.. _sphx_glr_wo_examples_models:

Models
=======

Run `pip install napari[all]` before running these examples.

This folder of `models` examples consists of a set of simulations that are being actively developed and will run as is.

Each model is named with the schema `<sample-angular-assumptions>_<sample-spatial-assumptions>_<data-shape>`.

For example, `isotropic_thin_3d.py` demonstrates a set of methods for simulating and reconstructing

- an isotropic object (i.e. an attenuating-phase object that has no diattenuation or birefringence) that is
- thin compared to the depth of field of the microscope from
- three-dimensional data (a defocus stack).



.. raw:: html

    <div class="sphx-glr-thumbnails">

.. thumbnail-parent-div-open

.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In plane oriented thick pol3d summary">

.. only:: html

  .. image:: /wo_examples/models/images/thumb/sphx_glr_inplane_oriented_thick_pol3d_thumb.png
    :alt:

  :ref:`sphx_glr_wo_examples_models_inplane_oriented_thick_pol3d.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">In plane oriented thick pol3d</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="Isotropic fluorescent thick 3d summary">

.. only:: html

  .. image:: /wo_examples/models/images/thumb/sphx_glr_isotropic_fluorescent_thick_3d_thumb.png
    :alt:

  :ref:`sphx_glr_wo_examples_models_isotropic_fluorescent_thick_3d.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Isotropic fluorescent thick 3d</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="# 3D partially coherent optical diffraction tomography (ODT) simulation # J. M. Soto, J. A. Rodrigo, and T. Alieva, &quot;Label-free quantitative # 3D tomographic imaging for partially coherent light microscopy,&quot; Opt. Express # 25, 15699-15712 (2017)">

.. only:: html

  .. image:: /wo_examples/models/images/thumb/sphx_glr_phase_thick_3d_thumb.png
    :alt:

  :ref:`sphx_glr_wo_examples_models_phase_thick_3d.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">phase thick 3d</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="In plane oriented thick pol3d vector summary">

.. only:: html

  .. image:: /wo_examples/models/images/thumb/sphx_glr_inplane_oriented_thick_pol3d_vector_thumb.png
    :alt:

  :ref:`sphx_glr_wo_examples_models_inplane_oriented_thick_pol3d_vector.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">In plane oriented thick pol3d vector</div>
    </div>


.. raw:: html

    <div class="sphx-glr-thumbcontainer" tooltip="# 3D partially coherent optical diffraction tomography (ODT) simulation # J. M. Soto, J. A. Rodrigo, and T. Alieva, &quot;Label-free quantitative # 3D tomographic imaging for partially coherent light microscopy,&quot; Opt. Express # 25, 15699-15712 (2017)">

.. only:: html

  .. image:: /wo_examples/models/images/thumb/sphx_glr_isotropic_thin_3d_thumb.png
    :alt:

  :ref:`sphx_glr_wo_examples_models_isotropic_thin_3d.py`

.. raw:: html

      <div class="sphx-glr-thumbnail-title">Isotropic thin 3d</div>
    </div>


.. thumbnail-parent-div-close

.. raw:: html

    </div>


.. toctree::
   :hidden:

   /wo_examples/models/inplane_oriented_thick_pol3d
   /wo_examples/models/isotropic_fluorescent_thick_3d
   /wo_examples/models/phase_thick_3d
   /wo_examples/models/inplane_oriented_thick_pol3d_vector
   /wo_examples/models/isotropic_thin_3d