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<section id="annotations">
<span id="notes"></span><h1>Annotations<a class="headerlink" href="#annotations" title="Permalink to this heading"></a></h1>
<p>Wonambi allows you to add annotations to your signal, such as sleep staging and signal quality (epochwise), highlighted events, cycle markers and bookmarks.</p>
<p>You must first create an Annotation File, by clicking on <code class="docutils literal notranslate"><span class="pre">New</span> <span class="pre">Annotations</span></code>.</p>
<p>You will be asked to provide a rater name. Annotation Files are divided into separate raters. Use the <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Rater</span></code> menu to create new raters and switch between them.</p>
<p>To load previously created annotations, click on <code class="docutils literal notranslate"><span class="pre">Load</span> <span class="pre">Annotations</span></code>:</p>
<img alt="../_images/notes_03_load.png" src="../_images/notes_03_load.png" />
<section id="import-sleep-staging-from-an-external-source">
<h2>Import sleep staging from an external source<a class="headerlink" href="#import-sleep-staging-from-an-external-source" title="Permalink to this heading"></a></h2>
<p>Wonambi can import sleep staging from files generated by Alice, Compumedics, Domino, FASST, PRANA, RemLogic or Sandman.</p>
<p>To import external sleep staging, click on <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Import</span> <span class="pre">staging</span></code>, and select the source program:</p>
<img alt="../_images/notes_04_import_fasst.png" src="../_images/notes_04_import_fasst.png" />
<p>For Compumedics staging, you will be prompted to provide the staging start time.</p>
<p>For all sources but FASST, you will be asked to provide a rater name, under which to save the staging in the Annotation File. You may create a new rater or overwrite the staging in an existing one.</p>
<p>For FASST staging, you’ll first be asked to load the <code class="docutils literal notranslate"><span class="pre">.mat</span></code> file containing the FASST sleep scores. Then you’ll need to indicate where to save the annotations in <code class="docutils literal notranslate"><span class="pre">.xml</span></code> format.</p>
<p>If importation is successful, the converted sleep staging will appear in the <code class="docutils literal notranslate"><span class="pre">Overview</span></code> panel:</p>
<img alt="../_images/notes_05_show_imported.png" src="../_images/notes_05_show_imported.png" />
<p>For RemLogic staging, make sure you select the following options when exporting from RemLogic:</p>
<img alt="gui/images/notes_21_remlogic_options.png" src="gui/images/notes_21_remlogic_options.png" />
</section>
<section id="stage-sleep">
<h2>Stage sleep<a class="headerlink" href="#stage-sleep" title="Permalink to this heading"></a></h2>
<p>You can also stage sleep within Wonambi. First, make sure you are lined up with an epoch. Make sure you are zoomed to the 30-s view with <code class="docutils literal notranslate"><span class="pre">View</span></code> -> <code class="docutils literal notranslate"><span class="pre">Window</span> <span class="pre">length</span></code> –> <code class="docutils literal notranslate"><span class="pre">Set</span> <span class="pre">to</span> <span class="pre">30.0</span></code>.</p>
<p>If you are not lined up with the epoch start, click on <code class="docutils literal notranslate"><span class="pre">Navigation</span></code> –> <code class="docutils literal notranslate"><span class="pre">Line</span> <span class="pre">Up</span> <span class="pre">with</span> <span class="pre">Epoch</span></code>.</p>
<p>Now you can use the <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Score</span></code> menu or the associated keyboard shortcuts to stage sleep per epoch.
Alternatively, you can select a stage from the <code class="docutils literal notranslate"><span class="pre">Stage</span> <span class="pre">Box</span></code>:</p>
<img alt="../_images/notes_09_stage_box.png" src="../_images/notes_09_stage_box.png" />
<p>The <code class="docutils literal notranslate"><span class="pre">Stage</span> <span class="pre">Box</span></code> always displays the stage of the current epoch (as long as you are lined up with one).</p>
<p>Wonambi provides two parallel sleep scoring tracks: one for sleep stages, the other for signal quality.
