IDAT Colocalization Analysis

This Docker container performs classic image colocalization analysis including Pearson correlation and Manders overlap coefficients. It accepts masks for background subtraction. Thresholding methods can be either Otsu or Costes.

Inputs

Expects three directories:
first_images should contain the first set of images (in alphabetical order) to be compared.
second_images contains the set of images (in alphabetical order) against which the first set will be compared.
masks (Optional) contains the masks used for background subtraction.

Outputs

Analysis results are output to a CSV file in the results directory.

Usage

The default usage calculates Pearson correlation, and Manders overlap coefficients using Otsu thresholding.

docker run -it \
    -v "$(pwd)<first_images_dir>:/code/data/first_images" \
    -v "$(pwd)<second_images_dir>:/code/data/second_images" \
    -v "$(pwd)<masks_dir>:/code/data/masks" \
    -v "$(pwd)<results_dir>:/code/results" \
    ghcr.io/turku-bioimaging/idt-colocalization-analysis:0.3.0

Disable masks for background subtraction:

    ...
    ghcr.io/turku-bioimaging/idt-colocalization-analysis:0.3.0 --disable-masks

Disable Pearson correlation:

    ...
    ghcr.io/turku-bioimaging/idt-colocalization-analysis:0.3.0 --disable-pearson

Disable Otsu thresholding for Manders overlap coefficients:

    ...
    ghcr.io/turku-bioimaging/idt-colocalization-analysis:0.3.0 --disable-manders-otsu

Enable Costes auto thresholding for Manders overlap coefficients:

    ...
    ghcr.io/turku-bioimaging/idt-colocalization-analysis:0.3.0 --manders-costes

Credits

Image Data Team - Turku BioImaging
Joanna Pylvänäinen - [email protected]
Junel Solis - [email protected]
Dado Tokic - [email protected]
Pasi Kankaanpää - [email protected]

Turku BioImaging
https://bioimaging.fi