Skip to content

tutorials v2 #63

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
josenimo merged 3 commits into from
Jul 9, 2025
Merged

tutorials v2 #63

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
a218bf3
all tutorials v2, +rankplot
josenimo Jul 9, 2025
bd76453
refresh plottings
josenimo Jul 9, 2025
3f7b511
Update src/opendvp/plotting/rankplot.py
josenimo Jul 9, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
55 changes: 27 additions & 28 deletions docs/Tutorials/T1_ImageAnalysis.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
"id": "29cad22f",
"metadata": {},
"source": [
"# Image single-cell analysis"
"# T1: Image single-cell analysis"
]
},
{
Expand All @@ -28,7 +28,7 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": null,
"id": "8e40b139",
"metadata": {},
"outputs": [
Expand All @@ -42,7 +42,6 @@
}
],
"source": [
"#lets take a quick look\n",
"import skimage.io as io\n",
"import numpy as np\n",
"import opendvp as dvp\n",
Expand Down Expand Up @@ -70,7 +69,7 @@
"outputs": [],
"source": [
"url = \"https://zenodo.org/records/15830141/files/data.tar.gz?download=1\"\n",
"output_path = \"demodata.gz\" \n",
"output_path = \"../data/demodata.gz\" \n",
"\n",
"import requests\n",
"response = requests.get(url, stream=True)\n",
Expand Down Expand Up @@ -112,13 +111,13 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": null,
"id": "2383e316",
"metadata": {},
"outputs": [],
"source": [
"# let's perform some quick QC\n",
"path_to_segmentation = \"data/segmentation/segmentation_mask.tif\"\n",
"path_to_segmentation = \"../data/segmentation/segmentation_mask.tif\"\n",
"seg = io.imread(path_to_segmentation)"
]
},
Expand Down Expand Up @@ -367,7 +366,7 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": null,
"id": "b84aeade",
"metadata": {},
"outputs": [
Expand All @@ -382,7 +381,7 @@
],
"source": [
"# now lets write that geodataframe into a file\n",
"gdf.to_file(\"outputs/segmentation_for_qupath.geojson\")"
"gdf.to_file(\"../outputs/segmentation_for_qupath.geojson\")"
]
},
{
Expand Down Expand Up @@ -411,13 +410,13 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": null,
"id": "28c2f46e",
"metadata": {},
"outputs": [],
"source": [
"#load image\n",
"image = io.imread(\"data/image/mIF.ome.tif\")"
"image = io.imread(\"../data/image/mIF.ome.tif\")"
]
},
{
Expand Down Expand Up @@ -472,7 +471,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": null,
"id": "ed1f9c70",
"metadata": {},
"outputs": [
Expand All @@ -487,7 +486,7 @@
],
"source": [
"#transform the .csv matrix to an AnnData object\n",
"adata = dvp.io.quant_to_adata(\"data/quantification/quant.csv\")"
"adata = dvp.io.quant_to_adata(\"../data/quantification/quant.csv\")"
]
},
{
Expand Down Expand Up @@ -1014,13 +1013,13 @@
},
{
"cell_type": "code",
"execution_count": 21,
"execution_count": null,
"id": "6ad690cd",
"metadata": {},
"outputs": [],
"source": [
"#check annotations\n",
"gdf = gpd.read_file(\"data/manual_artefact_annotations/artefacts.geojson\")"
"gdf = gpd.read_file(\"../data/manual_artefact_annotations/artefacts.geojson\")"
]
},
{
Expand Down Expand Up @@ -1156,7 +1155,7 @@
},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": null,
"id": "07e5d802",
"metadata": {},
"outputs": [
Expand All @@ -1173,7 +1172,7 @@
"source": [
"adata = dvp.tl.filter_by_annotation(\n",
" adata=adata, \n",
" path_to_geojson=\"data/manual_artefact_annotations/artefacts.geojson\")"
" path_to_geojson=\"../data/manual_artefact_annotations/artefacts.geojson\")"
]
},
{
Expand Down Expand Up @@ -1414,7 +1413,7 @@
},
{
"cell_type": "code",
"execution_count": 28,
"execution_count": null,
"id": "482a0b18",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -1494,7 +1493,7 @@
}
],
"source": [
"gdf = gpd.read_file(\"outputs/segmentation_for_qupath.geojson\")\n",
"gdf = gpd.read_file(\"../outputs/segmentation_for_qupath.geojson\")\n",
"gdf.head()"
]
},
Expand Down Expand Up @@ -1527,13 +1526,13 @@
},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": null,
"id": "44441f39",
"metadata": {},
"outputs": [],
"source": [
"# let's save the file to drag it into qupath\n",
"cells.to_file(\"outputs/filtered_cells.geojson\")"
"cells.to_file(\"../outputs/filtered_cells.geojson\")"
]
},
{
Expand Down Expand Up @@ -1587,7 +1586,7 @@
},
{
"cell_type": "code",
"execution_count": 31,
"execution_count": null,
"id": "0da35a57",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -1693,7 +1692,7 @@
],
"source": [
"# this function loads and processes the values ready for the phenotyping\n",
"thresholds = dvp.io.import_thresholds(gates_csv_path=\"data/phenotyping/gates.csv\")\n",
"thresholds = dvp.io.import_thresholds(gates_csv_path=\"../data/phenotyping/gates.csv\")\n",
"thresholds"
]
},
Expand Down Expand Up @@ -1779,7 +1778,7 @@
},
{
"cell_type": "code",
"execution_count": 34,
"execution_count": null,
"id": "fd0f28f3",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -1925,7 +1924,7 @@
"# we must load the phenotyping workflow\n",
"# this is the set of biological knowledge we have about the markers\n",
"# and what they mean to classify the cells\n",
"phenotype = pd.read_csv('data/phenotyping/celltype_matrix.csv')\n",
"phenotype = pd.read_csv('../data/phenotyping/celltype_matrix.csv')\n",
"# this just shows you the table \n",
"phenotype.style.format(na_rep='')"
]
Expand Down Expand Up @@ -2255,12 +2254,12 @@
},
{
"cell_type": "code",
"execution_count": 42,
"execution_count": null,
"id": "a7598b49",
"metadata": {},
"outputs": [],
"source": [
"phenotypes.to_file(\"outputs/phenotypes.geojson\")"
"phenotypes.to_file(\"../outputs/phenotypes.geojson\")"
]
},
{
Expand Down Expand Up @@ -2453,7 +2452,7 @@
},
{
"cell_type": "code",
"execution_count": 136,
"execution_count": null,
"id": "a0164589",
"metadata": {},
"outputs": [
Expand All @@ -2468,7 +2467,7 @@
],
"source": [
"#save to file\n",
"voronoi.to_file(\"outputs/voronoi_neighborhoods.geojson\")"
"voronoi.to_file(\"../outputs/voronoi_neighborhoods.geojson\")"
]
}
],
Expand Down
Loading
Loading