Answers.Body: <p>We published <a href="http://www.nature.com/articles/s41598-020-78995-8" rel="nofollow noreferrer">a paper (Miller et al 2021)</a> and <a href="https://data.aad.gov.au/metadata/AcousticTrends_BlueFinLibrary" rel="nofollow noreferrer">a dataset (Miller et al 2020)</a> a few years back where we used PAMGuard's Ishmael Spectrogram Correlation and Energy Sum detectors for Antarctic blue and fin whale sounds. The paper described the overall detection process and settings, and I believe the open-access dataset included the PAMGuard settings files.</p>
  <p>Ultimately, for our Antarctic datasets the results of these detectors were at best mediocre, with low recall for &quot;acceptable&quot; levels of precision. So, it would be worth checking out if your goal is to education and learning a bit about how to use PAMGuard and these modules, but may not be great for a real-world/ecological application.</p>
  <p>If your main interest is in efficient and accurate detection of fin whale, and you're skilled with Matlab and/or Python, then you might be better off checking out the work of
  <a href="https://royalsocietypublishing.org/doi/10.1098/rsif.2021.0297" rel="nofollow noreferrer">Madhusudhana et al (2020)</a> and their <a href="https://github.com/shyamblast/TemporalContext-2021" rel="nofollow noreferrer">associated code</a>, <a href="https://doi.org/10.5281/zenodo.4661494" rel="nofollow noreferrer">model</a> and <a href="https://zenodo.org/records/4661495" rel="nofollow noreferrer">dataset</a>.</p>
  <p>Additionally, there's a nice comparison of ML detectors for this task in the hot-off-the-press <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/rse2.392" rel="nofollow noreferrer">paper on deep-learning algorithms by Schall et al (2024)</a></p>
  <p>References</p>
  <ul>
  <li><p>Madhusudhana, S., Shiu, Y., Klinck, H., Fleishman, E., Liu, X., Nosal, E. M., et al. (2021). Improve automatic detection of animal
  call sequences with temporal context. Journal of the Royal Society Interface 18. doi: 10.1098/rsif.2021.0297</p>
  </li>
  <li><p>Miller, B. S., Stafford, K. M., Van Opzeeland, I., Harris, D., Samaran, F., Širović, A., et al. (2020). An annotated library of    underwater acoustic recordings for testing and training automated algorithms for detecting Antarctic blue and fin whale sounds. doi:    10.26179/5e6056035c01b</p>
  </li>
  <li><p>Miller, B. S., IWC SORP Acoustic Trends Working Group, Kathleen M. Stafford, Ilse Van Opzeeland, Danielle Harris, Flore Samaran, Ana
  Širović, Susannah Buchan, Ken Findlay, Balcazar, N., Nieukirk, S., Leroy, E. C., et al. (2021). An open access dataset for developing    automated detectors of Antarctic baleen whale sounds and performance evaluation of two commonly used detectors. Scientific Reports 11, 806. doi: 10.1038/s41598-020-78995-8</p>
  </li>
  <li><p>Schall, E., Kaya, I. I., Debusschere, E., Devos, P., and Parcerisas,  C. (2024). Deep learning in marine bioacoustics: a benchmark for
  baleen whale detection. Remote Sens Ecol Conserv n/a, 13pp. doi: 10.1002/rse2.392</p>
  </li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-26T16:43:30.503Z
Answers.Text: Thank you so much for these references Brian Miller! These are super helpful to my research since we are trying to validate a different Python built detection software and our eventual goal is ML applications but with the North Pacific Fin Whale and ships. I have two of your papers already saved in Mendeley so I knew they were important, but I hadn't made the connection yet (early PhD student here).
Answers.UserDisplayName: Carla
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-04-26T04:00:35.823Z
Answers.LastActivityDate: 2024-04-26T04:00:35.823Z
Answers.UserDisplayName: Brian Miller
