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LucaMarconato merged 27 commits into from
Mar 24, 2024
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Improved documentation #79

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b27eda0
improved squidpy notebook
LucaMarconato Mar 18, 2024
ff9cb8e
fix import
LucaMarconato Mar 18, 2024
b2236aa
fixed densenet and query notebooks
Mar 21, 2024
431b0cf
fixed aggregation notebook
Mar 21, 2024
fc54769
fixed alignment using landmarks
Mar 21, 2024
1883979
Merge branch 'main' into fix/notebooks
Mar 21, 2024
5611fb9
fixed alignment notebook
Mar 21, 2024
fdbae15
wip visium xenium
Mar 21, 2024
19f53d5
Merge branch 'fix/notebooks' into improve/docs
LucaMarconato Mar 21, 2024
144a13d
tiny fixes squidpy notebook
LucaMarconato Mar 21, 2024
ebbef74
fixed 00_xenium_and_visium
LucaMarconato Mar 21, 2024
189bf58
cleanup cosmx notebook before warnings are fixed
Mar 21, 2024
ce9f42a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 21, 2024
9edc0e3
fixes notebooks speed_up_illustration and cosmx
Mar 21, 2024
fe7af95
Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…
Mar 21, 2024
6760350
fixed notebook speed_up_illustration
Mar 21, 2024
ce87b30
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 21, 2024
63c452a
reduced size plot speed_up_illustration notebook
Mar 21, 2024
4784b27
reduced size plot speed_up_illustration notebook
Mar 21, 2024
f8aefc1
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 21, 2024
c6dd4db
reproducibility check xenium_visium notebooks
LucaMarconato Mar 23, 2024
c0dea5a
fixed notebook 00
Mar 24, 2024
8614be9
correct outlines
melonora Mar 24, 2024
9ea096f
example of assigning cells to rois and computing fractional overlap
LucaMarconato Mar 24, 2024
4b80dd5
Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…
LucaMarconato Mar 24, 2024
77a6d73
removed fractional overlap approach
LucaMarconato Mar 24, 2024
6e98986
update limitation
melonora Mar 24, 2024
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349 changes: 222 additions & 127 deletions notebooks/examples/aggregation.ipynb
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70 changes: 41 additions & 29 deletions notebooks/examples/alignment_using_landmarks.ipynb
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Original file line numberDiff line numberDiff line change
Expand Up@@ -72,7 +72,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/macbook/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:183: ImplicitModificationWarning: Transforming to str index.\n",
"/mnt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67: ImplicitModificationWarning: Transforming to str index.\n",
" warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
]
},
Expand All@@ -88,19 +88,14 @@
"├── Shapes\n",
"│ ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
"│ ├── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
"│ ├── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
"│ └── 'xenium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
"└── Table\n",
" └── AnnData object with n_obs × n_vars = 167780 × 313\n",
" obs: 'cell_id', 'transcript_counts', 'control_probe_counts', 'control_codeword_counts', 'total_counts', 'cell_area', 'nucleus_area', 'region'\n",
" var: 'gene_ids', 'feature_types', 'genome'\n",
" uns: 'spatialdata_attrs'\n",
" obsm: 'spatial': AnnData (167780, 313)\n",
"│ └── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
"└── Tables\n",
" └── 'table': AnnData (167780, 313)\n",
"with coordinate systems:\n",
"▸ 'aligned', with elements:\n",
" morphology_mip (Images)\n",
"▸ 'global', with elements:\n",
" morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes), xenium_landmarks (Shapes)"
" morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)"
]
},
"execution_count": 2,
Expand DownExpand Up@@ -133,27 +128,19 @@
"│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_full_image': MultiscaleSpatialImage[cyx] (3, 21571, 19505), (3, 10785, 9752), (3, 5392, 4876), (3, 2696, 2438), (3, 1348, 1219)\n",
"│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_hires_image': SpatialImage[cyx] (3, 2000, 1809)\n",
"│ └── 'CytAssist_FFPE_Human_Breast_Cancer_lowres_image': SpatialImage[cyx] (3, 600, 543)\n",
"├── Points\n",
"│ ├── 'Points': DataFrame with shape: (3, 2) (2D points)\n",
"│ └── 'Points_1': DataFrame with shape: (1, 2) (2D points)\n",
"├── Shapes\n",
"│ ├── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
"│ └── 'visium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
"└── Table\n",
" └── AnnData object with n_obs × n_vars = 4992 × 18085\n",
" obs: 'in_tissue', 'array_row', 'array_col', 'spot_id', 'region', 'dataset', 'clone'\n",
" var: 'gene_ids', 'feature_types', 'genome'\n",
" uns: 'spatial', 'spatialdata_attrs'\n",
" obsm: 'spatial': AnnData (4992, 18085)\n",
"│ └── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
"└── Tables\n",
" └── 'table': AnnData (4992, 18085)\n",
"with coordinate systems:\n",
"▸ 'aligned', with elements:\n",
" CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), Points (Points), Points_1 (Points), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)\n",
" CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
"▸ 'downscaled_hires', with elements:\n",
" CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
"▸ 'downscaled_lowres', with elements:\n",
" CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
"▸ 'global', with elements:\n",
" CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)"
" CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)"
]
},
"execution_count": 3,
Expand DownExpand Up@@ -184,7 +171,10 @@
"end_time": "2023-04-10T18:59:26.909684Z",
"start_time": "2023-04-10T18:59:25.642148Z"
},
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"source": [
"Interactive([visium_sdata, xenium_sdata], points=False, shapes=False)"
Expand DownExpand Up@@ -335,6 +325,9 @@
"id": "e71718a2",
"metadata": {
"collapsed": false,
"jupyter": {
"outputs_hidden": false
},
"tags": []
},
"outputs": [
Expand DownExpand Up@@ -498,25 +491,44 @@
"id": "be9277db",
"metadata": {},
"source": [
"### Saving the alignment back to Zarr\n"
"### Saving the landmarks and the alignment back to Zarr\n"
]
},
{
"cell_type": "markdown",
"id": "2e98374c-85cd-45ad-ac62-b2bc075c9631",
"metadata": {},
"source": [
"We will now save the transformations to disk. Notice that this is a lightweight operation because we are just mofiying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
"We will now save the landmark points and the transformations of the other elements to disk. \n",
"\n",
"Notice that these are both lightweight operations because the two sets of landmark points are small, and when saving the transformation of the other elements we are modifying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
]
},
{
"cell_type": "markdown",
"id": "a30ee131-40a4-44a2-b736-763532cf570e",
"metadata": {},
"source": [
"WARNING: unfortunately the modular saving of transformation and elements have been refactored out of the latest release and is still not finalized. This function will be re-enabled with high priority, please see the issue tracker here: https://github.com/scverse/spatialdata/issues/496."
]
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 10,
"id": "474410bd-2d02-45c1-b073-eba1152ab615",
"metadata": {
"tags": []
},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/visium_landmarks as it is not found in Zarr storage \n",
"\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/xenium_landmarks as it is not found in Zarr storage \n"
]
}
],
"source": [
"from spatialdata import save_transformations\n",
"\n",
Expand All@@ -541,7 +553,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.10.12"
"version": "3.10.13"
},
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Expand Down
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Improved documentation by LucaMarconato · Pull Request #79 · scverse/spatialdata-tutorials · GitHub
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Improved documentation#79

