"""GlassCut data module for downloading and loading sample histology slides."""
from pathlib import Path
from typing import Tuple
import openslide
from .fetcher import DataFetcher
# ===== Data Loading Functions =====
_fetcher = DataFetcher()
[docs]
def aorta_tissue() -> Tuple[openslide.OpenSlide, Path]:
"""Load aorta tissue sample.
Aorta tissue, brightfield, JPEG 2000, YCbCr format from OpenSlide test data.
Source: http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/
Returns
-------
Tuple[openslide.OpenSlide, Path]
H&E-stained WSI of aortic tissue and its file path
"""
return _fetcher.load_slide("aperio/JP2K-33003-1.svs")
[docs]
def breast_tissue() -> Tuple[openslide.OpenSlide, Path]:
"""Load breast tissue sample from TCGA-BRCA.
Source: TCGA-A8-A082-01A-01-TS1.3cad4a77-47a6-4658-becf-d8cffa161d3a.svs
Access: open
Returns
-------
Tuple[openslide.OpenSlide, Path]
H&E-stained WSI of breast tissue and its file path
"""
return _fetcher.load_slide(
"tcga/breast/TCGA-A8-A082-01A-01-TS1.3cad4a77-47a6-4658-becf-d8cffa161d3a.svs"
)
[docs]
def breast_tissue_diagnostic_green_pen() -> Tuple[openslide.OpenSlide, Path]:
"""Load breast tissue diagnostic slide with green pen marks.
Source: TCGA-A1-A0SH-01Z-00-DX1.90E71B08-E1D9-4FC2-85AC-062E56DDF17C.svs
Access: open
Returns
-------
Tuple[openslide.OpenSlide, Path]
H&E-stained WSI with green pen annotations and its file path
"""
return _fetcher.load_slide(
"tcga/breast/TCGA-A1-A0SH-01Z-00-DX1.90E71B08-E1D9-4FC2-85AC-062E56DDF17C.svs"
)
[docs]
def breast_tissue_diagnostic_red_pen() -> Tuple[openslide.OpenSlide, Path]:
"""Load breast tissue diagnostic slide with red pen marks.
Source: TCGA-E9-A24A-01Z-00-DX1.F0342837-5750-4172-B60D-5F902E2A02FD.svs
Access: open
Returns
-------
Tuple[openslide.OpenSlide, Path]
H&E-stained WSI with red pen annotations and its file path
"""
return _fetcher.load_slide(
"tcga/breast/TCGA-E9-A24A-01Z-00-DX1.F0342837-5750-4172-B60D-5F902E2A02FD.svs"
)
[docs]
def breast_tissue_diagnostic_black_pen() -> Tuple[openslide.OpenSlide, Path]:
"""Load breast tissue diagnostic slide with black pen marks.
Source: TCGA-BH-A201-01Z-00-DX1.6D6E3224-50A0-45A2-B231-EEF27CA7EFD2.svs
Access: open
Returns
-------
Tuple[openslide.OpenSlide, Path]
H&E-stained WSI with black pen annotations and its file path
"""
return _fetcher.load_slide(
"tcga/breast/TCGA-BH-A201-01Z-00-DX1.6D6E3224-50A0-45A2-B231-EEF27CA7EFD2.svs"
)
[docs]
def cmu_small_region() -> Tuple[openslide.OpenSlide, Path]:
"""Load Carnegie Mellon University MRXS sample tissue.
Small region from CMU test data.
Source: http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/
Licensed under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Returns
-------
Tuple[openslide.OpenSlide, Path]
H&E-stained WSI and its file path
"""
return _fetcher.load_slide("data/cmu_small_region.svs")
[docs]
def heart_tissue() -> Tuple[openslide.OpenSlide, Path]:
"""Load heart tissue sample.
Heart tissue, brightfield, JPEG 2000, YCbCr format from OpenSlide test data.
Source: http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/
Returns
-------
Tuple[openslide.OpenSlide, Path]
H&E-stained WSI of heart tissue and its file path
"""
return _fetcher.load_slide("aperio/JP2K-33003-2.svs")
[docs]
def ihc_breast() -> Tuple[openslide.OpenSlide, Path]:
"""Load breast cancer resection with IHC staining.
Staining: CD3 (brown) and CD20 (red)
Source: https://idr.openmicroscopy.org/ (accession idr0073, ID breastCancer12)
Returns
-------
Tuple[openslide.OpenSlide, Path]
IHC-stained WSI of breast tissue and its file path
"""
return _fetcher.load_slide("9798433/?format=tif")
[docs]
def ihc_kidney() -> Tuple[openslide.OpenSlide, Path]:
"""Load kidney tissue with IHC staining.
Renal allograft staining: CD3 (brown) and CD20 (red)
Source: https://idr.openmicroscopy.org/ (accession idr0073, ID kidney_46_4)
Returns
-------
Tuple[openslide.OpenSlide, Path]
IHC-stained WSI of kidney tissue and its file path
"""
return _fetcher.load_slide("9798554/?format=tif")
[docs]
def ovarian_tissue() -> Tuple[openslide.OpenSlide, Path]:
"""Load ovarian tissue from TCGA-OV (Serous Cystadenocarcinoma).
Source: TCGA-13-1404-01A-01-TS1.cecf7044-1d29-4d14-b137-821f8d48881e.svs
Access: open
Returns
-------
Tuple[openslide.OpenSlide, Path]
H&E-stained WSI of ovarian tissue and its file path
"""
return _fetcher.load_slide(
"tcga/ovarian/TCGA-13-1404-01A-01-TS1.cecf7044-1d29-4d14-b137-821f8d48881e.svs"
)
[docs]
def prostate_tissue() -> Tuple[openslide.OpenSlide, Path]:
"""Load prostate tissue from TCGA-PRAD (Adenocarcinoma).
Source: TCGA-CH-5753-01A-01-BS1.4311c533-f9c1-4c6f-8b10-922daa3c2e3e.svs
Access: open
Returns
-------
Tuple[openslide.OpenSlide, Path]
H&E-stained WSI of prostate tissue and its file path
"""
return _fetcher.load_slide(
"tcga/prostate/TCGA-CH-5753-01A-01-BS1.4311c533-f9c1-4c6f-8b10-922daa3c2e3e.svs"
)
# ===== Public API =====
__all__ = [
"aorta_tissue",
"breast_tissue",
"breast_tissue_diagnostic_green_pen",
"breast_tissue_diagnostic_red_pen",
"breast_tissue_diagnostic_black_pen",
"cmu_small_region",
"heart_tissue",
"ihc_breast",
"ihc_kidney",
"ovarian_tissue",
"prostate_tissue",
]
GlassCut