The idea is to keep sleep annotation separate from signal annotation, so that signal quality does not affect physiological parameters like sleep efficiency and relative stage durations.</p>
<p>We recommend that you first stage sleep, disregarding signal quality
(except of course when it is unintelligible, in which case you can mark it as <code class="docutils literal notranslate"><span class="pre">Artefact</span></code>).
Then, you can make a second pass only evaluating signal quality, using the <code class="docutils literal notranslate"><span class="pre">o</span></code> and <code class="docutils literal notranslate"><span class="pre">p</span></code> keys for <code class="docutils literal notranslate"><span class="pre">Good</span></code> and <code class="docutils literal notranslate"><span class="pre">Poor</span></code> signal, respectively.
Similarly to the <code class="docutils literal notranslate"><span class="pre">Stage</span> <span class="pre">Box</span></code>, the <code class="docutils literal notranslate"><span class="pre">Quality</span> <span class="pre">Box</span></code> displays the quality of the current epoch, and can be used to change it:</p>
<img alt="../_images/notes_10_quality_box.png" src="../_images/notes_10_quality_box.png" />
<p>Epochs marked as <code class="docutils literal notranslate"><span class="pre">Poor</span></code> signal are excluded from <code class="docutils literal notranslate"><span class="pre">Analysis</span></code>, namely event detections and tools in the analysis console.</p>
<p>Epochs staged as <code class="docutils literal notranslate"><span class="pre">Artefact</span></code> are automatically marked as <code class="docutils literal notranslate"><span class="pre">Poor</span></code> signal.</p>
<p>You can view staging and signal quality summary parameters by clicking <code class="docutils literal notranslate"><span class="pre">Summary</span></code> in the <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> panel.</p>
</section>
<section id="mark-cycles">
<h2>Mark cycles<a class="headerlink" href="#mark-cycles" title="Permalink to this heading"></a></h2>
<p>The stages of sleep are normally segregated into cycles (N1; N2; N3; then REM). After staging, you can segment the hypnogram into cycles for use in analysis.</p>
<p>To mark a cycle start, line yourself up with the first epoch of the cycle and click on <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Cycle</span></code> -> <code class="docutils literal notranslate"><span class="pre">Set</span> <span class="pre">cycle</span> <span class="pre">start</span></code>.</p>
<img alt="../_images/notes_11_set_cycle_start.png" src="../_images/notes_11_set_cycle_start.png" />
<p>A cycle start marker will appear as a red square bracket on the <code class="docutils literal notranslate"><span class="pre">Overview</span></code> panel:</p>
<img alt="../_images/notes_12_cycle_marker.png" src="../_images/notes_12_cycle_marker.png" />
<p>To mark a cycle end, line yourself up with the first epoch after the end of the cycle. Here, you can either use <code class="docutils literal notranslate"><span class="pre">Set</span> <span class="pre">cycle</span> <span class="pre">end</span></code> or, if this epoch is the start of the next cycle, simply use <code class="docutils literal notranslate"><span class="pre">Set</span> <span class="pre">cycle</span> <span class="pre">start</span></code> again.</p>
<p>Repeat for each cycle, and make sure to mark the end of the last cycle with <code class="docutils literal notranslate"><span class="pre">Set</span> <span class="pre">cycle</span> <span class="pre">end</span></code>. Omitting this will result in illegible cycle data.</p>
<img alt="../_images/notes_13_all_cycle_markers.png" src="../_images/notes_13_all_cycle_markers.png" />
<p>To remove a cycle marker, line yourself up with that epoch and click <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Cycle</span></code> -> <code class="docutils literal notranslate"><span class="pre">Remove</span> <span class="pre">cycle</span> <span class="pre">marker</span></code>.</p>
<p>You can clear all cycle markers in the rater profile with <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Cycle</span></code> -> <code class="docutils literal notranslate"><span class="pre">Clear</span> <span class="pre">cycle</span> <span class="pre">markers</span></code>.</p>
</section>
<section id="mark-events">
<h2>Mark events<a class="headerlink" href="#mark-events" title="Permalink to this heading"></a></h2>
<p>In addition to epoch annotation, Wonambi allows you to mark events of varying duration directly on the trace.</p>