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to your account

 Merged

LucaMarconato
merged 27 commits into

from

Mar 24, 2024
 Merged


Improved documentation
#79
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27 commits


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b27eda0

improved squidpy notebook


LucaMarconato Mar 18, 2024
ff9cb8e

fix import


LucaMarconato Mar 18, 2024
b2236aa

fixed densenet and query notebooks

Mar 21, 2024
431b0cf

fixed aggregation notebook

Mar 21, 2024
fc54769

fixed alignment using landmarks

Mar 21, 2024
1883979

Merge branch 'main' into fix/notebooks

Mar 21, 2024
5611fb9

fixed alignment notebook

Mar 21, 2024
fdbae15

wip visium xenium

Mar 21, 2024
19f53d5

Merge branch 'fix/notebooks' into improve/docs


LucaMarconato Mar 21, 2024
144a13d

tiny fixes squidpy notebook


LucaMarconato Mar 21, 2024
ebbef74

fixed 00_xenium_and_visium


LucaMarconato Mar 21, 2024
189bf58

cleanup cosmx notebook before warnings are fixed

Mar 21, 2024
ce9f42a

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
9edc0e3

fixes notebooks speed_up_illustration and cosmx

Mar 21, 2024
fe7af95

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…

Mar 21, 2024
6760350

fixed notebook speed_up_illustration

Mar 21, 2024
ce87b30

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
63c452a

reduced size plot speed_up_illustration notebook

Mar 21, 2024
4784b27

reduced size plot speed_up_illustration notebook

Mar 21, 2024
f8aefc1

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
c6dd4db

reproducibility check xenium_visium notebooks


LucaMarconato Mar 23, 2024
c0dea5a

fixed notebook 00

Mar 24, 2024
8614be9

correct outlines


melonora Mar 24, 2024
9ea096f

example of assigning cells to rois and computing fractional overlap


LucaMarconato Mar 24, 2024
4b80dd5

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…


LucaMarconato Mar 24, 2024
77a6d73

removed fractional overlap approach


LucaMarconato Mar 24, 2024
6e98986

update limitation


melonora Mar 24, 2024

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349 changes: 222 additions & 127 deletions
notebooks/examples/aggregation.ipynb

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70 changes: 41 additions & 29 deletions
notebooks/examples/alignment_using_landmarks.ipynb

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -72,7 +72,7 @@
 "name": "stderr",
 "output_type": "stream",
 "text": [
 "/Users/macbook/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:183: ImplicitModificationWarning: Transforming to str index.\n",
 "/mnt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67: ImplicitModificationWarning: Transforming to str index.\n",
 " warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
 ]
 },
Expand All@@ -88,19 +88,14 @@
 "├── Shapes\n",
 "│ ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ ├── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
 "│ ├── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ └── 'xenium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 167780 × 313\n",
 " obs: 'cell_id', 'transcript_counts', 'control_probe_counts', 'control_codeword_counts', 'total_counts', 'cell_area', 'nucleus_area', 'region'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (167780, 313)\n",
 "│ └── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (167780, 313)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " morphology_mip (Images)\n",
 "▸ 'global', with elements:\n",
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes), xenium_landmarks (Shapes)"
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)"
 ]
 },
 "execution_count": 2,
Expand DownExpand Up@@ -133,27 +128,19 @@
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_full_image': MultiscaleSpatialImage[cyx] (3, 21571, 19505), (3, 10785, 9752), (3, 5392, 4876), (3, 2696, 2438), (3, 1348, 1219)\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_hires_image': SpatialImage[cyx] (3, 2000, 1809)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer_lowres_image': SpatialImage[cyx] (3, 600, 543)\n",
 "├── Points\n",
 "│ ├── 'Points': DataFrame with shape: (3, 2) (2D points)\n",
 "│ └── 'Points_1': DataFrame with shape: (1, 2) (2D points)\n",
 "├── Shapes\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "│ └── 'visium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 4992 × 18085\n",
 " obs: 'in_tissue', 'array_row', 'array_col', 'spot_id', 'region', 'dataset', 'clone'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatial', 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (4992, 18085)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (4992, 18085)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), Points (Points), Points_1 (Points), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_hires', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_lowres', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'global', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)"
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)"
 ]
 },
 "execution_count": 3,
Expand DownExpand Up@@ -184,7 +171,10 @@
 "end_time": "2023-04-10T18:59:26.909684Z",
 "start_time": "2023-04-10T18:59:25.642148Z"
 },
 "collapsed": false
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 }
 },
 "source": [
 "Interactive([visium_sdata, xenium_sdata], points=False, shapes=False)"
Expand DownExpand Up@@ -335,6 +325,9 @@
 "id": "e71718a2",
 "metadata": {
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 },
 "tags": []
 },
 "outputs": [
Expand DownExpand Up@@ -498,25 +491,44 @@
 "id": "be9277db",
 "metadata": {},
 "source": [
 "### Saving the alignment back to Zarr\n"
 "### Saving the landmarks and the alignment back to Zarr\n"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "2e98374c-85cd-45ad-ac62-b2bc075c9631",
 "metadata": {},
 "source": [
 "We will now save the transformations to disk. Notice that this is a lightweight operation because we are just mofiying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 "We will now save the landmark points and the transformations of the other elements to disk. \n",
 "\n",
 "Notice that these are both lightweight operations because the two sets of landmark points are small, and when saving the transformation of the other elements we are modifying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "a30ee131-40a4-44a2-b736-763532cf570e",
 "metadata": {},
 "source": [
 "WARNING: unfortunately the modular saving of transformation and elements have been refactored out of the latest release and is still not finalized. This function will be re-enabled with high priority, please see the issue tracker here: https://github.com/scverse/spatialdata/issues/496."
 ]
 },
 {
 "cell_type": "code",
 "execution_count": 8,
 "execution_count": 10,
 "id": "474410bd-2d02-45c1-b073-eba1152ab615",
 "metadata": {
 "tags": []
 },
 "outputs": [],
 "outputs": [
 {
 "name": "stdout",
 "output_type": "stream",
 "text": [
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/visium_landmarks as it is not found in Zarr storage \n",
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/xenium_landmarks as it is not found in Zarr storage \n"
 ]
 }
 ],
 "source": [
 "from spatialdata import save_transformations\n",
 "\n",
Expand All@@ -541,7 +553,7 @@
 "name": "python",
 "nbconvert_exporter": "python",
 "pygments_lexer": "ipython3",
 "version": "3.10.12"
 "version": "3.10.13"
 },
 "vscode": {
 "interpreter": {
Expand Down
Loading

