imctoolkit.ImageSingleCellData¶

class ImageSingleCellData(img, mask, channel_names=None, region_properties=None)¶

Single-cell data accessor for multi-channel images

Variables

img – intensity image, as xarray.DataArray with dimensions (c, y, x) and, optionally, channel names as coordinate for the c dimension
mask – cell mask, as numpy.ndarray of shape (y, x), where 0 indicates background pixels and non-zero pixels indicate the cell ID
region_properties – list of RegionProperties computed by the current instance, see regionprops()

class RegionProperties(value)¶

Enumeration of regionprops properties supported by this class, see https://scikit-image.org/docs/0.17.x/api/skimage.measure.html#skimage.measure.regionprops

AREA = 'area'¶

BBOX = 'bbox'¶

BBOX_AREA = 'bbox_area'¶

CONVEX_AREA = 'convex_area'¶

CONVEX_IMAGE = 'convex_image'¶

COORDS = 'coords'¶

ECCENTRICITY = 'eccentricity'¶

EQUIVALENT_DIAMETER = 'equivalent_diameter'¶

EULER_NUMBER = 'euler_number'¶

EXTENT = 'extent'¶

FILLED_AREA = 'filled_area'¶

FILLED_IMAGE = 'filled_image'¶

IMAGE = 'image'¶

INERTIA_TENSOR = 'inertia_tensor'¶

INERTIA_TENSOR_EIGVALS = 'inertia_tensor_eigvals'¶

LOCAL_CENTROID = 'local_centroid'¶

MAJOR_AXIS_LENGTH = 'major_axis_length'¶

MINOR_AXIS_LENGTH = 'minor_axis_length'¶

MOMENTS = 'moments'¶

MOMENTS_CENTRAL = 'moments_central'¶

MOMENTS_HU = 'moments_hu'¶

MOMENTS_NORMALIZED = 'moments_normalized'¶

ORIENTATION = 'orientation'¶

PERIMETER = 'perimeter'¶

SLICE = 'slice'¶

SOLIDITY = 'solidity'¶

DEFAULT_REGION_PROPERTIES = [<RegionProperties.AREA: 'area'>, <RegionProperties.ECCENTRICITY: 'eccentricity'>, <RegionProperties.MAJOR_AXIS_LENGTH: 'major_axis_length'>, <RegionProperties.MINOR_AXIS_LENGTH: 'minor_axis_length'>, <RegionProperties.ORIENTATION: 'orientation'>]¶: List of RegionProperties computed by default, see __init__()

__init__(img, mask, channel_names=None, region_properties=None)¶

Parameters

img¶ (image file path, MultichannelImage or array-like) – intensity image, shape: (c, y, x)
mask¶ (mask file path or array-like) – (path to) cell mask of shape: (y, x)
channel_names¶ (Optional[Sequence[str]]) – channel names
region_properties¶ (Optional[Sequence[RegionProperties]]) – list of RegionProperties to compute, defaults to DEFAULT_REGION_PROPERTIES when None

property image_width¶

Image width in pixels

Return type: int

property image_height¶

Image height in pixels

Return type: int

property num_channels¶

Number of channels

Return type: int

property channel_names¶

Channel names

Return type: List[str]

property num_cells¶

Number of cells

Return type: int

property cell_ids¶

Integer cell IDs

Return type: ndarray

property cell_centroids¶

Cell centroids, shape: (cells, dimensions=2)

Return type: DataArray

property min_intensities¶

Minimum cell intensities

Returns: DataArray with coordinates (cell IDs, channel names)

property min_intensities_table¶

Minimum cell intensities

Return type: DataFrame
Returns: DataFrame (index: cell IDs, columns: channel names)

property max_intensities¶

Maximum cell intensities

Returns: DataArray with coordinates (cell IDs, channel names)

property max_intensities_table¶

Maximum cell intensities

Return type: DataFrame
Returns: DataFrame (index: cell IDs, columns: channel names)

property mean_intensities¶

Mean cell intensities

Returns: DataArray with coordinates (cell IDs, channel names)

property mean_intensities_table¶

Mean cell intensities

Return type: DataFrame
Returns: DataFrame (index: cell IDs, columns: channel names)

property median_intensities¶

Median cell intensities

Returns: DataArray with coordinates (cell IDs, channel names)

property median_intensities_table¶

Median cell intensities

Return type: DataFrame
Returns: DataFrame (index: cell IDs, columns: channel names)

property std_intensities¶

Standard deviations of cell intensities

Returns: DataArray with coordinates (cell IDs, channel names)

property std_intensities_table¶

Standard deviations of cell intensities

Return type: DataFrame
Returns: DataFrame (index: cell IDs, columns: channel names)

property var_intensities¶

Variances of cell intensities

Returns: DataArray with coordinates (cell IDs, channel names)

property var_intensities_table¶

Variances of cell intensities

Return type: DataFrame
Returns: DataFrame (index: cell IDs, columns: channel names)

property regionprops¶

Region properties

For a list of computed properties, see region_properties.

