from ._utils import DataSet
[docs]def imc(force_download=False):
"""Pre-processed zurich cohort IMC dataset from *Jackson, H.W., Fischer, J.R., Zanotelli, V.R.T. et al. The single-cell pathology landscape of breast cancer.* `Nature <https://doi.org/10.1038/s41586-019-1876-x>`_
"""
print('warning: to get the latest version of this dataset use `so = sh.dataset.imc(force_download=True)`')
so = DataSet(
name='imc',
url='https://figshare.com/ndownloader/files/34877643',
doc_header='Pre-processed subset IMC dataset from `Jackson et al '
)
return so(force_download=force_download)
[docs]def imc_sample(force_download=False):
"""Pre-processed samples from the cohort IMC dataset from *Jackson, H.W., Fischer, J.R., Zanotelli, V.R.T. et al. The single-cell pathology landscape of breast cancer.* `Nature <https://doi.org/10.1038/s41586-019-1876-x>`_
"""
print('warning: to get the latest version of this dataset use `so = sh.dataset.imc(force_download=True)`')
so = DataSet(
name='imc_sample',
url='https://figshare.com/ndownloader/files/36150798',
doc_header='Pre-processed subset IMC dataset from `Jackson et al '
)
return so(force_download=force_download)
[docs]def imc_quickstart(force_download=False):
"""Pre-processed samples from the cohort IMC dataset from *Jackson, H.W., Fischer, J.R., Zanotelli, V.R.T. et al. The single-cell pathology landscape of breast cancer.* `Nature <https://doi.org/10.1038/s41586-019-1876-x>`_
"""
print('warning: to get the latest version of this dataset use `so = sh.dataset.imc(force_download=True)`')
so = DataSet(
name='imc_quickstart',
url='https://figshare.com/ndownloader/files/36418257',
doc_header='Pre-processed subset IMC dataset from `Jackson et al '
)
return so(force_download=force_download)
# def imc_basel():
# """Pre-processed subset IMC dataset from *Jackson, H.W., Fischer, J.R., Zanotelli, V.R.T. et al. The single-cell pathology landscape of breast cancer.* `Nature <https://doi.org/10.1038/s41586-019-1876-x>`_
# """
# so = DataSet(
# name='imc',
# url='https://figshare.com/ndownloader/files/31750769',
# doc_header='Pre-processed subset IMC dataset from `Jackson et al '
# )
# return so()
[docs]def mibi():
"""
Processed data from *A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging.* `Cell <https://doi.org/10.1016/j.cell.2018.08.039>`_.
Normalised expression values of segmented cells and cell masks from `here <https://www.angelolab.com/mibi-data>`_ and tiff stacks from `here <https://mibi-share.ionpath.com/tracker/imageset/>`_
"""
so = DataSet(
name='mibi',
url='https://figshare.com/ndownloader/files/34148859',
doc_header='Processed data from https://www.angelolab.com/mibi-data and https://mibi-share.ionpath.com/tracker/imageset'
)
return so()
# mibi_pop = DataSet(
# name='mibi',
# url=None,
# doc_header='Processed and populated data (graphs, metrics) from https://www.angelolab.com/mibi-data and https://mibi-share.ionpath.com/tracker/imageset'
# )