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Improved documentation by LucaMarconato · Pull Request #79 · scverse/spatialdata-tutorials · GitHub
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Improved documentation#79

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LucaMarconato
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Mar 24, 2024
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Improved documentation
#79
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b27eda0

improved squidpy notebook


LucaMarconato Mar 18, 2024
ff9cb8e

fix import


LucaMarconato Mar 18, 2024
b2236aa

fixed densenet and query notebooks

Mar 21, 2024
431b0cf

fixed aggregation notebook

Mar 21, 2024
fc54769

fixed alignment using landmarks

Mar 21, 2024
1883979

Merge branch 'main' into fix/notebooks

Mar 21, 2024
5611fb9

fixed alignment notebook

Mar 21, 2024
fdbae15

wip visium xenium

Mar 21, 2024
19f53d5

Merge branch 'fix/notebooks' into improve/docs


LucaMarconato Mar 21, 2024
144a13d

tiny fixes squidpy notebook


LucaMarconato Mar 21, 2024
ebbef74

fixed 00_xenium_and_visium


LucaMarconato Mar 21, 2024
189bf58

cleanup cosmx notebook before warnings are fixed

Mar 21, 2024
ce9f42a

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
9edc0e3

fixes notebooks speed_up_illustration and cosmx

Mar 21, 2024
fe7af95

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…

Mar 21, 2024
6760350

fixed notebook speed_up_illustration

Mar 21, 2024
ce87b30

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
63c452a

reduced size plot speed_up_illustration notebook

Mar 21, 2024
4784b27

reduced size plot speed_up_illustration notebook

Mar 21, 2024
f8aefc1

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
c6dd4db

reproducibility check xenium_visium notebooks


LucaMarconato Mar 23, 2024
c0dea5a

fixed notebook 00

Mar 24, 2024
8614be9

correct outlines


melonora Mar 24, 2024
9ea096f

example of assigning cells to rois and computing fractional overlap


LucaMarconato Mar 24, 2024
4b80dd5

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…


LucaMarconato Mar 24, 2024
77a6d73

removed fractional overlap approach


LucaMarconato Mar 24, 2024
6e98986

update limitation


melonora Mar 24, 2024

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349 changes: 222 additions & 127 deletions
notebooks/examples/aggregation.ipynb

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70 changes: 41 additions & 29 deletions
notebooks/examples/alignment_using_landmarks.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -72,7 +72,7 @@
 "name": "stderr",
 "output_type": "stream",
 "text": [
 "/Users/macbook/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:183: ImplicitModificationWarning: Transforming to str index.\n",
 "/mnt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67: ImplicitModificationWarning: Transforming to str index.\n",
 " warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
 ]
 },
Expand All@@ -88,19 +88,14 @@
 "├── Shapes\n",
 "│ ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ ├── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
 "│ ├── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ └── 'xenium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 167780 × 313\n",
 " obs: 'cell_id', 'transcript_counts', 'control_probe_counts', 'control_codeword_counts', 'total_counts', 'cell_area', 'nucleus_area', 'region'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (167780, 313)\n",
 "│ └── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (167780, 313)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " morphology_mip (Images)\n",
 "▸ 'global', with elements:\n",
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes), xenium_landmarks (Shapes)"
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)"
 ]
 },
 "execution_count": 2,
Expand DownExpand Up@@ -133,27 +128,19 @@
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_full_image': MultiscaleSpatialImage[cyx] (3, 21571, 19505), (3, 10785, 9752), (3, 5392, 4876), (3, 2696, 2438), (3, 1348, 1219)\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_hires_image': SpatialImage[cyx] (3, 2000, 1809)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer_lowres_image': SpatialImage[cyx] (3, 600, 543)\n",
 "├── Points\n",
 "│ ├── 'Points': DataFrame with shape: (3, 2) (2D points)\n",
 "│ └── 'Points_1': DataFrame with shape: (1, 2) (2D points)\n",
 "├── Shapes\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "│ └── 'visium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 4992 × 18085\n",
 " obs: 'in_tissue', 'array_row', 'array_col', 'spot_id', 'region', 'dataset', 'clone'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatial', 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (4992, 18085)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (4992, 18085)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), Points (Points), Points_1 (Points), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_hires', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_lowres', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'global', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)"
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)"
 ]
 },
 "execution_count": 3,
Expand DownExpand Up@@ -184,7 +171,10 @@
 "end_time": "2023-04-10T18:59:26.909684Z",
 "start_time": "2023-04-10T18:59:25.642148Z"
 },
 "collapsed": false
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 }
 },
 "source": [
 "Interactive([visium_sdata, xenium_sdata], points=False, shapes=False)"
Expand DownExpand Up@@ -335,6 +325,9 @@
 "id": "e71718a2",
 "metadata": {
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 },
 "tags": []
 },
 "outputs": [
Expand DownExpand Up@@ -498,25 +491,44 @@
 "id": "be9277db",
 "metadata": {},
 "source": [
 "### Saving the alignment back to Zarr\n"
 "### Saving the landmarks and the alignment back to Zarr\n"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "2e98374c-85cd-45ad-ac62-b2bc075c9631",
 "metadata": {},
 "source": [
 "We will now save the transformations to disk. Notice that this is a lightweight operation because we are just mofiying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 "We will now save the landmark points and the transformations of the other elements to disk. \n",
 "\n",
 "Notice that these are both lightweight operations because the two sets of landmark points are small, and when saving the transformation of the other elements we are modifying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "a30ee131-40a4-44a2-b736-763532cf570e",
 "metadata": {},
 "source": [
 "WARNING: unfortunately the modular saving of transformation and elements have been refactored out of the latest release and is still not finalized. This function will be re-enabled with high priority, please see the issue tracker here: https://github.com/scverse/spatialdata/issues/496."
 ]
 },
 {
 "cell_type": "code",
 "execution_count": 8,
 "execution_count": 10,
 "id": "474410bd-2d02-45c1-b073-eba1152ab615",
 "metadata": {
 "tags": []
 },
 "outputs": [],
 "outputs": [
 {
 "name": "stdout",
 "output_type": "stream",
 "text": [
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/visium_landmarks as it is not found in Zarr storage \n",
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/xenium_landmarks as it is not found in Zarr storage \n"
 ]
 }
 ],
 "source": [
 "from spatialdata import save_transformations\n",
 "\n",
Expand All@@ -541,7 +553,7 @@
 "name": "python",
 "nbconvert_exporter": "python",
 "pygments_lexer": "ipython3",
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Expand Down
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Improved documentation by LucaMarconato · Pull Request #79 · scverse/spatialdata-tutorials · GitHub
Skip to content
Improved documentation#79

