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.. _tutorials:


Tutorials
=========


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.. _general-tutorials:


General tutorials
-----------------


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    <div class="sphx-glr-thumbcontainer" tooltip="This example will focus on the basics of working with an :py~pynwb.file.NWBFile object, including writing and reading of an NWB file, and giving you an introduction to the basic data types. Before we dive into code showing how to use an :py~pynwb.file.NWBFile, we first provide a brief overview of the basic concepts of NWB.">

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  .. image:: /tutorials/general/images/thumb/sphx_glr_plot_file_thumb.png
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  :doc:`/tutorials/general/plot_file`

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      <div class="sphx-glr-thumbnail-title">NWB File Basics</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial explains how to add and remove containers from an existing NWB file and either write the data back to the same file or export the data to a new file.">

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  :doc:`/tutorials/general/add_remove_containers`

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      <div class="sphx-glr-thumbnail-title">Adding/Removing Containers from an NWB File</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Annotating events in time is a common need in neuroscience, e.g. to describes epochs, trials, and invalid times during an experimental session. NWB supports annotation of time intervals via the :py~pynwb.epoch.TimeIntervals type. The :py~pynwb.epoch.TimeIntervals type is a :py~hdmf.common.table.DynamicTable with the following columns:">

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  .. image:: /tutorials/general/images/thumb/sphx_glr_plot_timeintervals_thumb.png
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  :doc:`/tutorials/general/plot_timeintervals`

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      <div class="sphx-glr-thumbnail-title">Annotating Time Intervals</div>
    </div>


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    <div class="sphx-glr-thumbcontainer" tooltip="This example will focus on the basics of working with an :py~pynwb.file.NWBFile to do more than storing standardized data for use and exchange. For example, you may want to store results from intermediate analyses or one-off analyses with unknown utility. This functionality is primarily accomplished with linking and scratch space.">

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  :doc:`/tutorials/general/scratch`

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      <div class="sphx-glr-thumbnail-title">Exploratory Data Analysis with NWB</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The NWB format was designed to be easily extendable. Here we discuss some of the basic functionality in PyNWB for creating  Neurodata Extensions (NDX).">

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  :doc:`/tutorials/general/extensions`

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      <div class="sphx-glr-thumbnail-title">Extending NWB</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This is a user guide for how to curate and take advantage of configuration files in order to more easily validate terms within datasets or attributes.">

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  :doc:`/tutorials/general/plot_configurator`

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      <div class="sphx-glr-thumbnail-title">How to Configure Term Validations</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example focuses on how to access object IDs from NWB container objects and NWB container objects by object ID. Every NWB container object has an object ID that is a UUID_ string, such as &quot;123e4567-e89b-12d3-a456-426655440000&quot;. These IDs have a non-zero probability of being duplicated, but are practically unique and used widely across computing platforms as if they are unique.">

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  .. image:: /tutorials/general/images/thumb/sphx_glr_object_id_thumb.png
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  :doc:`/tutorials/general/object_id`

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      <div class="sphx-glr-thumbnail-title">Object IDs in NWB</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial will demonstrate how to read, explore, and do basic visualizations with an NWB File using different tools.">

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  .. image:: /tutorials/general/images/thumb/sphx_glr_plot_read_basics_thumb.png
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  :doc:`/tutorials/general/plot_read_basics`

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      <div class="sphx-glr-thumbnail-title">Reading and Exploring an NWB File</div>
    </div>


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.. toctree::
   :hidden:

   /tutorials/general/plot_file
   /tutorials/general/add_remove_containers
   /tutorials/general/plot_timeintervals
   /tutorials/general/scratch
   /tutorials/general/extensions
   /tutorials/general/plot_configurator
   /tutorials/general/object_id
   /tutorials/general/plot_read_basics



.. _domain-tutorials:


Domain-specific tutorials
-------------------------


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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial describes storage of extracellular electrophysiology data in NWB in four main steps:">

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  :doc:`/tutorials/domain/ecephys`

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      <div class="sphx-glr-thumbnail-title">Extracellular Electrophysiology Data</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial will demonstrate how to write calcium imaging data. The workflow demonstrated here involves five main steps:">

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  :doc:`/tutorials/domain/ophys`

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      <div class="sphx-glr-thumbnail-title">Calcium Imaging Data</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The following tutorial describes storage of intracellular electrophysiology data in NWB. NWB supports storage of the time series describing the stimulus and response, information about the electrode and device used, as well as metadata about the organization of the experiment.">

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  .. image:: /tutorials/domain/images/thumb/sphx_glr_plot_icephys_thumb.png
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  :doc:`/tutorials/domain/plot_icephys`

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      <div class="sphx-glr-thumbnail-title">Intracellular Electrophysiology</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial focuses on using pandas to query experiment metadata for intracellular electrophysiology experiments using the metadata tables from the :py~pynwb.icephys module. See the icephys_tutorial_new tutorial for an introduction to the intracellular electrophysiology metadata tables and how to create an NWBFile for intracellular electrophysiology data.">

