:orphan:

Tutorials
===================

This gallery contains demonstrations of various image processing tools
from the ASPIRE package, implemented using simulated data.

API Introduction
----------------

Newcomers should start here to get an overview of ASPIRE's primitive
structures and interfaces, building up to a short simulated ab-initio
pipeline.



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


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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial reviews the default ASPIRE configuration and common patterns for overriding.">

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  .. image:: /auto_tutorials/images/thumb/sphx_glr_configuration_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_configuration.py`

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      <div class="sphx-glr-thumbnail-title">ASPIRE Configuration</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this notebook we will introduce the core API components, then demonstrate basic usage corres...">

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  .. image:: /auto_tutorials/images/thumb/sphx_glr_aspire_introduction_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_aspire_introduction.py`

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      <div class="sphx-glr-thumbnail-title">ASPIRE-Python Introduction</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial demonstrates some key components of an ab-initio reconstruction pipeline using sy...">

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  .. image:: /auto_tutorials/images/thumb/sphx_glr_pipeline_demo_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_pipeline_demo.py`

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      <div class="sphx-glr-thumbnail-title">Ab-initio Pipeline Demonstration</div>
    </div>


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    </div>


.. toctree::
   :hidden:

   /auto_tutorials/configuration
   /auto_tutorials/aspire_introduction
   /auto_tutorials/pipeline_demo

Component Examples
------------------

Selected components demonstrate some common tasks while discussing
usage and configuration.




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


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    <div class="sphx-glr-thumbcontainer" tooltip="This script illustrates 2D covariance Wiener filtering functionality in the ASPIRE package, imp...">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_cov2d_simulation_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_cov2d_simulation.py`

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      <div class="sphx-glr-thumbnail-title">2D Covariance Estimation</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This script illustrates the estimation of orientation angles using a synchronization matrix and...">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_orient3d_simulation_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_orient3d_simulation.py`

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      <div class="sphx-glr-thumbnail-title">3D Image Orientation</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial demonstrates some methods of the ASPIRE Image class">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_image_class_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_image_class.py`

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      <div class="sphx-glr-thumbnail-title">ASPIRE Image Class</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="We demonstrate ASPIRE&#x27;s particle picking methods using the Apple class.">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_apple_picker_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_apple_picker.py`

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      <div class="sphx-glr-thumbnail-title">Apple Picker</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this example we will demonstrate some of ASPIRE&#x27;s image processing functionality. We will ad...">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_basic_image_array_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_basic_image_array.py`

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      <div class="sphx-glr-thumbnail-title">Basic Image Array</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial demonstrates the CTF and corresponds to lecture notes from MATH586 at Princeton.">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_ctf_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_ctf.py`

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      <div class="sphx-glr-thumbnail-title">CTF: Contrast Transfer Function</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="We demonstrate class averaging using the rotationally invariant representation algorithm.">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_class_averaging_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_class_averaging.py`

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      <div class="sphx-glr-thumbnail-title">Class Averaging</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This script illustrates the example of Covariance 3D estimation using simulation images generat...">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_cov3d_simulation_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_cov3d_simulation.py`

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      <div class="sphx-glr-thumbnail-title">Covariance 3D Estimation</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial reviews ASPIRE&#x27;s data downloading utility.">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_data_downloader_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_data_downloader.py`

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      <div class="sphx-glr-thumbnail-title">Data Downloader</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This script illustrates using ASPIRE&#x27;s Simulation source to generate projections of a Volume us...">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_generating_volume_projections_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_generating_volume_projections.py`

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      <div class="sphx-glr-thumbnail-title">Generating 3D Volume Projections</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This script illustrates several expansion methods for 2D images developed in ASPIRE package bas...">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_image_expansion_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_image_expansion.py`

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      <div class="sphx-glr-thumbnail-title">Image Expansion</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This script illustrates the preprocess steps implemented prior to starting the pipeline of reco...">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_preprocess_imgs_sim_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_preprocess_imgs_sim.py`

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      <div class="sphx-glr-thumbnail-title">Image Preprocessing</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial will demonstrate how to set up and use ASPIRE&#x27;s MicrographSource classes.">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_micrograph_source_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_micrograph_source.py`

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      <div class="sphx-glr-thumbnail-title">Micrograph Sources</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="In this tutorial we compare projections generated by Relion with projections generated by ASPIR...">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_relion_projection_interop_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_relion_projection_interop.py`

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      <div class="sphx-glr-thumbnail-title">Relion Projection Interoperability</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="Starfile">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_starfile_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_starfile.py`

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      <div class="sphx-glr-thumbnail-title">Starfile</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial demonstrates a weighted volume reconstruction, using a published reference datase...">

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  .. image:: /auto_tutorials/tutorials/images/thumb/sphx_glr_weighted_volume_estimation_thumb.png
    :alt:

  :ref:`sphx_glr_auto_tutorials_tutorials_weighted_volume_estimation.py`

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      <div class="sphx-glr-thumbnail-title">Weighted Volume Reconstruction</div>
    </div>


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    </div>


.. toctree::
   :hidden:
   :includehidden:


   /auto_tutorials/tutorials/index.rst



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

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