New issue

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 Merged

LucaMarconato
merged 27 commits into

from

Mar 24, 2024
 Merged


Improved documentation
#79
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b27eda0

improved squidpy notebook


LucaMarconato Mar 18, 2024
ff9cb8e

fix import


LucaMarconato Mar 18, 2024
b2236aa

fixed densenet and query notebooks

Mar 21, 2024
431b0cf

fixed aggregation notebook

Mar 21, 2024
fc54769

fixed alignment using landmarks

Mar 21, 2024
1883979

Merge branch 'main' into fix/notebooks

Mar 21, 2024
5611fb9

fixed alignment notebook

Mar 21, 2024
fdbae15

wip visium xenium

Mar 21, 2024
19f53d5

Merge branch 'fix/notebooks' into improve/docs


LucaMarconato Mar 21, 2024
144a13d

tiny fixes squidpy notebook


LucaMarconato Mar 21, 2024
ebbef74

fixed 00_xenium_and_visium


LucaMarconato Mar 21, 2024
189bf58

cleanup cosmx notebook before warnings are fixed

Mar 21, 2024
ce9f42a

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
9edc0e3

fixes notebooks speed_up_illustration and cosmx

Mar 21, 2024
fe7af95

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…

Mar 21, 2024
6760350

fixed notebook speed_up_illustration

Mar 21, 2024
ce87b30

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
63c452a

reduced size plot speed_up_illustration notebook

Mar 21, 2024
4784b27

reduced size plot speed_up_illustration notebook

Mar 21, 2024
f8aefc1

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
c6dd4db

reproducibility check xenium_visium notebooks


LucaMarconato Mar 23, 2024
c0dea5a

fixed notebook 00

Mar 24, 2024
8614be9

correct outlines


melonora Mar 24, 2024
9ea096f

example of assigning cells to rois and computing fractional overlap


LucaMarconato Mar 24, 2024
4b80dd5

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…


LucaMarconato Mar 24, 2024
77a6d73

removed fractional overlap approach


LucaMarconato Mar 24, 2024
6e98986

update limitation


melonora Mar 24, 2024

File filter

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349 changes: 222 additions & 127 deletions
notebooks/examples/aggregation.ipynb

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70 changes: 41 additions & 29 deletions
notebooks/examples/alignment_using_landmarks.ipynb

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -72,7 +72,7 @@
 "name": "stderr",
 "output_type": "stream",
 "text": [
 "/Users/macbook/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:183: ImplicitModificationWarning: Transforming to str index.\n",
 "/mnt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67: ImplicitModificationWarning: Transforming to str index.\n",
 " warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
 ]
 },
Expand All@@ -88,19 +88,14 @@
 "├── Shapes\n",
 "│ ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ ├── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
 "│ ├── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ └── 'xenium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 167780 × 313\n",
 " obs: 'cell_id', 'transcript_counts', 'control_probe_counts', 'control_codeword_counts', 'total_counts', 'cell_area', 'nucleus_area', 'region'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (167780, 313)\n",
 "│ └── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (167780, 313)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " morphology_mip (Images)\n",
 "▸ 'global', with elements:\n",
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes), xenium_landmarks (Shapes)"
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)"
 ]
 },
 "execution_count": 2,
Expand DownExpand Up@@ -133,27 +128,19 @@
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_full_image': MultiscaleSpatialImage[cyx] (3, 21571, 19505), (3, 10785, 9752), (3, 5392, 4876), (3, 2696, 2438), (3, 1348, 1219)\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_hires_image': SpatialImage[cyx] (3, 2000, 1809)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer_lowres_image': SpatialImage[cyx] (3, 600, 543)\n",
 "├── Points\n",
 "│ ├── 'Points': DataFrame with shape: (3, 2) (2D points)\n",
 "│ └── 'Points_1': DataFrame with shape: (1, 2) (2D points)\n",
 "├── Shapes\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "│ └── 'visium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 4992 × 18085\n",
 " obs: 'in_tissue', 'array_row', 'array_col', 'spot_id', 'region', 'dataset', 'clone'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatial', 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (4992, 18085)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (4992, 18085)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), Points (Points), Points_1 (Points), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_hires', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_lowres', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'global', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)"
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)"
 ]
 },
 "execution_count": 3,
Expand DownExpand Up@@ -184,7 +171,10 @@
 "end_time": "2023-04-10T18:59:26.909684Z",
 "start_time": "2023-04-10T18:59:25.642148Z"
 },
 "collapsed": false
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 }
 },
 "source": [
 "Interactive([visium_sdata, xenium_sdata], points=False, shapes=False)"
Expand DownExpand Up@@ -335,6 +325,9 @@
 "id": "e71718a2",
 "metadata": {
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 },
 "tags": []
 },
 "outputs": [
Expand DownExpand Up@@ -498,25 +491,44 @@
 "id": "be9277db",
 "metadata": {},
 "source": [
 "### Saving the alignment back to Zarr\n"
 "### Saving the landmarks and the alignment back to Zarr\n"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "2e98374c-85cd-45ad-ac62-b2bc075c9631",
 "metadata": {},
 "source": [
 "We will now save the transformations to disk. Notice that this is a lightweight operation because we are just mofiying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 "We will now save the landmark points and the transformations of the other elements to disk. \n",
 "\n",
 "Notice that these are both lightweight operations because the two sets of landmark points are small, and when saving the transformation of the other elements we are modifying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "a30ee131-40a4-44a2-b736-763532cf570e",
 "metadata": {},
 "source": [
 "WARNING: unfortunately the modular saving of transformation and elements have been refactored out of the latest release and is still not finalized. This function will be re-enabled with high priority, please see the issue tracker here: https://github.com/scverse/spatialdata/issues/496."
 ]
 },
 {
 "cell_type": "code",
 "execution_count": 8,
 "execution_count": 10,
 "id": "474410bd-2d02-45c1-b073-eba1152ab615",
 "metadata": {
 "tags": []
 },
 "outputs": [],
 "outputs": [
 {
 "name": "stdout",
 "output_type": "stream",
 "text": [
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/visium_landmarks as it is not found in Zarr storage \n",
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/xenium_landmarks as it is not found in Zarr storage \n"
 ]
 }
 ],
 "source": [
 "from spatialdata import save_transformations\n",
 "\n",
Expand All@@ -541,7 +553,7 @@
 "name": "python",
 "nbconvert_exporter": "python",
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Improved documentation by LucaMarconato · Pull Request #79 · scverse/spatialdata-tutorials · GitHub
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LucaMarconato
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Improved documentation
#79
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b27eda0

