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Original file line number | Diff line number | Diff line change |
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Converting a Single Session | ||
======================================= | ||
Coming soon... | ||
=========================== | ||
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As a researcher, you’ve just completed an experimental session and you’d like to convert your data to NWB right away. | ||
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Upon launching the GUIDE, you'll begin on the Conversions page. If you’re opening the application for the first time, there should be no pipelines listed on this page. | ||
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.. figure:: ../assets/tutorials/home-page.png | ||
:align: center | ||
:alt: Home page | ||
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Press the **Create a new conversion pipeline** button to start the conversion process. | ||
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Project Structure | ||
----------------- | ||
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Project Setup | ||
^^^^^^^^^^^^^ | ||
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The Project Setup page will have you define two pieces of information about your pipeline: the **name** and, optionally, the **output location** for your NWB files. | ||
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.. note:: | ||
Choosing a good output location is important for two reasons, namely **conversion speed** and **disk space**. | ||
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1. SSDs will be much faster than HDDs. We’d recommend moving the output location to an SSD if available. | ||
2. If you don’t have much disk space available on your main drive, we recommend changing the output location to a drive that has ample space. | ||
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You’ll notice that the name property has a red asterisk next to it, which identifies it as a required property. | ||
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.. figure:: ../assets/tutorials/single/info-page.png | ||
:align: center | ||
:alt: Project Setup page with no name (invalid) | ||
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After specifying a unique project name, the colored background and error message will disappear, allowing you to advance to the next page. | ||
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.. figure:: ../assets/tutorials/single/valid-name.png | ||
:align: center | ||
:alt: Project Setup page with valid name | ||
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Workflow Configuration | ||
^^^^^^^^^^^^^^^^^^^^^^ | ||
On this page, you’ll specify the type of **workflow** you’d like to follow for this conversion pipeline. | ||
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Since this is a single-session workflow, you’ll need to specify a **Subject ID** and **Session ID** to identify the data you’ll be converting. | ||
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.. figure:: ../assets/tutorials/single/workflow-page.png | ||
:align: center | ||
:alt: Workflow page | ||
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Additionally, we’ll turn off the option to upload to the DANDI Archive and approach this in a later tutorial. | ||
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Data Formats | ||
^^^^^^^^^^^^ | ||
Next, you’ll specify the data formats you’re working with on the Data Formats page. The GUIDE supports 40+ total neurophysiology formats. A full registry of available formats is available :doc:`here </format_support>`. | ||
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.. figure:: ../assets/tutorials/single/formats-page.png | ||
:align: center | ||
:alt: Date Formats page | ||
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The tutorial we're working with uses the SpikeGLX and Phy formats, a common output for NeuroPixel recordings and subsequent spike sorting. To specify that your pipeline will handle these files, you’ll press the “Add Format” button. | ||
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.. figure:: ../assets/tutorials/single/format-options.png | ||
:align: center | ||
:alt: Format pop-up on the Data Formats page | ||
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Then, select the relevant formats—in this case, **SpikeGLX Recording** and **Phy Sorting**—from the pop-up list. Use the search bar to filter for the format you need. | ||
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.. figure:: ../assets/tutorials/single/search-behavior.png | ||
:align: center | ||
:alt: Searching for SpikeGLX in the format pop-up | ||
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The selected formats will then display above the button. | ||
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.. figure:: ../assets/tutorials/single/interface-added.png | ||
:align: center | ||
:alt: Data Formats page with SpikeGLX Recording added to the list | ||
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Advance to the next page when you have **SpikeGLX Recording** and **Phy Sorting** selected. | ||
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.. figure:: ../assets/tutorials/single/all-interfaces-added.png | ||
:align: center | ||
:alt: Data Formats page with both SpikeGLX Recording and Phy Sorting added to the list | ||
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Data Entry | ||
----------- | ||
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Source Data Information | ||
^^^^^^^^^^^^^^^^^^^^^^^ | ||
On this page, specify the relevant **.bin** (Spikeglx) file and **phy** folder so that the GUIDE can find this source data to complete the conversion. | ||
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As discussed in the :doc:`Dataset Generation </tutorials/dataset>` tutorial, these can be found in the `~/NWB_GUIDE/test-data/data` directory. | ||
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You can either click the file selector to navigate to the file or drag-and-drop into the GUIDE from your file navigator. | ||
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.. figure:: ../assets/tutorials/single/sourcedata-page-specified.png | ||
:align: center | ||
:alt: Source Data page with source locations specified | ||
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Session Metadata | ||
^^^^^^^^^^^^^^^^ | ||
The file metadata page is a great opportunity to add rich annotations to the file, which will be read by anyone reusing your data in the future! | ||
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The Session Start Time in the General Metadata section is already specified because this field was automatically extracted from the SpikeGLX source data. | ||
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.. figure:: ../assets/tutorials/single/metadata-nwbfile.png | ||
:align: center | ||
:alt: Metadata page with invalid Subject information | ||
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However, we still need to add the Subject information—as noted by the red accents around that item. Let’s say that our subject is a male mouse with an age of P30D. | ||
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.. figure:: ../assets/tutorials/single/metadata-subject-complete.png | ||
:align: center | ||
:alt: Metadata page with valid Subject information | ||
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The status of the Subject information will update in real-time as you fill out the form. | ||
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This dataset will also have **Ecephys** metadata extracted from the SpikeGLX source data. | ||
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.. figure:: ../assets/tutorials/single/metadata-ecephys.png | ||
:align: center | ||
:alt: Ecephys metadata extracted from the SpikeGLX source data | ||
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Let's leave this as-is and advance to the next page. | ||
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The next step generates a preview file and displays real-time progress throughout the conversion process. | ||
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File Conversion | ||
--------------- | ||
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Inspector Report | ||
^^^^^^^^^^^^^^^^ | ||
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The Inspector Report page allows you to validate the preview file against the latest Best Practices and make suggestions to improve the content or representations. | ||
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.. figure:: ../assets/tutorials/single/inspect-page.png | ||
:align: center | ||
:alt: NWB Inspector report | ||
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Conversion Preview | ||
^^^^^^^^^^^^^^^^^^ | ||
On the Conversion Preview, Neurosift allows you to explore the structure of the NWB file and ensure the packaged data matches your expectations. | ||
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.. figure:: ../assets/tutorials/single/preview-page.png | ||
:align: center | ||
:alt: Neurosift preview visualization | ||
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Advancing from this page will trigger the full conversion of your data to the NWB format, a process that may take some time depending on the dataset size. | ||
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Conversion Review | ||
^^^^^^^^^^^^^^^^^ | ||
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Congratulations on finishing your first conversion of neurophysiology files using the NWB GUIDE! | ||
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.. figure:: ../assets/tutorials/single/conversion-results-page.png | ||
:align: center | ||
:alt: Conversion results page with a list of converted files | ||
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This was a straightforward workflow with only a single session... But what if you have multiple sessions to convert? |
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