tdm.raw.breast_imc#

IMC breast-cancer dataset by Fischer et. al., Cell Reports Medicine 2023 https://www.nature.com/articles/s41588-022-01041-y

Not automatically testing these functions because data requires some preprocessing in R.

Functions

all_image_numbers()

read_clinical_df()

read_image_single_cell_df(img_num)

read_single_cell_df([tissue_type, ...])

Reads the SingleCells.csv dataframe, persistent_cache for fast reading.
tdm.raw.breast_imc.all_image_numbers()[source]#
tdm.raw.breast_imc.read_clinical_df()[source]#
tdm.raw.breast_imc.read_image_single_cell_df(img_num)[source]#
tdm.raw.breast_imc.read_single_cell_df(tissue_type: Literal['primary tumor', 'lymph node mts', 'both'] = 'primary tumor', ki67_threshold: float = 0.5, download: bool = True) → DataFrame[source]#

Reads the SingleCells.csv dataframe, persistent_cache for fast reading.

Note

There were some additional types in the data, including ‘normal breast tissue’ (~30K cells from 37 patients)