improved squidpy notebook


LucaMarconato Mar 18, 2024
ff9cb8e

fix import


LucaMarconato Mar 18, 2024
b2236aa

fixed densenet and query notebooks

Mar 21, 2024
431b0cf

fixed aggregation notebook

Mar 21, 2024
fc54769

fixed alignment using landmarks

Mar 21, 2024
1883979

Merge branch 'main' into fix/notebooks

Mar 21, 2024
5611fb9

fixed alignment notebook

Mar 21, 2024
fdbae15

wip visium xenium

Mar 21, 2024
19f53d5

Merge branch 'fix/notebooks' into improve/docs


LucaMarconato Mar 21, 2024
144a13d

tiny fixes squidpy notebook


LucaMarconato Mar 21, 2024
ebbef74

fixed 00_xenium_and_visium


LucaMarconato Mar 21, 2024
189bf58

cleanup cosmx notebook before warnings are fixed

Mar 21, 2024
ce9f42a

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
9edc0e3

fixes notebooks speed_up_illustration and cosmx

Mar 21, 2024
fe7af95

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…

Mar 21, 2024
6760350

fixed notebook speed_up_illustration

Mar 21, 2024
ce87b30

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
63c452a

reduced size plot speed_up_illustration notebook

Mar 21, 2024
4784b27

reduced size plot speed_up_illustration notebook

Mar 21, 2024
f8aefc1

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
c6dd4db

reproducibility check xenium_visium notebooks


LucaMarconato Mar 23, 2024
c0dea5a

fixed notebook 00

Mar 24, 2024
8614be9

correct outlines


melonora Mar 24, 2024
9ea096f

example of assigning cells to rois and computing fractional overlap


LucaMarconato Mar 24, 2024
4b80dd5

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…


LucaMarconato Mar 24, 2024
77a6d73

removed fractional overlap approach


LucaMarconato Mar 24, 2024
6e98986

update limitation


melonora Mar 24, 2024

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349 changes: 222 additions & 127 deletions
notebooks/examples/aggregation.ipynb

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70 changes: 41 additions & 29 deletions
notebooks/examples/alignment_using_landmarks.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -72,7 +72,7 @@
 "name": "stderr",
 "output_type": "stream",
 "text": [
 "/Users/macbook/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:183: ImplicitModificationWarning: Transforming to str index.\n",
 "/mnt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67: ImplicitModificationWarning: Transforming to str index.\n",
 " warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
 ]
 },
Expand All@@ -88,19 +88,14 @@
 "├── Shapes\n",
 "│ ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ ├── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
 "│ ├── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ └── 'xenium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 167780 × 313\n",
 " obs: 'cell_id', 'transcript_counts', 'control_probe_counts', 'control_codeword_counts', 'total_counts', 'cell_area', 'nucleus_area', 'region'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (167780, 313)\n",
 "│ └── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (167780, 313)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " morphology_mip (Images)\n",
 "▸ 'global', with elements:\n",
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes), xenium_landmarks (Shapes)"
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)"
 ]
 },
 "execution_count": 2,
Expand DownExpand Up@@ -133,27 +128,19 @@
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_full_image': MultiscaleSpatialImage[cyx] (3, 21571, 19505), (3, 10785, 9752), (3, 5392, 4876), (3, 2696, 2438), (3, 1348, 1219)\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_hires_image': SpatialImage[cyx] (3, 2000, 1809)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer_lowres_image': SpatialImage[cyx] (3, 600, 543)\n",
 "├── Points\n",
 "│ ├── 'Points': DataFrame with shape: (3, 2) (2D points)\n",
 "│ └── 'Points_1': DataFrame with shape: (1, 2) (2D points)\n",
 "├── Shapes\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "│ └── 'visium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 4992 × 18085\n",
 " obs: 'in_tissue', 'array_row', 'array_col', 'spot_id', 'region', 'dataset', 'clone'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatial', 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (4992, 18085)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (4992, 18085)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), Points (Points), Points_1 (Points), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_hires', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_lowres', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'global', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)"
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)"
 ]
 },
 "execution_count": 3,
Expand DownExpand Up@@ -184,7 +171,10 @@
 "end_time": "2023-04-10T18:59:26.909684Z",
 "start_time": "2023-04-10T18:59:25.642148Z"
 },
 "collapsed": false
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 }
 },
 "source": [
 "Interactive([visium_sdata, xenium_sdata], points=False, shapes=False)"
Expand DownExpand Up@@ -335,6 +325,9 @@
 "id": "e71718a2",
 "metadata": {
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 },
 "tags": []
 },
 "outputs": [
Expand DownExpand Up@@ -498,25 +491,44 @@
 "id": "be9277db",
 "metadata": {},
 "source": [
 "### Saving the alignment back to Zarr\n"
 "### Saving the landmarks and the alignment back to Zarr\n"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "2e98374c-85cd-45ad-ac62-b2bc075c9631",
 "metadata": {},
 "source": [
 "We will now save the transformations to disk. Notice that this is a lightweight operation because we are just mofiying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 "We will now save the landmark points and the transformations of the other elements to disk. \n",
 "\n",
 "Notice that these are both lightweight operations because the two sets of landmark points are small, and when saving the transformation of the other elements we are modifying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "a30ee131-40a4-44a2-b736-763532cf570e",
 "metadata": {},
 "source": [
 "WARNING: unfortunately the modular saving of transformation and elements have been refactored out of the latest release and is still not finalized. This function will be re-enabled with high priority, please see the issue tracker here: https://github.com/scverse/spatialdata/issues/496."
 ]
 },
 {
 "cell_type": "code",
 "execution_count": 8,
 "execution_count": 10,
 "id": "474410bd-2d02-45c1-b073-eba1152ab615",
 "metadata": {
 "tags": []
 },
 "outputs": [],
 "outputs": [
 {
 "name": "stdout",
 "output_type": "stream",
 "text": [
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/visium_landmarks as it is not found in Zarr storage \n",
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/xenium_landmarks as it is not found in Zarr storage \n"
 ]
 }
 ],
 "source": [
 "from spatialdata import save_transformations\n",
 "\n",
Expand All@@ -541,7 +553,7 @@
 "name": "python",
 "nbconvert_exporter": "python",
 "pygments_lexer": "ipython3",
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 },
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Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
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Improved documentation by LucaMarconato · Pull Request #79 · scverse/spatialdata-tutorials · GitHub
Skip to content
Improved documentation#79