<p>To mark an event on the trace, enter <em>event edit mode</em> by clicking on the <code class="docutils literal notranslate"><span class="pre">Event</span> <span class="pre">Mode</span></code> icon:</p>
<img alt="../_images/notes_07_event_mode.png" src="../_images/notes_07_event_mode.png" />
<p>Next, select an event type in the <code class="docutils literal notranslate"><span class="pre">Event</span> <span class="pre">Type</span> <span class="pre">box</span></code>:</p>
<img alt="../_images/notes_08_evt_type_box.png" src="../_images/notes_08_evt_type_box.png" />
<p>You can create a new event type with <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Event</span></code> –> <code class="docutils literal notranslate"><span class="pre">New</span> <span class="pre">Event</span> <span class="pre">Type</span></code>.</p>
<p>Now, click and drag along a segment of the signal from the desired channel to create a new event:</p>
<img alt="../_images/notes_14_mark_event.png" src="../_images/notes_14_mark_event.png" />
<p>Events belong to the channel on which they were marked, and appear as a darker colour on that channel. The colours themselves are automatically generated from the event label text.</p>
<p>By default, the events are also highlighted on all other channels in a lighter colour. You can disable this option by toggling <code class="docutils literal notranslate"><span class="pre">View</span></code> -> <code class="docutils literal notranslate"><span class="pre">Full-length</span> <span class="pre">markers</span></code>.</p>
<p>To delete an event, make sure you are in <em>event edit mode</em>, and click on it, so that it becomes highlighted in bright yellow:</p>
<img alt="../_images/notes_15_highlight_event.png" src="../_images/notes_15_highlight_event.png" />
<p>Now press the <code class="docutils literal notranslate"><span class="pre">Delete</span></code> key. Note: The event will be removed from both the trace and the Annotation File.</p>
<p>Events are visible both highlighted on the trace and in table form in the <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> tab of the <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> panel.</p>
<p>Double-click on an event in the table to jump to its position on the trace.</p>
<p>You can also delete an event from the table by clicking it and pressing the <code class="docutils literal notranslate"><span class="pre">Delete</span></code> button below the table.</p>
</section>
<section id="mark-artefacts">
<h2>Mark artefacts<a class="headerlink" href="#mark-artefacts" title="Permalink to this heading"></a></h2>
<p>Events marked using the event type <code class="docutils literal notranslate"><span class="pre">Artefact</span></code> are used for data exclusion in analysis.</p>
<p>For detections and analysis, if the artefact exclusion option is selected, artefacts marked on any channel will exclude concurrent signal on all channels.</p>
<p>To mark <code class="docutils literal notranslate"><span class="pre">Artefact</span></code> events, click on <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Event</span></code> –> <code class="docutils literal notranslate"><span class="pre">New</span> <span class="pre">Event</span> <span class="pre">Type</span></code> and type in <em>Artefact</em>.
Then in <code class="docutils literal notranslate"><span class="pre">Event</span> <span class="pre">Mode</span></code>, mark the artefacts on any channel in the channel group.
This channel must still be in the channel group at the moment of detection or analysis in order for the artefact events to be found.</p>
</section>
<section id="export-sleep-scores-as-csv">
<h2>Export sleep scores as csv<a class="headerlink" href="#export-sleep-scores-as-csv" title="Permalink to this heading"></a></h2>
<p>You can export the current sleep scores as <code class="docutils literal notranslate"><span class="pre">.csv</span></code> file to disk.
To do so, click on <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Export</span> <span class="pre">staging</span></code>:</p>
<img alt="../_images/notes_06_export.png" src="../_images/notes_06_export.png" />
<p>then select the file where you want to store the sleep scores.</p>
</section>
<section id="export-sleep-statistics-as-csv">
<h2>Export sleep statistics as csv<a class="headerlink" href="#export-sleep-statistics-as-csv" title="Permalink to this heading"></a></h2>
<p>You can export some sleep statistics (such as Total Sleep Time, WASO, etc) as <code class="docutils literal notranslate"><span class="pre">.csv</span></code> file to disk.
