imctools.data¶

imctools.data.acquisition¶

class AblationImageType(value)¶

Before / after ablation types of images

BEFORE = 'before'¶

AFTER = 'after'¶

class AcquisitionDict¶

slide_id: int¶

id: int¶

origin: str¶

source_path: str¶

max_x: int¶

max_y: int¶

signal_type: Optional[str]¶

segment_data_format: Optional[str]¶

ablation_frequency: Optional[float]¶

ablation_power: Optional[float]¶

start_timestamp: Optional[str]¶

end_timestamp: Optional[str]¶

movement_type: Optional[str]¶

ablation_distance_between_shots_x: Optional[float]¶

ablation_distance_between_shots_y: Optional[float]¶

template: Optional[str]¶

roi_start_x_pos_um: Optional[float]¶

roi_start_y_pos_um: Optional[float]¶

roi_end_x_pos_um: Optional[float]¶

roi_end_y_pos_um: Optional[float]¶

description: Optional[str]¶

has_before_ablation_image: bool¶

has_after_ablation_image: bool¶

metadata: Optional[Dict[str, str]]¶

is_valid: bool¶

class Acquisition(slide_id, id, origin, source_path, max_x, max_y, signal_type=None, segment_data_format=None, ablation_frequency=None, ablation_power=None, start_timestamp=None, end_timestamp=None, movement_type=None, ablation_distance_between_shots_x=None, ablation_distance_between_shots_y=None, template=None, roi_start_x_pos_um=None, roi_start_y_pos_um=None, roi_end_x_pos_um=None, roi_end_y_pos_um=None, description=None, has_before_ablation_image=False, has_after_ablation_image=False, metadata=None, is_valid=True)¶

IMC acquisition as a collection of acquisition channels.

symbol = 'a'¶

static from_dict(d)¶: Recreate an object from dictionary

property metaname¶: Meta name fully describing the entity

property n_channels¶: Number of channels

property channel_names¶: Channel names

property channel_labels¶: Channel labels

property channel_masses¶: Channel masses

get_name_indices(names)¶: Returns a list with the indices from names

get_mass_indices(masses)¶: Returns the channel indices from the queried mass

get_csv_dict()¶: Returns dictionary for CSV tables

imctools.data.acquisitiondata¶

class AcquisitionData(acquisition, image_data)¶

Container for IMC acquisition binary image data.

property acquisition¶: Acquisition metadata

property image_data¶: Binary image data as numpy array

to_xarray()¶: Get binary image data as xarray

property is_valid¶

property n_channels¶: Number of channels

property channel_names¶: Channel names

property channel_labels¶: Channel labels

property channel_masses¶: Channel masses

get_image_stack_by_indices(indices)¶: Get image stack by channel indices

get_image_by_index(index)¶: Get channel image by its index

get_image_stack_by_names(names)¶: Get image stack by channel names

get_image_by_name(name)¶: Get channel image by its name

get_image_stack_by_labels(labels)¶: Get image stack by channel labels

get_image_by_label(label)¶: Get channel image by its label

save_ome_tiff(filename, names=None, masses=None, xml_metadata=None, dtype=None)¶

Save OME TIFF file.

Parameters

filename¶ (Union[str, Path]) – .ome.tiff file name.
names¶ (Optional[Sequence[str]]) – Channel names (metals / tags).
masses¶ (Optional[Sequence[str]]) – Channel masses.
xml_metadata¶ (Optional[str]) – Original MCD-XML metadata.
dtype¶ (Optional[object]) – Output numpy format.

save_tiff(filename, names=None, imagej=False, bigtiff=False, dtype=None, compression=0)¶

save_tiffs(output_folder, names=None, masses=None, basename=None, imagej=True, bigtiff=False, dtype=None, compression=0)¶

Save ImageJ TIFF files in a folder.

Parameters

output_folder¶ (Union[str, Path]) – Output folder.
names¶ (Optional[Sequence[str]]) – Channel names (metals / tags).
masses¶ (Optional[Sequence[str]]) – Channel masses.
basename¶ (Optional[str]) – Base file name.
imagej¶ – Save TIFF file compatible with ImageJ format.
bigtiff¶ – BigTIFF format.
dtype¶ (Optional[object]) – Output numpy format.
compression¶ (int) – Compression level.

imctools.data.channel¶

class ChannelDict¶

acquisition_id: int¶

id: int¶

order_number: int¶

name: str¶

label: Optional[str]¶

mass: Optional[int]¶

min_intensity: Optional[float]¶

max_intensity: Optional[float]¶

metadata: Optional[Dict[str, str]]¶

class Channel(acquisition_id, id, order_number, name, label=None, mass=None, min_intensity=None, max_intensity=None, metadata=None)¶

IMC acquisition channel. Represents an image intensity.

symbol = 'c'¶

static from_dict(d)¶: Recreate an object from dictionary

property metaname¶: Meta name fully describing the entity

get_csv_dict()¶: Returns dictionary for CSV tables

imctools.data.panorama¶

class PanoramaDict¶

slide_id: int¶

id: int¶

image_type: str¶

description: str¶

x1: float¶

y1: float¶

x2: float¶

y2: float¶

x3: float¶

y3: float¶

x4: float¶

y4: float¶

rotation_angle: float¶

metadata: Optional[Dict[str, str]]¶

class Panorama(slide_id, id, image_type, description, x1, y1, x2, y2, x3, y3, x4, y4, rotation_angle, metadata=None)¶

Panoramic image (manually attached or automatically generated).

symbol = 'p'¶

static from_dict(d)¶: Recreate an object from dictionary

property metaname¶: Meta name fully describing the entity

get_csv_dict()¶: Returns dictionary for CSV tables

imctools.data.session¶

class SessionDict¶

id: str¶

name: str¶

imctools_version: str¶

created: str¶

metadata: Optional[Dict[str, Any]]¶

slides: List[imctools.data.slide.SlideDict]¶

acquisitions: List[imctools.data.acquisition.AcquisitionDict]¶

panoramas: List[imctools.data.panorama.PanoramaDict]¶

channels: List[imctools.data.channel.ChannelDict]¶

class Session(id, name, imctools_version, created, metadata=None)¶

IMC session data. Container for all slides, acquisitions, panoramas, etc.

static from_dict(d)¶: Recreate an object from dictionary

get_csv_dict()¶: Returns dictionary for CSV tables

save(filepath)¶

Save session data in JSON format.

Parameters: filepath¶ (str) – Output JSON file path

save_meta_csv(output_folder)¶: Writes the metadata as CSV tables

static load(filepath)¶

Load IMC session data from JSON file

Parameters: filepath¶ (Union[str, Path]) – Input JSON file path.

property metaname¶: Meta name fully describing the entity

property acquisition_ids¶

Return type: Tuple[int, …]

imctools.data.slide¶

class SlideDict¶

session_id: str¶

id: int¶

description: Optional[str]¶

width_um: Optional[int]¶

height_um: Optional[int]¶

has_slide_image: Optional[bool]¶

metadata: Optional[Dict[str, str]]¶

class Slide(session_id, id, description=None, width_um=None, height_um=None, has_slide_image=None, metadata=None)¶