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DeepSqueak v3.0 was designed and tested with MATLAB 2020a.

To run DeepSqueak, navigate to the main DeepSqueak folder in MATLAB, and type "DeepSqueak" into the command line.

DeepSqueak will add itself to the MATLAB path after running.

Table of Contents:

• Installation
• Main Window
• USV Detection
  • Selecting Audio Files
  • Output
  • Training Detection Networks
• Selection Review
  • Keyboard Shortcuts
  • Contour Detection
  • Post Hoc Denoising
• Call Classification
  • Unsupervised Clustering
  • Supervised Classification
  • Syntax Analysis
• Other Tools
• Import & Export
  • Export to Excel

                                   +-----------------+
                            v-----<| Export to Raven |<--------<
                            |      +-----------------+         |
                            v                                  |
              +-------------+---+                              |
       >----->| Raven Table     |>---v                         |
       |      +-----------------+    |                         |
       |                             |                         |
       |      +-----------------+    |                         |         +-----------------------------+   
       >----->| MUPET Output    |>---v                         |         | Syntax Analysis             |   
       |      +-----------------+    |   +--------------+      |         +-----------------------------+   
       |                             >-->| Import Calls |>--v  |         | Transition probabilities    |   
       |      +-----------------+    |   +--------------+   |  |   >-----| between call classification |<------<
       >----->| Ultravox Output |>---^                      |  |   |     |                             |       |  
       |      +-----------------+    |                      |  |   |     +-----------------------------+       |  
       |                             |                      |  |   |                                           |  
       |      +-----------------+    |                      |  |   |                                           |  
       >----->| XBAT Output     |>---^                      |  |   |                                           |  
       |      +-----------------+                           |  |   |                                           |  
       |                                                    |  |   |                                           |  
       |                                                    |  |   |                                           |  
       ^                                                    v  ^   ^                                           ^   
+------+------+                              +--------------+--+---+--+                               +--------+--------+     
| Audio Files |     +----------------+       | Detected Call Files    |                               |   Excel Table   |     
+-------------+     | "Detect Calls  |       +------------------------+      +-----------------+      +-----------------+     
|   *.wmf     +>---------------------------->| *.m file containing    +>---->| Export to Excel |>---->| Call Statistics |
|   *.wav     |     | "Multi Detect" |       | Audio and call box     |      +-----------------+      |                 |     
|   *.flac    |     +----------------+       |                        |                               |                 |     
|   *.UVD     |                              |                        |                               |                 |     
+-------------+                              +-+-+---------+-----+----+                               +-----------------+     
                                               ^ v         ^     v
                                               | |         |     |
                                               | |         |     |
                                               | |         |     |
                                               ^ v         |  +--+-----------------+        +-------------+
                            +------------------+-+-+       |  | Contour Extraction |>------>| t-SNE Plot  |
                            | Call Refinement      |       |  +--+-----------------+        +-------------+
                            +----------------------+       |     |
                            | Manual Review        |       |     |
                            | Post-hoc Denoising   |       ^     v
                            | Threshold Adjustment |     +-+-----+-------------------+
                            +----------------------+     | Call Classification       |
                                                         +---------------------------+
                                                         | K+means Clustering        |
                                                         | Supervised Classification |
                                                         |                           |
                                                         +---------------------------+