.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "3d_tfm/auto_examples/3_BeadMeasurement.py"
.. LINE NUMBERS ARE GIVEN BELOW.

.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        :ref:`Go to the end <sphx_glr_download_3d_tfm_auto_examples_3_BeadMeasurement.py>`
        to download the full example code

.. rst-class:: sphx-glr-example-title

.. _sphx_glr_3d_tfm_auto_examples_3_BeadMeasurement.py:


Microbeads to Detect Matrix Deformations
==============================================

This example calculates matrix deformations around a Human Umbilical Vein Endothelial Cells (HUVECs) that invades 
in a polyethylene glycol (PEG) hydrogel cell as measured and described in `[Jorge Barrasa-Fano et al., 2021] <https://www.sciencedirect.com/science/article/pii/S2352711021000625>`_.                                                
The data is available from the authors website `here <https://www.mech.kuleuven.be/en/bme/research/mechbio/lab/tfmlab>`_.
Images of microbeads (channel 'ch01') between a relaxed and deformed stacks are used to calculate matrix deformations (image on the right).


 .. figure:: ../images/examples/bead_measurement/microbeads.png

.. GENERATED FROM PYTHON SOURCE LINES 15-21

.. code-block:: default
   :lineno-start: 16


    import saenopy





.. GENERATED FROM PYTHON SOURCE LINES 23-32

Loading the Stacks
------------------

Saenopy is very flexible in loading stacks from any filename structure.
We replace the number of the channels "ch00" with a channel placeholder "ch{c:01}" to indicate that this refers to
the channels and which channel to use as the first channel where the deformations should be detected.
We replace the number of the z slice "z000" with a z placeholder "z{z}" to indicate that this number refers to the
z slice. We do the same for the deformed state and for the reference stack.
Here images of microbeads (channel 'ch01') are used to calculate matrix deformation.

.. GENERATED FROM PYTHON SOURCE LINES 32-43

.. code-block:: default
   :lineno-start: 33


    # load the relaxed and the contracted stack
    # {z} is the placeholder for the z stack
    # {c} is the placeholder for the channels
    # {t} is the placeholder for the time points
    results = saenopy.get_stacks( 
        'TestDataTFMlabKULeuven\Stressed_z{z}_ch{c:01}.tif',
        reference_stack='TestDataTFMlabKULeuven\Relaxed_z{z}_ch{c:01}.tif',
        output_path='3_BeadMeasurement/example_output',
        voxel_size=[0.567, 0.567, 0.493])


.. GENERATED FROM PYTHON SOURCE LINES 44-61

Detecting the Deformations
--------------------------
Saenopy uses 3D Particle Image Velocimetry (PIV) with the following parameters 
to calculate matrix deformations between a deformed and relaxed state.  

+------------------+-------+
| Piv Parameter    | Value |
+==================+=======+
| element_size     |    5  |
+------------------+-------+
| window_size      |    25 |
+------------------+-------+
| signal_to_noise  |   1.1 |
+------------------+-------+
| drift_correction | True  |
+------------------+-------+


.. GENERATED FROM PYTHON SOURCE LINES 61-90

.. code-block:: default
   :lineno-start: 62


    # define the parameters for the piv deformation detection
    piv_parameters = {'element_size': 5.0, 'window_size': 25.0, 'signal_to_noise': 1.1, 'drift_correction': True}


    # iterate over all the results objects
    for result in results:
        # set the parameters
        result.piv_parameters = piv_parameters
        # get count
        count = len(result.stacks)
        if result.stack_reference is None:
            count -= 1
        # iterate over all stack pairs
        for i in range(count):
            # get two consecutive stacks 
            if result.stack_reference is None:
                stack1, stack2 = result.stacks[i], result.stacks[i + 1]
            # or reference stack and one from the list
            else:
                stack1, stack2 = result.stack_reference, result.stacks[i]
            # and calculate the displacement between them
            result.mesh_piv[i] = saenopy.get_displacements_from_stacks(stack1, stack2,
                                                                       piv_parameters["window_size"],
                                                                       piv_parameters["element_size"],
                                                                       piv_parameters["signal_to_noise"],
                                                                       piv_parameters["drift_correction"])
        # save the displacements
        result.save()


.. _sphx_glr_download_3d_tfm_auto_examples_3_BeadMeasurement.py:

.. only:: html

  .. container:: sphx-glr-footer sphx-glr-footer-example




    .. container:: sphx-glr-download sphx-glr-download-python

      :download:`Download Python source code: 3_BeadMeasurement.py <3_BeadMeasurement.py>`

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      :download:`Download Jupyter notebook: 3_BeadMeasurement.ipynb <3_BeadMeasurement.ipynb>`


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 .. rst-class:: sphx-glr-signature

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