457
]
454458
},
455459
{
@@ -467,7 +471,7 @@
467471
"metadata": {},
468472
"outputs": [],
469473
"source": [
470-
"sc.pp.normalize_total(visium_hd_mouse_brain.tables[\"cell_segmentations\"], target_sum = None)\n",
474+
"sc.pp.normalize_total(visium_hd_mouse_brain.tables[\"cell_segmentations\"], target_sum=None)\n",
471475
"sc.pp.log1p(visium_hd_mouse_brain.tables[\"cell_segmentations\"])\n",
472476
"sc.tl.pca(visium_hd_mouse_brain.tables[\"cell_segmentations\"])"
473477
]
@@ -489,14 +493,22 @@
489493
],
490494
"source": [
491495
"# neighborhood and clustering resolution\n",
492-
"RES = 0.5 # clustering resolution\n",
496+
"RES = 0.5 # clustering resolution\n",
493497
"NEIGHBORS = 30 # number of neighbors\n",
494498
"\n",
495-
"MIN_DIST=0.5 #default 0.5\n",
496-
"SPREAD=2 #default 1\n",
499+
"MIN_DIST = 0.5 # default 0.5\n",
500+
"SPREAD = 2 # default 1\n",
497501
"\n",
498-
"sc.pp.neighbors(visium_hd_mouse_brain.tables[\"cell_segmentations\"], n_neighbors=NEIGHBORS, use_rep=\"X_pca\",metric=\"correlation\")\n",
499-
"sc.tl.leiden(visium_hd_mouse_brain.tables[\"cell_segmentations\"], flavor=\"igraph\", key_added=\"clusters\", resolution=RES,random_state=0)"
502+
"sc.pp.neighbors(\n",
503+
" visium_hd_mouse_brain.tables[\"cell_segmentations\"], n_neighbors=NEIGHBORS, use_rep=\"X_pca\", metric=\"correlation\"\n",
504+
")\n",
505+
"sc.tl.leiden(\n",
506+
" visium_hd_mouse_brain.tables[\"cell_segmentations\"],\n",
507+
" flavor=\"igraph\",\n",
508+
" key_added=\"clusters\",\n",
509+
" resolution=RES,\n",
510+
" random_state=0,\n",
511+
")"
500512
]
501513
},
502514
{
@@ -549,9 +561,7 @@
549561
"source": [
550562
"(\n",
551563
" visium_hd_mouse_brain.pl.render_images(\"Visium_HD_3prime_Mouse_Brain_lowres_image\")\n",
552-
" .pl.render_shapes(\"Visium_HD_3prime_Mouse_Brain_cell_segmentations\",\n",
553-
" color=\"clusters\"\n",
554-
" )\n",
564+
" .pl.render_shapes(\"Visium_HD_3prime_Mouse_Brain_cell_segmentations\", color=\"clusters\")\n",
555565
" .pl.show(title=\"clusters over H&E image\", coordinate_systems=\"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
556566
")"
557567
]
@@ -611,11 +621,10 @@
611621
"(\n",
612622
" crop0_lowres(visium_hd_mouse_brain, 150, 250, 300, 500, \"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
613623
" .pl.render_images(\"Visium_HD_3prime_Mouse_Brain_lowres_image\")\n",
614-
" .pl.render_shapes(\"Visium_HD_3prime_Mouse_Brain_cell_segmentations\",\n",
615-
" color=\"clusters\",\n",
616-
" outline_width = 0.10,\n",
617-
" outline_alpha = 1)\n",
618-
" .pl.show(title=f\"Mouse Hypothalamus Clusters\", coordinate_systems=\"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
624+
" .pl.render_shapes(\n",
625+
" \"Visium_HD_3prime_Mouse_Brain_cell_segmentations\", color=\"clusters\", outline_width=0.10, outline_alpha=1\n",
626+
" )\n",
627+
" .pl.show(title=\"Mouse Hypothalamus Clusters\", coordinate_systems=\"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
619628
")"
620629
]
621630
},
@@ -670,8 +679,11 @@
670679
}
671680
],
672681
"source": [
673-
"centroids = sdata.get_centroids(visium_hd_mouse_brain.shapes['Visium_HD_3prime_Mouse_Brain_nucleus_segmentations'], coordinate_system=\"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
674-
"visium_hd_mouse_brain.points['Visium_HD_3prime_Mouse_Brain_nucleus_centroids'] = centroids\n",
682+
"centroids = sdata.get_centroids(\n",
683+
" visium_hd_mouse_brain.shapes[\"Visium_HD_3prime_Mouse_Brain_nucleus_segmentations\"],\n",
684+
" coordinate_system=\"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\",\n",
685+
")\n",
686+
"visium_hd_mouse_brain.points[\"Visium_HD_3prime_Mouse_Brain_nucleus_centroids\"] = centroids\n",
675687
"visium_hd_mouse_brain"
676688
]
677689
},
@@ -730,7 +742,7 @@
730742
"source": [
731743
"(\n",
732744
" visium_hd_mouse_brain.pl.render_images(\"Visium_HD_3prime_Mouse_Brain_lowres_image\")\n",
733-
" .pl.render_points(\"Visium_HD_3prime_Mouse_Brain_nucleus_centroids\", size = 0.2, color = \"black\")\n",
745+
" .pl.render_points(\"Visium_HD_3prime_Mouse_Brain_nucleus_centroids\", size=0.2, color=\"black\")\n",
734746
" .pl.show(title=\"Centroids over H&E image\", coordinate_systems=\"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
735747
")"
736748
]
@@ -788,8 +800,8 @@
788800
"(\n",
789801
" crop0_lowres(visium_hd_mouse_brain, 150, 250, 300, 500, \"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
790802
" .pl.render_images(\"Visium_HD_3prime_Mouse_Brain_lowres_image\")\n",
791-
" .pl.render_points(\"Visium_HD_3prime_Mouse_Brain_nucleus_centroids\", size = 0.2, color = \"black\")\n",
792-
" .pl.show(title=f\"Mouse Hypothalamus Centroids\", coordinate_systems=\"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
803+
" .pl.render_points(\"Visium_HD_3prime_Mouse_Brain_nucleus_centroids\", size=0.2, color=\"black\")\n",
804+
" .pl.show(title=\"Mouse Hypothalamus Centroids\", coordinate_systems=\"Visium_HD_3prime_Mouse_Brain_downscaled_lowres\")\n",
793805
")"
794806
]
795807
}

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