Converting a Single Session

Let’s imagine you’ve just completed an experimental session and you’d like to convert your data to NWB right away.

Upon launching the GUIDE, you’ll begin on the Convert page. If you’re opening the application for the first time, there should be no pipelines listed on this page.

Press the Create a new conversion pipeline button to start the conversion process.

Project Structure

Project Setup

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.

You’ll notice that the name property has a red asterisk next to it, which identifies it as a required property.

After specifying a unique project name, the colored background and error message will disappear, allowing you to advance to the next page.

Workflow Configuration

On this page, you’ll specify the type of workflow you’d like to follow for this conversion pipeline.

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.

Additionally, we’ll turn off the option to upload to the DANDI Archive and approach this in a later tutorial.

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 here.

The tutorial we’re working with uses the SpikeGLX and Phy formats, a common output for Neuropixels recordings and subsequent spike sorting. To specify that your pipeline will handle these files, you’ll press the “Add Format” button.

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.

The selected formats will then display above the button.

Advance to the next page when you have SpikeGLX Recording and Phy Sorting selected.

Data Entry

Source Data Information

On this page, specify the .ap.bin (SpikeGLX) file and phy folder so that the GUIDE can find this source data to complete the conversion.

As discussed in the Dataset Generation tutorial, these can be found in the ~/NWB_GUIDE/test-data/data directory, where ~ is the home directory of your system.

You can either click the file selector to navigate to the file or drag-and-drop into the GUIDE from your file navigator.

Advance to the next page to extract metadata from the source data.

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!

The Session Start Time in the General Metadata section is already specified because this field was automatically extracted from the SpikeGLX source data.

While the General Metadata section is complete, take some time to fill out additional information such as the Institutional Info box and the Experimenter field.

We also 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 P25W, which represents 25 weeks old.

The status of the Subject information will update in real-time as you fill out the form.

This dataset will also have Ecephys metadata extracted from the SpikeGLX source data, though we aren’t interested in modifying this information at the moment.

Let’s leave this as-is and advance to the next page. This will trigger the conversion of your source data into a preview NWB file.

File Conversion

Inspector Report

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.

Advance to the next page when you are satisfied with the Inspector Report.

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.

In particular, take a look at the lefthand metadata table and check that the information provided on the previous pages is present in the NWB file.

Neurosift can be useful for many other exploration tasks—but this will not be covered in this tutorial.

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.

Conversion Review

Congratulations on finishing your first conversion of neurophysiology files using the NWB GUIDE!

This was a straightforward workflow with only a single session… But what if you have multiple sessions to convert?