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

    Click :ref:`here <sphx_glr_download_gallery_bonc_natural_images.py>` to download the full example code
.. rst-class:: sphx-glr-example-title

.. _sphx_glr_gallery_bonc_natural_images.py:


natural scene decoding ophys
==============================

This is an example of how to decode natural images from ophys traces in V1




.. code-block:: python


    OEID = 541206592


First, let's download an experiment from the Allen Institute Brain Observatory



.. code-block:: python


    from allensdk.core.brain_observatory_cache import BrainObservatoryCache
    nwb_dataset = boc.get_ophys_experiment_data(OEID)


Next, we'll load the dF/F traces and put them in a DataFrame



.. code-block:: python


    timestamps, dff = nwb_dataset.get_dff_traces()
    neuron_ids = nwb_dataset.get_cell_specimen_ids()

    traces = pd.DataFrame(
        dff.T,
        columns=neuron_ids,
        index=timestamps,
    )

    print(traces.head())


Next, we'll load stim_table



.. code-block:: python


    stim_table = nwb_dataset.get_stimulus_table('natural_scenes')
    print(stim_table.head())


The stim_table lists stimulus times in terms of the start and end frames of
the calcium traces, but we need start times and durations for neuroglia, so
we'll need to reshape



.. code-block:: python


    stim_table['time'] = timestamps[stim_table['Start']]
    stim_tabel['End']  = timestamps[stim_table['End']]

    stim_table['duration'] = stim_tabel['End'] - stim_tabel['time']

    print(stim_table.head())


.. _sphx_glr_download_gallery_bonc_natural_images.py:


.. only :: html

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



  .. container:: sphx-glr-download

     :download:`Download Python source code: bonc_natural_images.py <bonc_natural_images.py>`



  .. container:: sphx-glr-download

     :download:`Download Jupyter notebook: bonc_natural_images.ipynb <bonc_natural_images.ipynb>`


.. only:: html

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

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.readthedocs.io>`_