API Reference

Main Package

import kintsugi

Functions

kintsugi.check_dependencies

kintsugi.check_dependencies(verbose: bool = True) -> dict

Check all KINTSUGI dependencies and return status.

Parameters:

verbose (bool): If True, print status messages. Default: True

Returns:

dict: Dictionary with dependency status information.

kintsugi.get_config_template

kintsugi.get_config_template() -> dict

Get a template configuration dictionary for registration workflow.

Returns:

dict: Template configuration with all available options.

Kreg Module (Registration)

from kintsugi import Kreg
# or
from kintsugi.kreg import Valis

Valis Class

The main class for image registration.

from kintsugi.kreg import Valis

registrar = Valis(
    src_dir="/path/to/images",
    dst_dir="/path/to/output",
    reference_img_f="reference.tif",
    **kwargs
)

Parameters:

src_dir (str): Path to source image directory
dst_dir (str): Path to output directory
reference_img_f (str): Filename of reference image
align_to_reference (bool): Align all images to reference. Default: True
max_image_dim_px (int): Maximum image dimension. Default: 2048
compose_non_rigid (bool): Enable non-rigid registration. Default: True
crop_to_overlap (bool): Crop output to overlapping region. Default: True

Methods:

register(): Perform initial registration
register_micro(): Perform micro (fine) registration
warp_and_merge_slides(): Warp images and save results

Kview2 Module (Visualization)

from kintsugi import Kview2
# or
from kintsugi.kview2 import imshow, curtain, crop

imshow

Display an image interactively.

from kintsugi.kview2 import imshow

imshow(image, **kwargs)

curtain

Compare two images with an interactive curtain view.

from kintsugi.kview2 import curtain

curtain(image1, image2, **kwargs)

crop

Interactively crop an image.

from kintsugi.kview2 import crop

cropped = crop(image)

Kstitch Module (Stitching)

from kintsugi import Kstitch

Provides tile stitching functionality for large tiled images.

signal Module

from kintsugi.signal import (
    subtract_autofluorescence,
    analyze_for_subtraction,
    AutofluorescenceSubtractor,
)

Provides autofluorescence subtraction with intelligent parameter suggestion and learning capabilities.

qc Module

from kintsugi.qc import ImageQC, CellQC, MarkerQC, BatchQC

Quality control and assessment tools for image processing pipelines.

denoise Module

from kintsugi.denoise import (
    adaptive_denoise,
    denoise_median,
    denoise_nlm,
    denoise_bilateral,
)

Advanced denoising algorithms including adaptive, NLM, bilateral, and N2V methods.

deps Module

from kintsugi import deps

DependencyChecker Class

from kintsugi.deps import DependencyChecker

checker = DependencyChecker()
results = checker.check_all(verbose=True)

Check and report on all external dependencies.