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docs/docs/getting-started-gui.md

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+These are tutorials to get started using the SanPy desktop GUI.
+
+Please watch the videos as you follow along with a recipes.
+
+## Load a file, detect spikes, and run some plugins
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/OtxpjSrgPjY?si=tMCUb8qrjRdNwvd8" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+**Recipe** for remaking the SanPy manuscript figure 3 from the GUI. Here we will load a raw data file, detect some spikes, and run some plugins.
+
+1. Run SanPy
+2. Select menu `File -> Open ...`
+3. Open data file `2021_07_20_0010.abf` from the `data/` folder
+4. Select a sweep with a number of spikes (for example, sweep 14)
+5. Select `Fast Neuron` in the `Detection - Presets` popup
+6. If it is not already shown, display the derivative of the recording with the `View - Derivative` menu
+7. In the derivative plot, click and drag the horizontal cursor (C) to set the desired dvdt threshold for spike detection
+8. Right click the derivative plot and select the  `Set dvdt Threshold` menu
+9. Click the `Detect dV/dt` button in the `Detection` panel.
+
+Finally, run the plugins to genarate Figure 3 a/b
+
+10. Select the `Plugins - Plot Recording` menu, this will generate panel (a)
+11. Select the `Plugins - Plot FI` menu, this will generate panel (b)
+
+Screen shot of the main GUI.
+![Figure 3](../img/figure-3/main-gui.png)
+
+Right click the dvdt plot and select `Set dvdt Threshold`.
+<IMG SRC="../img/figure-3/set-dvdt-threshold.png" width=200>
+
+Figure 3a, the `Plot Recording` plugin.
+![Figure 3a](../img/figure-3/plot-recording-plugin.png)
+
+Figure 3b, the `Plot FI` plugin.
+![Figure 3a](../img/figure-3/plot-fi-plugin.png)
+
+## Loading a folder, detect spikes in multiple files, and run the Plot Tool (pool) plugin
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/Z4_dgWxxPB0?si=IaVfZRSm-gNqQziY" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+**Recipe** for remaking the SanPy manuscript Figure 4 from the GUI.
+
+Please note, this will not be the same exact data but the plots will be similar.
+
+1. Run SanPy
+2. Use `Load Folder ...` to load the provided sample data in the `data/` folder.
+3. Load and analyze two raw data files. Try with `19114001.abf` and `20191009_0005.abf`
+4. Use the `Set Meta Data` plugin to set the `Condition1` of one file to `Control`, and the other file to `Drug`
+3. Run the `Plot Tool (pool)` plugin
+4. Set the interface as follows
+    - Plot Type: Violin Plot
+    - Hue: Condition1
+    - X-Stat: Condition1
+    - Y-Stat: Spike Frequency (Hz)
+
+The plot in the plugin should look something like this
+
+<IMG SRC="../img/figure-4/violin-spike-freq.png" width=200>
+
+The step above can be repeated for any `Y-Stat` such as `Take Off Potential (mV)` or other.
+
+Likewise, a scatter plot is easily created by selecting Plot Type `Scatter Plot` and choosing the desired X-Stat and Y-Stat.
+
+<IMG SRC="../img/figure-4/scatter-spike-freq.png" width=200>
+
+