diff --git a/docs/tutorials/dataset.rst b/docs/tutorials/dataset.rst index c0b2aca0a..0995f918d 100644 --- a/docs/tutorials/dataset.rst +++ b/docs/tutorials/dataset.rst @@ -17,7 +17,7 @@ Navigate to the **Settings** page using the main sidebar. Then press the **Gener Press the Generate button on the Settings page to create the dataset. -The generated data will populate in the `~/NWB_GUIDE/test_data` directory and include a `data` folder with the original data as well as a `dataset` folder that duplicates this `data` across multiple subjects and sessions. +The generated data will populate in the ``~/NWB_GUIDE/test_data`` directory and include a ``data`` folder with the original data as well as a ``dataset`` folder that duplicates this ``data`` across multiple subjects and sessions. .. code-block:: bash diff --git a/docs/tutorials/next_steps.rst b/docs/tutorials/next_steps.rst index ce80155c6..daf330370 100644 --- a/docs/tutorials/next_steps.rst +++ b/docs/tutorials/next_steps.rst @@ -1,3 +1,13 @@ What's Next? ======================================= -Coming soon... + +Considerations when Using Your Own Data +--------------------------------------- +When using your own data, there are a few things to consider: + +Choosing an Output Location +^^^^^^^^^^^^^^^^^^^^^^^^^^^ + Choosing a good output location is important for two reasons, namely **conversion speed** and **disk space**. + + 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. diff --git a/docs/tutorials/single_session.rst b/docs/tutorials/single_session.rst index 6f1ba5744..6eabe32d9 100644 --- a/docs/tutorials/single_session.rst +++ b/docs/tutorials/single_session.rst @@ -3,7 +3,7 @@ Converting a Single Session As a researcher, 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 Conversions page. If you’re opening the application for the first time, there should be no pipelines listed on this page. +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. .. figure:: ../assets/tutorials/home-page.png :align: center @@ -19,13 +19,6 @@ 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. -.. note:: - Choosing a good output location is important for two reasons, namely **conversion speed** and **disk space**. - - 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. - - You’ll notice that the name property has a red asterisk next to it, which identifies it as a required property. .. figure:: ../assets/tutorials/single/info-page.png @@ -59,7 +52,7 @@ Next, you’ll specify the data formats you’re working with on the Data Format :align: center :alt: Date Formats page -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. +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. .. figure:: ../assets/tutorials/single/format-options.png :align: center @@ -92,7 +85,7 @@ 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. -As discussed in the :doc:`Dataset Generation ` tutorial, these can be found in the `~/NWB_GUIDE/test-data/data` directory. +As discussed in the :doc:`Dataset Generation ` tutorial, these can be found in the ``~/NWB_GUIDE/test-data/data`` directory. You can either click the file selector to navigate to the file or drag-and-drop into the GUIDE from your file navigator. @@ -112,7 +105,7 @@ The Session Start Time in the General Metadata section is already specified beca :alt: Metadata page with invalid Subject information -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. +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, which represents 30 days old. .. figure:: ../assets/tutorials/single/metadata-subject-complete.png :align: center diff --git a/pyflask/manageNeuroconv/manage_neuroconv.py b/pyflask/manageNeuroconv/manage_neuroconv.py index 63b361673..e1ffbf67a 100644 --- a/pyflask/manageNeuroconv/manage_neuroconv.py +++ b/pyflask/manageNeuroconv/manage_neuroconv.py @@ -1063,7 +1063,7 @@ def generate_test_data(output_path: str): spikeglx_output_folder = base_path / "spikeglx" phy_output_folder = base_path / "phy" - # Define NeuroPixel-like values for sampling rates and conversion factors + # Define Neuropixels-like values for sampling rates and conversion factors duration_in_s = 3.0 number_of_units = 50 number_of_channels = 385 # Have to include 'sync' channel to be proper SpikeGLX. TODO: artificiate sync pulses