spared.datasets.get_dataset

spared.datasets.get_dataset(dataset_name: str, visualize: bool = True) → SpatialDataset[source]

Get a dataset from name.

This function receives the name of a dataset and retrieves a the correspondent SpatialDataset. This function will retrieve configuration files predefined for each dataset in SpaRED. The name of the dataset should be one of the following:

  • 10xgenomic_human_brain

  • 10xgenomic_human_breast_cancer

  • 10xgenomic_mouse_brain_coronal

  • 10xgenomic_mouse_brain_sagittal_anterior

  • 10xgenomic_mouse_brain_sagittal_posterior

  • abalo_human_squamous_cell_carcinoma

  • erickson_human_prostate_cancer_p1

  • erickson_human_prostate_cancer_p2

  • fan_mouse_brain_coronal

  • fan_mouse_olfatory_bulb

  • mirzazadeh_human_colon_p1

  • mirzazadeh_human_colon_p2

  • mirzazadeh_human_pediatric_brain_tumor_p1

  • mirzazadeh_human_pediatric_brain_tumor_p2

  • mirzazadeh_human_prostate_cancer

  • mirzazadeh_human_small_intestine

  • mirzazadeh_mouse_bone

  • mirzazadeh_mouse_brain_p1

  • mirzazadeh_mouse_brain_p2

  • mirzazadeh_mouse_brain

  • parigi_mouse_intestine

  • vicari_human_striatium

  • vicari_mouse_brain

  • villacampa_kidney_organoid

  • villacampa_lung_organoid

  • villacampa_mouse_brain

After the first load of each dataset, the data will be stored and the next time the function is called it will load the data from the stored file much faster.

Parameters:

  • dataset_name (str) – The name of the dataset.

  • visualize (bool, optional) – Whether to visualize the dataset or not. Can significantly increase run time of the command. Defaults to True.

Returns:

The specified dataset in a SpatialDataset object.

Return type:

SpatialDataset