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 Merged

LucaMarconato
merged 27 commits into

from

Mar 24, 2024
 Merged


Improved documentation
#79
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b27eda0

improved squidpy notebook


LucaMarconato Mar 18, 2024
ff9cb8e

fix import


LucaMarconato Mar 18, 2024
b2236aa

fixed densenet and query notebooks

Mar 21, 2024
431b0cf

fixed aggregation notebook

Mar 21, 2024
fc54769

fixed alignment using landmarks

Mar 21, 2024
1883979

Merge branch 'main' into fix/notebooks

Mar 21, 2024
5611fb9

fixed alignment notebook

Mar 21, 2024
fdbae15

wip visium xenium

Mar 21, 2024
19f53d5

Merge branch 'fix/notebooks' into improve/docs


LucaMarconato Mar 21, 2024
144a13d

tiny fixes squidpy notebook


LucaMarconato Mar 21, 2024
ebbef74

fixed 00_xenium_and_visium


LucaMarconato Mar 21, 2024
189bf58

cleanup cosmx notebook before warnings are fixed

Mar 21, 2024
ce9f42a

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
9edc0e3

fixes notebooks speed_up_illustration and cosmx

Mar 21, 2024
fe7af95

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…

Mar 21, 2024
6760350

fixed notebook speed_up_illustration

Mar 21, 2024
ce87b30

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
63c452a

reduced size plot speed_up_illustration notebook

Mar 21, 2024
4784b27

reduced size plot speed_up_illustration notebook

Mar 21, 2024
f8aefc1

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
c6dd4db

reproducibility check xenium_visium notebooks


LucaMarconato Mar 23, 2024
c0dea5a

fixed notebook 00

Mar 24, 2024
8614be9

correct outlines


melonora Mar 24, 2024
9ea096f

example of assigning cells to rois and computing fractional overlap


LucaMarconato Mar 24, 2024
4b80dd5

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…


LucaMarconato Mar 24, 2024
77a6d73

removed fractional overlap approach


LucaMarconato Mar 24, 2024
6e98986

update limitation


melonora Mar 24, 2024

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349 changes: 222 additions & 127 deletions
notebooks/examples/aggregation.ipynb

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70 changes: 41 additions & 29 deletions
notebooks/examples/alignment_using_landmarks.ipynb

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -72,7 +72,7 @@
 "name": "stderr",
 "output_type": "stream",
 "text": [
 "/Users/macbook/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:183: ImplicitModificationWarning: Transforming to str index.\n",
 "/mnt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67: ImplicitModificationWarning: Transforming to str index.\n",
 " warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
 ]
 },
Expand All@@ -88,19 +88,14 @@
 "├── Shapes\n",
 "│ ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ ├── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
 "│ ├── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ └── 'xenium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 167780 × 313\n",
 " obs: 'cell_id', 'transcript_counts', 'control_probe_counts', 'control_codeword_counts', 'total_counts', 'cell_area', 'nucleus_area', 'region'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (167780, 313)\n",
 "│ └── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (167780, 313)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " morphology_mip (Images)\n",
 "▸ 'global', with elements:\n",
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes), xenium_landmarks (Shapes)"
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)"
 ]
 },
 "execution_count": 2,
Expand DownExpand Up@@ -133,27 +128,19 @@
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_full_image': MultiscaleSpatialImage[cyx] (3, 21571, 19505), (3, 10785, 9752), (3, 5392, 4876), (3, 2696, 2438), (3, 1348, 1219)\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_hires_image': SpatialImage[cyx] (3, 2000, 1809)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer_lowres_image': SpatialImage[cyx] (3, 600, 543)\n",
 "├── Points\n",
 "│ ├── 'Points': DataFrame with shape: (3, 2) (2D points)\n",
 "│ └── 'Points_1': DataFrame with shape: (1, 2) (2D points)\n",
 "├── Shapes\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "│ └── 'visium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 4992 × 18085\n",
 " obs: 'in_tissue', 'array_row', 'array_col', 'spot_id', 'region', 'dataset', 'clone'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatial', 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (4992, 18085)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (4992, 18085)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), Points (Points), Points_1 (Points), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_hires', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_lowres', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'global', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)"
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)"
 ]
 },
 "execution_count": 3,
Expand DownExpand Up@@ -184,7 +171,10 @@
 "end_time": "2023-04-10T18:59:26.909684Z",
 "start_time": "2023-04-10T18:59:25.642148Z"
 },
 "collapsed": false
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 }
 },
 "source": [
 "Interactive([visium_sdata, xenium_sdata], points=False, shapes=False)"
Expand DownExpand Up@@ -335,6 +325,9 @@
 "id": "e71718a2",
 "metadata": {
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 },
 "tags": []
 },
 "outputs": [
Expand DownExpand Up@@ -498,25 +491,44 @@
 "id": "be9277db",
 "metadata": {},
 "source": [
 "### Saving the alignment back to Zarr\n"
 "### Saving the landmarks and the alignment back to Zarr\n"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "2e98374c-85cd-45ad-ac62-b2bc075c9631",
 "metadata": {},
 "source": [
 "We will now save the transformations to disk. Notice that this is a lightweight operation because we are just mofiying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 "We will now save the landmark points and the transformations of the other elements to disk. \n",
 "\n",
 "Notice that these are both lightweight operations because the two sets of landmark points are small, and when saving the transformation of the other elements we are modifying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "a30ee131-40a4-44a2-b736-763532cf570e",
 "metadata": {},
 "source": [
 "WARNING: unfortunately the modular saving of transformation and elements have been refactored out of the latest release and is still not finalized. This function will be re-enabled with high priority, please see the issue tracker here: https://github.com/scverse/spatialdata/issues/496."
 ]
 },
 {
 "cell_type": "code",
 "execution_count": 8,
 "execution_count": 10,
 "id": "474410bd-2d02-45c1-b073-eba1152ab615",
 "metadata": {
 "tags": []
 },
 "outputs": [],
 "outputs": [
 {
 "name": "stdout",
 "output_type": "stream",
 "text": [
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/visium_landmarks as it is not found in Zarr storage \n",
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/xenium_landmarks as it is not found in Zarr storage \n"
 ]
 }
 ],
 "source": [
 "from spatialdata import save_transformations\n",
 "\n",
Expand All@@ -541,7 +553,7 @@
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Improved documentation by LucaMarconato · Pull Request #79 · scverse/spatialdata-tutorials · GitHub
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Improved documentation#79

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Improved documentation
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b27eda0

improved squidpy notebook


LucaMarconato Mar 18, 2024
ff9cb8e

fix import


LucaMarconato Mar 18, 2024
b2236aa

fixed densenet and query notebooks

Mar 21, 2024
431b0cf

fixed aggregation notebook

Mar 21, 2024
fc54769

fixed alignment using landmarks

Mar 21, 2024
1883979

Merge branch 'main' into fix/notebooks

Mar 21, 2024
5611fb9

fixed alignment notebook

Mar 21, 2024
fdbae15

wip visium xenium

Mar 21, 2024
19f53d5

Merge branch 'fix/notebooks' into improve/docs


LucaMarconato Mar 21, 2024
144a13d

tiny fixes squidpy notebook


LucaMarconato Mar 21, 2024
ebbef74

fixed 00_xenium_and_visium


LucaMarconato Mar 21, 2024
189bf58

cleanup cosmx notebook before warnings are fixed

Mar 21, 2024
ce9f42a

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
9edc0e3

fixes notebooks speed_up_illustration and cosmx

Mar 21, 2024
fe7af95

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…

Mar 21, 2024
6760350

fixed notebook speed_up_illustration

Mar 21, 2024
ce87b30

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
63c452a

reduced size plot speed_up_illustration notebook

Mar 21, 2024
4784b27

reduced size plot speed_up_illustration notebook

Mar 21, 2024
f8aefc1

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
c6dd4db

reproducibility check xenium_visium notebooks


LucaMarconato Mar 23, 2024
c0dea5a

fixed notebook 00

Mar 24, 2024
8614be9

correct outlines


melonora Mar 24, 2024
9ea096f

example of assigning cells to rois and computing fractional overlap


LucaMarconato Mar 24, 2024
4b80dd5

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…


LucaMarconato Mar 24, 2024
77a6d73

removed fractional overlap approach


LucaMarconato Mar 24, 2024
6e98986

update limitation


melonora Mar 24, 2024

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349 changes: 222 additions & 127 deletions
notebooks/examples/aggregation.ipynb