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  .. image:: /tutorials/domain/images/thumb/sphx_glr_plot_icephys_pandas_thumb.png
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  :doc:`/tutorials/domain/plot_icephys_pandas`

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      <div class="sphx-glr-thumbnail-title">Query Intracellular Electrophysiology Metadata</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial will demonstrate the usage of the :pypynwb.behavior module for adding behavioral data to an :py~pynwb.file.NWBFile.">

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  :doc:`/tutorials/domain/plot_behavior`

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      <div class="sphx-glr-thumbnail-title">Behavior Data</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial will demonstrate the usage of the :pypynwb.image module for adding images to an :py~pynwb.file.NWBFile.">

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  :doc:`/tutorials/domain/images`

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      <div class="sphx-glr-thumbnail-title">Storing Image Data in NWB</div>
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    <div class="sphx-glr-thumbcontainer" tooltip=" This tutorial will demonstrate how to write optogenetics data.">

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  :doc:`/tutorials/domain/ogen`

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      <div class="sphx-glr-thumbnail-title">Optogenetics</div>
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.. toctree::
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   /tutorials/domain/ecephys
   /tutorials/domain/ophys
   /tutorials/domain/plot_icephys
   /tutorials/domain/plot_icephys_pandas
   /tutorials/domain/plot_behavior
   /tutorials/domain/images
   /tutorials/domain/ogen



.. _advanced-io-tutorials:


Advanced I/O
------------


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    <div class="sphx-glr-thumbcontainer" tooltip="The HDF5 storage backend supports a broad range of advanced dataset I/O options, such as, chunking and compression. Here we demonstrate how to use these features from PyNWB.">

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  .. image:: /tutorials/advanced_io/images/thumb/sphx_glr_h5dataio_thumb.png
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  :doc:`/tutorials/advanced_io/h5dataio`

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      <div class="sphx-glr-thumbnail-title">Defining HDF5 Dataset I/O Settings (chunking, compression, etc.)</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This tutorial demonstrates how to edit NWB files in-place to make small changes to existing containers. To add or remove containers from an NWB file, see modifying_data. How and whether it is possible to edit an NWB file depends on the storage backend and the type of edit.">

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  .. image:: /tutorials/advanced_io/images/thumb/sphx_glr_plot_editing_thumb.png
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  :doc:`/tutorials/advanced_io/plot_editing`

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      <div class="sphx-glr-thumbnail-title">Editing NWB files</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="This example demonstrate how to iteratively write data arrays with applications to writing large arrays without loading all data into memory and streaming data write.">

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  .. image:: /tutorials/advanced_io/images/thumb/sphx_glr_plot_iterative_write_thumb.png
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  :doc:`/tutorials/advanced_io/plot_iterative_write`

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      <div class="sphx-glr-thumbnail-title">Iterative Data Write</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="PyNWB supports linking between files using external links.">

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  .. image:: /tutorials/advanced_io/images/thumb/sphx_glr_plot_linking_data_thumb.png
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  :doc:`/tutorials/advanced_io/plot_linking_data`

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      <div class="sphx-glr-thumbnail-title">Modular Data Storage using External Files</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="The HDF5 storage backend supports parallel I/O using the Message Passing Interface (MPI). Using this feature requires that you install hdf5 and h5py against an MPI driver, and you install mpi4py. The basic installation of pynwb will not work. Setup can be tricky, and is outside the scope of this tutorial (for now), and the following assumes that you have HDF5 installed in a MPI configuration.">

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      <div class="sphx-glr-thumbnail-title">Parallel I/O using MPI</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="You can read specific sections within individual data files directly from remote stores such as the DANDI Archive. This is especially useful for reading small pieces of data from a large NWB file stored remotely. First, you will need to get the location of the file. The code below illustrates how to do this on DANDI using the dandi API library.">

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  :doc:`/tutorials/advanced_io/streaming`

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      <div class="sphx-glr-thumbnail-title">Streaming NWB files</div>
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    <div class="sphx-glr-thumbcontainer" tooltip="Zarr is an alternative backend option for NWB files. It is a Python package that provides an implementation of chunked, compressed, N-dimensional arrays. Zarr is a good option for large datasets because, like HDF5, it is designed to store data on disk and only load the data into memory when needed. Zarr is also a good option for parallel computing because it supports concurrent reads and writes.">

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  :doc:`/tutorials/advanced_io/plot_zarr_io`

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      <div class="sphx-glr-thumbnail-title">Zarr IO</div>
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.. toctree::
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   /tutorials/advanced_io/h5dataio
   /tutorials/advanced_io/plot_editing
   /tutorials/advanced_io/plot_iterative_write
   /tutorials/advanced_io/plot_linking_data
   /tutorials/advanced_io/parallelio
   /tutorials/advanced_io/streaming
   /tutorials/advanced_io/plot_zarr_io


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      :download:`Download all examples in Python source code: tutorials_python.zip </tutorials/tutorials_python.zip>`

    .. container:: sphx-glr-download sphx-glr-download-jupyter

      :download:`Download all examples in Jupyter notebooks: tutorials_jupyter.zip </tutorials/tutorials_jupyter.zip>`


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