Quickstart

There are a number of steps to preparing to run Breathe Easy. Below is a brief outline of the steps to set everything up within the GUI. Detailed instructions are linked within the outline and in the following sections of this guide.

1. Set input and output.

   • Set output folder for all processes in Breathe Easy. Individual folders will be automatically generated for each run within the selected folder.

   • Select input signal files that you would like analyzed. Help preparing data for analysis.

2. Review data for appropriate comments.

   • You may need to make corrections or adjustments based on the results of this check:

     • Missing Timestamp

     • Duplicate Timestamp

     • Novel Timestamp

3. Configure and load metadata for each animal and experiment.

4. Next you will need to configure settings for SASSI’s selection of breaths from your recordings. There are 3 different ways you can run SASSI, and each has a different type of configuration/ settings file associated with it.

   • Automated run: SASSI will select breaths using your settings. You will need 1) Basic Settings and 2) Automated Settings.

   • Manual run: SASSI will select breaths that were manually selected by the user. This will also require an additional export from your recording software that includes timestamps for your manual selections. You will need 1) Basic Settings and 2) a Manual Selections File.

   • Automated and Manual run: SASSI will perform two iterations of breath selection where one set of breaths will be those selected manually by the user and the other will be breaths that were selected by an automated run of SASSI with the same files. You will need 1) Basic Settings, 2) Automated Settings, and 3) a Manual Selections File.

     Note

     If you have existing configuration files for any or all of these settings, then you can click the Select SASSI settings files button (9) to select those files and load them in without using the subGUIs.

5. From this point you can continue on to establish STAGG settings to allow a full run of the program. Or you can run SASSI, then run STAGG separately.

   • Running SASSI independently allows you to interrogate whether the data produced enough “quality” breaths to allow for an accurate comparison between your groups. We recommend this kind of run if it is your first time running your data through the pipeline.