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70 changes: 41 additions & 29 deletions
notebooks/examples/alignment_using_landmarks.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -72,7 +72,7 @@
 "name": "stderr",
 "output_type": "stream",
 "text": [
 "/Users/macbook/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:183: ImplicitModificationWarning: Transforming to str index.\n",
 "/mnt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67: ImplicitModificationWarning: Transforming to str index.\n",
 " warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
 ]
 },
Expand All@@ -88,19 +88,14 @@
 "├── Shapes\n",
 "│ ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ ├── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
 "│ ├── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ └── 'xenium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 167780 × 313\n",
 " obs: 'cell_id', 'transcript_counts', 'control_probe_counts', 'control_codeword_counts', 'total_counts', 'cell_area', 'nucleus_area', 'region'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (167780, 313)\n",
 "│ └── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (167780, 313)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " morphology_mip (Images)\n",
 "▸ 'global', with elements:\n",
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes), xenium_landmarks (Shapes)"
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)"
 ]
 },
 "execution_count": 2,
Expand DownExpand Up@@ -133,27 +128,19 @@
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_full_image': MultiscaleSpatialImage[cyx] (3, 21571, 19505), (3, 10785, 9752), (3, 5392, 4876), (3, 2696, 2438), (3, 1348, 1219)\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_hires_image': SpatialImage[cyx] (3, 2000, 1809)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer_lowres_image': SpatialImage[cyx] (3, 600, 543)\n",
 "├── Points\n",
 "│ ├── 'Points': DataFrame with shape: (3, 2) (2D points)\n",
 "│ └── 'Points_1': DataFrame with shape: (1, 2) (2D points)\n",
 "├── Shapes\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "│ └── 'visium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 4992 × 18085\n",
 " obs: 'in_tissue', 'array_row', 'array_col', 'spot_id', 'region', 'dataset', 'clone'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatial', 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (4992, 18085)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (4992, 18085)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), Points (Points), Points_1 (Points), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_hires', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_lowres', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'global', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)"
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)"
 ]
 },
 "execution_count": 3,
Expand DownExpand Up@@ -184,7 +171,10 @@
 "end_time": "2023-04-10T18:59:26.909684Z",
 "start_time": "2023-04-10T18:59:25.642148Z"
 },
 "collapsed": false
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 }
 },
 "source": [
 "Interactive([visium_sdata, xenium_sdata], points=False, shapes=False)"
Expand DownExpand Up@@ -335,6 +325,9 @@
 "id": "e71718a2",
 "metadata": {
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 },
 "tags": []
 },
 "outputs": [
Expand DownExpand Up@@ -498,25 +491,44 @@
 "id": "be9277db",
 "metadata": {},
 "source": [
 "### Saving the alignment back to Zarr\n"
 "### Saving the landmarks and the alignment back to Zarr\n"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "2e98374c-85cd-45ad-ac62-b2bc075c9631",
 "metadata": {},
 "source": [
 "We will now save the transformations to disk. Notice that this is a lightweight operation because we are just mofiying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 "We will now save the landmark points and the transformations of the other elements to disk. \n",
 "\n",
 "Notice that these are both lightweight operations because the two sets of landmark points are small, and when saving the transformation of the other elements we are modifying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "a30ee131-40a4-44a2-b736-763532cf570e",
 "metadata": {},
 "source": [
 "WARNING: unfortunately the modular saving of transformation and elements have been refactored out of the latest release and is still not finalized. This function will be re-enabled with high priority, please see the issue tracker here: https://github.com/scverse/spatialdata/issues/496."
 ]
 },
 {
 "cell_type": "code",
 "execution_count": 8,
 "execution_count": 10,
 "id": "474410bd-2d02-45c1-b073-eba1152ab615",
 "metadata": {
 "tags": []
 },
 "outputs": [],
 "outputs": [
 {
 "name": "stdout",
 "output_type": "stream",
 "text": [
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/visium_landmarks as it is not found in Zarr storage \n",
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/xenium_landmarks as it is not found in Zarr storage \n"
 ]
 }
 ],
 "source": [
 "from spatialdata import save_transformations\n",
 "\n",
Expand All@@ -541,7 +553,7 @@
 "name": "python",
 "nbconvert_exporter": "python",
 "pygments_lexer": "ipython3",
 "version": "3.10.12"
 "version": "3.10.13"
 },
 "vscode": {
 "interpreter": {
Expand Down
Loading

, 'i');
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Improved documentation by LucaMarconato · Pull Request #79 · scverse/spatialdata-tutorials · GitHub
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Improved documentation#79

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 Merged

LucaMarconato
merged 27 commits into

from

Mar 24, 2024
 Merged


Improved documentation
#79
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b27eda0

improved squidpy notebook


LucaMarconato Mar 18, 2024
ff9cb8e

fix import


LucaMarconato Mar 18, 2024
b2236aa

fixed densenet and query notebooks

Mar 21, 2024
431b0cf

fixed aggregation notebook

Mar 21, 2024
fc54769

fixed alignment using landmarks

Mar 21, 2024
1883979

Merge branch 'main' into fix/notebooks

Mar 21, 2024
5611fb9

fixed alignment notebook

Mar 21, 2024
fdbae15

wip visium xenium

Mar 21, 2024
19f53d5

Merge branch 'fix/notebooks' into improve/docs


LucaMarconato Mar 21, 2024
144a13d

tiny fixes squidpy notebook


LucaMarconato Mar 21, 2024
ebbef74

fixed 00_xenium_and_visium


LucaMarconato Mar 21, 2024
189bf58

cleanup cosmx notebook before warnings are fixed

Mar 21, 2024
ce9f42a

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
9edc0e3

fixes notebooks speed_up_illustration and cosmx

Mar 21, 2024
fe7af95

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…

Mar 21, 2024
6760350

fixed notebook speed_up_illustration

Mar 21, 2024
ce87b30

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
63c452a

reduced size plot speed_up_illustration notebook

Mar 21, 2024
4784b27

reduced size plot speed_up_illustration notebook

Mar 21, 2024
f8aefc1

[pre-commit.ci] auto fixes from pre-commit.com hooks


pre-commit-ci[bot] Mar 21, 2024
c6dd4db

reproducibility check xenium_visium notebooks


LucaMarconato Mar 23, 2024
c0dea5a

fixed notebook 00

Mar 24, 2024
8614be9

correct outlines


melonora Mar 24, 2024
9ea096f

example of assigning cells to rois and computing fractional overlap


LucaMarconato Mar 24, 2024
4b80dd5

Merge branch 'improve/docs' of https://github.com/scverse/spatialdata…


LucaMarconato Mar 24, 2024
77a6d73

removed fractional overlap approach


LucaMarconato Mar 24, 2024
6e98986

update limitation


melonora Mar 24, 2024

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349 changes: 222 additions & 127 deletions
notebooks/examples/aggregation.ipynb

