scip.illumination_correction package#

Illumination correction methods

Submodules#

scip.illumination_correction.jones_2006 module#

Illumination correction as proposed by Jones et al. (2006)

scip.illumination_correction.jones_2006.correct(*, images: Bag, key: str, ngroups: int, median_filter_size: int = 50, downscale: int = 1, output: Path | None = None, precomputed: Path | None = None) → Bag#

Distributed implementation of retrospective illumination correction [1]. All images are averaged per batch, after which the image is filtered using a median filter. If requested, the image is downscaled prior to median filtering to reduce memory consumption.

[1] Singh, S., Bray, M. A., Jones, T. R., & Carpenter, A. E. (2014). Pipeline for illumination correction of images for high‐throughput microscopy. Journal of microscopy, 256(3), 231-236.

Parameters:

  • images – Collection containing images to be corrected. Each item in the collection a pixels and ‘key’ key.

  • key – Item key used for grouping.

  • ngroups – Number of groups in the images collection.

  • median_filter_size – Size of the window used in the median filter.

  • downscale – factor by which to downscale the image prior to median filtering

  • output – Path pointing to directory to save correction images.

  • precomputed – Path to pickle file with precomputed correction images in a dict.

Returns:

Collection with corrected images.