Body: <p>I want to use PAMGuard to detect 20 Hz fin whale vocalizations from audio files that I've created from low frequency (fs = 200 Hz) hydrophone data. I've figured out how to load the audio file and display the spectrogram. I want to use the Ishmael modules. While the PAMGuard tutorial was somewhat helpful, I'm not sure how I would use the spectrogram correlation module. I've searched all over Google for PAMGuard and Ishmael user guides. I've only found an Ishmael 1.0 user guide and the bioacoustics.us. site is no longer hosted.</p>
  <p>Does anyone have suggestions for how to use this module? I'm also considering trying the energy sum and building a kernel for the matched filter module.</p>
  <p>Thank you so much!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-25T06:04:02.713Z
Comments.Text: Do you have any aversion to simply try the different input options? IMO, they are straight forward. At least for the energy sum module. The Matched filter module needs only an audio file (e.g .wav).
Comments.UserDisplayName: WMXZ
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-25T17:43:18.370Z
Comments.Text: Thank you for your response @WMXZ! No, I don't have an aversion to different input options. I'm a newbie to PAMGuard and have done most of the processing on the raw  low frequency hydrophone data directly from Seismological Facility for the Advancement of Geoscience (SAGE), formerly IRIS, using their web services in Matlab or obspy in Python.
Comments.UserDisplayName: Carla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-25T21:30:05.353Z
Comments.Text: Are you committed to using Ishmael for fin whale detection? Or are you just trying to learn Ishmael? I ask because our lab has been successful using both the Whistle and Moan detector and the click detector to pick up fin whale 20Hz pulses
Comments.UserDisplayName: Cory Hom-Weaver
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-25T23:34:04.290Z
Comments.Text: Hi @CoryHom-Weaver, thank you for responding! No, I'm not committed to Ishmael. I'm just trying to find a more well-known detection capability to use for fin whale detection and classification. If you could provide some assistance on how to use the whistle & moan detector, that would be great. I found a presentation from Douglas Gillespie from my Google search, but I'm not sure how old it is & it stated that the performance with the whistle and moan detector was poor for blue & fin whales.
Comments.UserDisplayName: Carla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-26T16:13:56.033Z
Comments.Text: If you do want to play with Ishmael's standalone software, you can email David Mellinger at Oregon State (google will give you his email) and he can send you the Ishmael 3.0 installer which comes packaged with a user guide. He should also be able to share a workshop tutorial PDF. These all used to be on that bioacoustics.us site and he knows that is down but I'm not sure when it will be back up.
Comments.UserDisplayName: selene
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-26T16:30:18.283Z
Comments.Text: Thank you @selene! I emailed Dave Mellinger (OSU email address) back in December 2023 and didn't get a response. I'll try again.
Comments.UserDisplayName: Carla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-04-27T02:48:49.040Z
Comments.Text: I don't have a copy of the installer, but I'll talk to him and see if I can get one. If you email me at selene.fregosi at noaa.gov I can at least send you the most recent user guide and training documentation.
Comments.UserDisplayName: selene
Tags: <pamguard><automated-detection><underwater><spectrogram><marine-mammals>
Title: Detect 20 Hz Fin Whale Songs with PAMGuard
ThreadText: # Detect 20 Hz Fin Whale Songs with PAMGuard
  