Return type: DataArray
Returns: DataArray with coordinates (cell_id, property_name)

property regionprops_table¶

Region properties

For a list of computed properties, see region_properties.

Return type: DataFrame
Returns: DataFrame (index: cell IDs, columns: regionprops property names)

compute_cell_intensities(aggr)¶

Compute cell intensity values

Parameters: aggr¶ (Callable[[ndarray], Any]) – function for aggregating the pixel values of a cell
Return type: DataArray
Returns: DataArray with coordinates (cell IDs, channel names)

compute_cell_border_distances()¶

Compute the pairwise Euclidean distances between cell borders

Return type: DataArray
Returns: symmetric border distance matrix

to_dataset(cell_properties=False, cell_channel_properties=False)¶

Returns an xarray.Dataset representation of the current instance

At least one of cell_properties or cell_channel_properties has to be True

Parameters

cell_properties¶ (Union[bool, Sequence[str]]) – list of cell properties (e.g. regionprops) to include; set to True to include all
cell_channel_properties¶ (Union[bool, Sequence[str]]) – list of cell channel properties (e.g. intensity values) to include; set to True to include all

Return type

Dataset

Returns

Dataset with cell ID, channel name and/or property name as coordinates

compute_cell_centroid_distances(metric='euclidean')¶

Compute the pairwise distances between cell centroids

Parameters: metric¶ (str) – the distance metric to use, see https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html
Return type: DataArray
Returns: symmetric cell centroid distance matrix

to_anndata(cell_properties=False, cell_channel_properties=False, x_cell_channel_property=None)¶

Returns an anndata.AnnData representation of the current instance

Parameters

cell_properties¶ – list of cell properties (e.g. regionprops) to include; set to True to include all
cell_channel_properties¶ – list of cell channel properties (e.g. intensity values) to include; set to True to include all
x_cell_channel_property¶ – cell channel property to use for the main AnnData data matrix (X)

Returns

AnnData object, in which cell channel properties (e.g. intensity values) are stored as layers and cell properties (e.g. regionprops) are stored as observations

to_dataframe(cell_properties=False, cell_channel_properties=False)¶

Returns a pandas.DataFrame representation of the current instance

Column names for cell channel properties (e.g. intensity values) are prefixed by the property name, e.g. a mean_intensities property would be included as 'mean_intensities_{channel_name}'. Column names for cell properties (e.g. regionprops) are not prefixed.

Parameters

cell_properties¶ (Union[bool, Sequence[str]]) – list of cell properties (e.g. regionprops) to include; set to True to include all
cell_channel_properties¶ (Union[bool, Sequence[str]]) – list of cell channel properties (e.g. intensity values) to include; set to True to include all

Return type

DataFrame

Returns

DataFrame (index: cell IDs, columns: see description)

write_csv(path, cell_properties=False, cell_channel_properties=False, **kwargs)¶

Writes a CSV file, see to_dataframe() for format specifications

Parameters

path¶ (Union[str, Path]) – path to the .csv file to be written
cell_properties¶ (Union[bool, Sequence[str]]) – list of cell properties (e.g. regionprops) to include; set to True to include all
cell_channel_properties¶ (Union[bool, Sequence[str]]) – list of cell channel properties (e.g. intensity values) to include; set to True to include all
kwargs¶ – other arguments passed to pandas.DataFrame.to_csv()

write_fcs(path, cell_properties=False, cell_channel_properties=False, **kwargs)¶

Writes an FCS file, see to_dataframe() for format specifications

Uses fcswrite.write_fcs() for writing FCS 3.0 files.

Parameters

path¶ (Union[str, Path]) – path to the .fcs file to be written
cell_properties¶ (Union[bool, Sequence[str]]) – list of cell properties (e.g. regionprops) to include; set to True to include all
cell_channel_properties¶ (Union[bool, Sequence[str]]) – list of cell channel properties (e.g. intensity values) to include; set to True to include all
kwargs¶ – other arguments passed to fcswrite.write_fcs()