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70 changes: 41 additions & 29 deletions
notebooks/examples/alignment_using_landmarks.ipynb

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Original file line numberDiff line numberDiff line change
Expand Up@@ -72,7 +72,7 @@
 "name": "stderr",
 "output_type": "stream",
 "text": [
 "/Users/macbook/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/anndata.py:183: ImplicitModificationWarning: Transforming to str index.\n",
 "/mnt/miniconda3/envs/ome/lib/python3.10/site-packages/anndata/_core/aligned_df.py:67: ImplicitModificationWarning: Transforming to str index.\n",
 " warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
 ]
 },
Expand All@@ -88,19 +88,14 @@
 "├── Shapes\n",
 "│ ├── 'cell_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ ├── 'cell_circles': GeoDataFrame shape: (167780, 2) (2D shapes)\n",
 "│ ├── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "│ └── 'xenium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 167780 × 313\n",
 " obs: 'cell_id', 'transcript_counts', 'control_probe_counts', 'control_codeword_counts', 'total_counts', 'cell_area', 'nucleus_area', 'region'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (167780, 313)\n",
 "│ └── 'nucleus_boundaries': GeoDataFrame shape: (167780, 1) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (167780, 313)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " morphology_mip (Images)\n",
 "▸ 'global', with elements:\n",
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes), xenium_landmarks (Shapes)"
 " morphology_focus (Images), morphology_mip (Images), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)"
 ]
 },
 "execution_count": 2,
Expand DownExpand Up@@ -133,27 +128,19 @@
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_full_image': MultiscaleSpatialImage[cyx] (3, 21571, 19505), (3, 10785, 9752), (3, 5392, 4876), (3, 2696, 2438), (3, 1348, 1219)\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer_hires_image': SpatialImage[cyx] (3, 2000, 1809)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer_lowres_image': SpatialImage[cyx] (3, 600, 543)\n",
 "├── Points\n",
 "│ ├── 'Points': DataFrame with shape: (3, 2) (2D points)\n",
 "│ └── 'Points_1': DataFrame with shape: (1, 2) (2D points)\n",
 "├── Shapes\n",
 "│ ├── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "│ └── 'visium_landmarks': GeoDataFrame shape: (3, 2) (2D shapes)\n",
 "└── Table\n",
 " └── AnnData object with n_obs × n_vars = 4992 × 18085\n",
 " obs: 'in_tissue', 'array_row', 'array_col', 'spot_id', 'region', 'dataset', 'clone'\n",
 " var: 'gene_ids', 'feature_types', 'genome'\n",
 " uns: 'spatial', 'spatialdata_attrs'\n",
 " obsm: 'spatial': AnnData (4992, 18085)\n",
 "│ └── 'CytAssist_FFPE_Human_Breast_Cancer': GeoDataFrame shape: (4992, 2) (2D shapes)\n",
 "└── Tables\n",
 " └── 'table': AnnData (4992, 18085)\n",
 "with coordinate systems:\n",
 "▸ 'aligned', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), Points (Points), Points_1 (Points), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_hires', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_hires_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'downscaled_lowres', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_lowres_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)\n",
 "▸ 'global', with elements:\n",
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes), visium_landmarks (Shapes)"
 " CytAssist_FFPE_Human_Breast_Cancer_full_image (Images), CytAssist_FFPE_Human_Breast_Cancer (Shapes)"
 ]
 },
 "execution_count": 3,
Expand DownExpand Up@@ -184,7 +171,10 @@
 "end_time": "2023-04-10T18:59:26.909684Z",
 "start_time": "2023-04-10T18:59:25.642148Z"
 },
 "collapsed": false
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 }
 },
 "source": [
 "Interactive([visium_sdata, xenium_sdata], points=False, shapes=False)"
Expand DownExpand Up@@ -335,6 +325,9 @@
 "id": "e71718a2",
 "metadata": {
 "collapsed": false,
 "jupyter": {
 "outputs_hidden": false
 },
 "tags": []
 },
 "outputs": [
Expand DownExpand Up@@ -498,25 +491,44 @@
 "id": "be9277db",
 "metadata": {},
 "source": [
 "### Saving the alignment back to Zarr\n"
 "### Saving the landmarks and the alignment back to Zarr\n"
 ]
 },
 {
 "cell_type": "markdown",
 "id": "2e98374c-85cd-45ad-ac62-b2bc075c9631",
 "metadata": {},
 "source": [
 "We will now save the transformations to disk. Notice that this is a lightweight operation because we are just mofiying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 "We will now save the landmark points and the transformations of the other elements to disk. \n",
 "\n",
 "Notice that these are both lightweight operations because the two sets of landmark points are small, and when saving the transformation of the other elements we are modifying the objects metadata, not transforming the actual data. This is useful when dealing with large images and when one may need to reiterate multiple steps of landmark-based alignment in order to improve the spatial agreement of the alignment."
 ]
 },
 {
 "cell_type": "markdown",
 "id": "a30ee131-40a4-44a2-b736-763532cf570e",
 "metadata": {},
 "source": [
 "WARNING: unfortunately the modular saving of transformation and elements have been refactored out of the latest release and is still not finalized. This function will be re-enabled with high priority, please see the issue tracker here: https://github.com/scverse/spatialdata/issues/496."
 ]
 },
 {
 "cell_type": "code",
 "execution_count": 8,
 "execution_count": 10,
 "id": "474410bd-2d02-45c1-b073-eba1152ab615",
 "metadata": {
 "tags": []
 },
 "outputs": [],
 "outputs": [
 {
 "name": "stdout",
 "output_type": "stream",
 "text": [
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/visium_landmarks as it is not found in Zarr storage \n",
 "\u001b[34mINFO \u001b[0m Not saving the transformation to element shapes/xenium_landmarks as it is not found in Zarr storage \n"
 ]
 }
 ],
 "source": [
 "from spatialdata import save_transformations\n",
 "\n",
Expand All@@ -541,7 +553,7 @@
 "name": "python",
 "nbconvert_exporter": "python",
 "pygments_lexer": "ipython3",
 "version": "3.10.12"
 "version": "3.10.13"
 },
 "vscode": {
 "interpreter": {
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