spatialtis.read_ROIs¶
- class spatialtis.read_ROIs(entry, obs_names, var, mask_pattern=None, img_pattern=None)[source]¶
Extract single cell expression matrix and geometry information from stacked images and masks
For details, please refer to Multiplexed images to AnnData.
>>> import spatialtis as st
>>> var = pd.read_csv("panel_markers.csv")
>>> reader = st.read_ROIs(entry="IMC_images", obs_names=['ROI'], var=var, mask_pattern="mask", img_pattern="full") >>> data = reader.to_anndata()
- Parameters
entry (Union[pathlib.Path, str]) – The root folder to start with
obs_names (Sequence) – Array of names correspond to each level of your folders
var (pandas.core.frame.DataFrame) – Describe the order of layers in your stacked image
mask_pattern (Optional[str]) – Name pattern for all of your mask
img_pattern (Optional[str]) – Name pattern for all of your image
- anndata¶
The processed AnnData object