https://github.com/grfrederic/deconvolution

Python module for performing (automatic) colour deconvolution.
https://github.com/grfrederic/deconvolution

Last synced: 18 days ago
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Python module for performing (automatic) colour deconvolution.

• Host: GitHub
• URL: https://github.com/grfrederic/deconvolution
• Owner: grfrederic
• License: bsd-3-clause
• Created: 2017-05-27T18:50:18.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2022-11-20T19:29:40.000Z (about 2 years ago)
• Last Synced: 2024-12-13T13:58:49.714Z (24 days ago)
• Language: Python
• Size: 424 KB
• Stars: 4
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.txt

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README

        
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deconvolution

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A Python module providing Deconvolution class that implements and generalises Ruifrok-Johnston color deconvolution algorithm [RJ]_, [IJ]_. It allows one to split an image into distinct color layers in just

a few lines of code:

.. code:: python

  from deconvolution import Deconvolution

  from PIL import Image

  img = Image.open("image.jpg")

  

  # Declare an instance of Deconvolution, with image loaded and with color basis defining what layers are interesting

  decimg = Deconvolution(image=img, basis=[[1, 0.1, 0.2], [0, 0.1, 0.8]])

  

  # Constructs new PIL Images, with different color layers

  layer1, layer2 = decimg.out_images(mode=[1, 2])

Installation

------------

You can install the package using pip:

.. code:: bash

  pip install deconvolution

Alternatively, you can clone the repository and run:

.. code:: bash

  make install

Since then you can import use the module in your scripts:

.. code:: python

  from deconvolution import Deconvolution

  d = Deconvolution()

Testing

-------

.. code:: bash

  

  # For Python 3 users

  make test

  

  # For Python 2 users

  make comp

  # Check the code coverage

  make coverage

  # Check the coverage interactively, using a web browser

  make html

Deconvolve

----------

For better usage experience we created a script allowing one to deconvolve images from the shell. Copy `deconvolve.py` file into `/usr/local/bin` or, if you want to use it locally:

.. code:: bash

  mkdir ~/bin

  cp deconvolve.py ~/bin

  export PATH=~/bin:$PATH

Since then you can deconvolve images using:

.. code:: bash

  deconvolve.py image1.png image2.png ...

  # For help

  deconvolve.py -h

Documentation

-------------

Check out our documentation at `Read The Docs

`_.

Contributors

------------

Method developed by Frederic Grabowski generalising Ruifrok-Johnston algorithm [RJ]_. and implemented by Frederic Grabowski [FG]_ and Paweł Czyż [PC]_.

We are very grateful to prof. Daniel Wójcik and dr Piotr Majka [N1]_, [N2]_ who supervised the project. We also would like to thank prof. Gabriel Landini [GL]_, who

implemented the colour deconvolution in ImageJ [IJ]_ and allowed us to test the algorithm on his data.

References

----------

.. [RJ] `Research paper by Ruifrok and Johnston 

  `_

.. [IJ] `ImageJ webpage

  `_

.. [N1] `Laboratory of Neuroinformatics webpage

  `_

.. [GL] `Prof. Gabriel Landini's webpage

  `_

.. [N2] https://github.com/Neuroinflab/

.. [FG] https://github.com/grfrederic

.. [PC] https://github.com/pawel-czyz