To do so, click on <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Sleep</span> <span class="pre">statistics</span></code>:</p>
<img alt="../_images/analysis_02_statistics.png" src="../_images/analysis_02_statistics.png" />
<p>then select the file where you want to store the sleep scores.</p>
<p>In addition, you need to specify at what time the lights went off (<code class="docutils literal notranslate"><span class="pre">Lights</span> <span class="pre">OUT</span></code>) and when the lights went on (<code class="docutils literal notranslate"><span class="pre">Lights</span> <span class="pre">ON</span></code>):</p>
<img alt="../_images/analysis_02_timedialog.png" src="../_images/analysis_02_timedialog.png" />
<div class="admonition note">
<p class="admonition-title">Note</p>
<p><code class="docutils literal notranslate"><span class="pre">Lights</span> <span class="pre">OUT</span></code> and <code class="docutils literal notranslate"><span class="pre">Lights</span> <span class="pre">ON</span></code> are to be used as delimiters of the <em>time spent intending to sleep</em>, not as markers of actual luminosity change in the room.</p>
</div>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>If any epochs are scored as sleep before <code class="docutils literal notranslate"><span class="pre">Lights</span> <span class="pre">OUT</span></code> or after <code class="docutils literal notranslate"><span class="pre">Lights</span> <span class="pre">ON</span></code>, sleep efficiency may exceed 1.</p>
</div>
</section>
<section id="import-markers-as-events">
<h2>Import markers as events<a class="headerlink" href="#import-markers-as-events" title="Permalink to this heading"></a></h2>
<p>Some EEG file formats such as Brain Vision come with timeline markers, and these are automatically displayed in Wonambi.
Markers are immutable, so if you would like to modify them in Wonambi, you’ll need to convert them to events, which are saved in the Annotations File.</p>
<p>To do this, make sure you have an Annotations File loaded. Now click <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Event</span></code> -> <code class="docutils literal notranslate"><span class="pre">Markers</span> <span class="pre">to</span> <span class="pre">events</span></code> and choose among the options.</p>
<p>To convert all markers into a single event type, select <code class="docutils literal notranslate"><span class="pre">New</span> <span class="pre">name</span></code>, and enter the event type name when prompted.</p>
<p>To convert markers into new event types named from the marker labels, select <code class="docutils literal notranslate"><span class="pre">Keep</span> <span class="pre">marker</span> <span class="pre">names</span></code>.
A new event type will be created for each unique marker label.</p>
</section>
<section id="merge-events">
<h2>Merge events<a class="headerlink" href="#merge-events" title="Permalink to this heading"></a></h2>
<p>You may want to merge events outside of the automatic detection process.
For instance, you may want to merge spindles detected by different algorithms, or you may want to merge manually marked events with automatically detected ones.</p>
<p>To do this, click on <code class="docutils literal notranslate"><span class="pre">Annotations</span></code> -> <code class="docutils literal notranslate"><span class="pre">Event</span></code> -> <code class="docutils literal notranslate"><span class="pre">Merge</span> <span class="pre">Events...</span></code> to open the <em>merge events dialog</em>:</p>
<img alt="../_images/notes_19_mergedialog.png" src="../_images/notes_19_mergedialog.png" />
<p>You may choose to merge events from one or several event types using the <code class="docutils literal notranslate"><span class="pre">Event</span> <span class="pre">type(s)</span></code> box.
If you select several, you will be prompted to provide a label for the new event type created by the merger.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The selected event types will be deleted and replaced with the new event type.</p>
</div>
<p>Events marked within a same channel will be merged if they are separated by up to a certain interval.
This interval is set with <code class="docutils literal notranslate"><span class="pre">Minimum</span> <span class="pre">interval</span></code>.</p>
<p>In addition to merging events from within a same channel, you may choose to merge events marked on different channels.
To do so, check the <code class="docutils literal notranslate"><span class="pre">Merge</span> <span class="pre">across</span> <span class="pre">channels</span></code> box.
With this option checked, events on any channel separated by <code class="docutils literal notranslate"><span class="pre">Minimum</span> <span class="pre">interval</span></code> or less will be merged.</p>
<p>When events are merged across channels, only one channel keeps the event.
That channel can either be the one that had the earliest onset event, or the longest event.
You can choose the channel selection rule with the <code class="docutils literal notranslate"><span class="pre">Merge</span> <span class="pre">to...</span></code> drop-down menu.</p>
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