  (Asked by: username_0 on 2024-04-25)
  
  I want to use PAMGuard to detect 20 Hz fin whale vocalizations from audio files that I've created from low frequency (fs = 200 Hz) hydrophone data. I've figured out how to load the audio file and display the spectrogram. I want to use the Ishmael modules. While the PAMGuard tutorial was somewhat helpful, I'm not sure how I would use the spectrogram correlation module. I've searched all over Google for PAMGuard and Ishmael user guides. I've only found an Ishmael 1.0 user guide and the bioacoustics.us. site is no longer hosted.
  
  Does anyone have suggestions for how to use this module? I'm also considering trying the energy sum and building a kernel for the matched filter module.
  
  Thank you so much!
  
  **Tags:** pamguard, automated-detection, underwater, spectrogram, marine-mammals
  
  > **Comments:**
  > **username_1**: Do you have any aversion to simply try the different input options? IMO, they are straight forward. At least for the energy sum module. The Matched filter module needs only an audio file (e.g .wav).  
  > **username_0**: Thank you for your response @username_1! No, I don't have an aversion to different input options. I'm a newbie to PAMGuard and have done most of the processing on the raw  low frequency hydrophone data directly from Seismological Facility for the Advancement of Geoscience (SAGE), formerly IRIS, using their web services in Matlab or obspy in Python.  
  > **username_2**: Are you committed to using Ishmael for fin whale detection? Or are you just trying to learn Ishmael? I ask because our lab has been successful using both the Whistle and Moan detector and the click detector to pick up fin whale 20Hz pulses  
  > **username_0**: Hi @CoryHom-Weaver, thank you for responding! No, I'm not committed to Ishmael. I'm just trying to find a more well-known detection capability to use for fin whale detection and classification. If you could provide some assistance on how to use the whistle & moan detector, that would be great. I found a presentation from Douglas Gillespie from my Google search, but I'm not sure how old it is & it stated that the performance with the whistle and moan detector was poor for blue & fin whales.  
  > **username_3**: If you do want to play with Ishmael's standalone software, you can email David Mellinger at Oregon State (google will give you his email) and he can send you the Ishmael 3.0 installer which comes packaged with a user guide. He should also be able to share a workshop tutorial PDF. These all used to be on that bioacoustics.us site and he knows that is down but I'm not sure when it will be back up.  
  > **username_0**: Thank you @username_3! I emailed Dave Mellinger (OSU email address) back in December 2023 and didn't get a response. I'll try again.  
  > **username_3**: I don't have a copy of the installer, but I'll talk to him and see if I can get one. If you email me at username_3.fregosi at noaa.gov I can at least send you the most recent user guide and training documentation.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_4 on 2024-04-26. Score: 3 | Accepted answer
  
  We published [a paper (Miller et al 2021)](http://www.nature.com/articles/s41598-020-78995-8) and [a dataset (Miller et al 2020)](https://data.aad.gov.au/metadata/AcousticTrends_BlueFinLibrary) a few years back where we used PAMGuard's Ishmael Spectrogram Correlation and Energy Sum detectors for Antarctic blue and fin whale sounds. The paper described the overall detection process and settings, and I believe the open-access dataset included the PAMGuard settings files.
  
  Ultimately, for our Antarctic datasets the results of these detectors were at best mediocre, with low recall for "acceptable" levels of precision. So, it would be worth checking out if your goal is to education and learning a bit about how to use PAMGuard and these modules, but may not be great for a real-world/ecological application.
  
  If your main interest is in efficient and accurate detection of fin whale, and you're skilled with Matlab and/or Python, then you might be better off checking out the work of
  [Madhusudhana et al (2020)](https://royalsocietypublishing.org/doi/10.1098/rsif.2021.0297) and their [associated code](https://github.com/shyamblast/TemporalContext-2021), [model](https://doi.org/10.5281/zenodo.4661494) and [dataset](https://zenodo.org/records/4661495).
  
  Additionally, there's a nice comparison of ML detectors for this task in the hot-off-the-press [paper on deep-learning algorithms by Schall et al (2024)](https://onlinelibrary.wiley.com/doi/abs/10.1002/rse2.392)
  
  References
  
  * Madhusudhana, S., Shiu, Y., Klinck, H., Fleishman, E., Liu, X., Nosal, E. M., et al. (2021). Improve automatic detection of animal
    call sequences with temporal context. Journal of the Royal Society Interface 18. doi: 10.1098/rsif.2021.0297
  * Miller, B. S., Stafford, K. M., Van Opzeeland, I., Harris, D., Samaran, F., Širović, A., et al. (2020). An annotated library of underwater acoustic recordings for testing and training automated algorithms for detecting Antarctic blue and fin whale sounds. doi: 10.26179/5e6056035c01b
  * Miller, B. S., IWC SORP Acoustic Trends Working Group, Kathleen M. Stafford, Ilse Van Opzeeland, Danielle Harris, Flore Samaran, Ana
    Širović, Susannah Buchan, Ken Findlay, Balcazar, N., Nieukirk, S., Leroy, E. C., et al. (2021). An open access dataset for developing automated detectors of Antarctic baleen whale sounds and performance evaluation of two commonly used detectors. Scientific Reports 11, 806. doi: 10.1038/s41598-020-78995-8
  * Schall, E., Kaya, I. I., Debusschere, E., Devos, P., and Parcerisas, C. (2024). Deep learning in marine bioacoustics: a benchmark for
    baleen whale detection. Remote Sens Ecol Conserv n/a, 13pp. doi: 10.1002/rse2.392
  
  > **Comments:**
  > **username_0**: Thank you so much for these references username_4! These are super helpful to my research since we are trying to validate a different Python built detection software and our eventual goal is ML applications but with the North Pacific Fin Whale and ships. I have two of your papers already saved in Mendeley so I knew they were important, but I hadn't made the connection yet (early PhD student here).  
  
  ---
  
  