rhine3 / bioacoustics-software Goto Github PK

Name: Deepsqueak

A Matlab package

https://github.com/DrCoffey/DeepSqueak

Open Source

As discussed in #1 - it would be great to create a filterable website (and possibly an automatically updated README?) for the bioacoustics software list. @NickleDave suggested potentially basing this off of the system that @vsoch used to create the Research Software Encyclopedia.

Hi @rhine3 thank you again for putting together this great resource

• Wanted to ask if you'd accept a PR adding tweetynet?
  https://github.com/yardencsGitHub/tweetynet

The model both segments and classifies the segments -- diff't people have diff't schema but I think on the README it would make sense under classification

• Also wanted to ask about changing the links to crowsetta and vak -- we set up a GitHub org so they live here now: https://github.com/vocalpy
  Again I'm happy to make a quick pull request to change them just to save you the effort

Last thing: very minor but I don't think AVA does detection or segmenting per se? (You have it under "detection"). I say this because they used tweetynet with vak to do some of the segmenting (see methods of eLife paper). The main goal of AVA as I understand it is to do dimensionality reduction by mapping existing sounds/segments to a latent space with fewer dimensions. Similar (but not the same) as models from Tim Sainburg (https://github.com/timsainb/avgn_paper). Maybe you could consider adding a section like "Unsupervised / clustering / dimensionality reduction"?

Add the following:

• Pykanto: https://arxiv.org/pdf/2302.10340v1.pdf
• Nighthawk: https://github.com/bmvandoren/Nighthawk/
• pypam: https://github.com/lifewatch/pypam for long-term underwater acoustics data visualization, focused on ML for bioacoustics
• pyporcc: https://github.com/lifewatch/pyporcc a python version of the PAMGuard click detector, together with a published click classifier
• a collection of jupyter notebooks to categorize soundscapes in an unsupervised way: https://github.com/lifewatch/categorizing_soundscapes/tree/main
• https://github.com/earthspecies/aves (and maybe other packages from ESP? https://github.com/earthspecies)
• https://github.com/earthspecies/cocktail-party-problem
• https://git-dev.cs.dal.ca/meridian/NARW_detection_tool
• https://bitbucket.org/CLO-BRP/manta-wiki/wiki/Home
• https://github.com/schonkopf/soundscape_IR
• https://ecosound-web.de/ecosound_web/
• Detector and Classifier https://github.com/htleblond/PAMGuardMIRRF
• Revision tool for hourly detection SoundScope: https://github.com/xaviermouy/SoundScope
• Tethys: https://tethys.sdsu.edu/ detections and metadata management, also good for exploring detections
• DAS data processing https://github.com/leabouffaut/DAS4Whales
• Some guidelines for people starting with python: https://github.com/leabouffaut/bioacoustics_python
• ENSTA-Bretagne annotation tool: https://github.com/Project-OSmOSE/osmose-app/tree/1.8.3
• https://github.com/david-rx/BioLingual
• General: add a column in the excel sheet which indicates ecosystem the software is suitable for (Marine/Terrestrial/Both)

Make this document easier to cite using a DOI and Zenodo versioning

https://synergy.st-andrews.ac.uk/soundanalysis/ is a dead link.

The new page is:
https://soundanalysis.wp.st-andrews.ac.uk/

Thanks for the work done! Very useful compilation.

Do you think our packages (under development) would meet the criteria to be on this list?
pypam: https://github.com/lifewatch/pypam for long-term underwater acoustics data visualization, focused on ML for bioacoustics
pyporcc: https://github.com/lifewatch/pyporcc a python version of the PAMGuard click detector, together with a published click classifier

We also published a collection of jupyter notebooks to categorize soundscapes in an unsupervised way:
https://github.com/lifewatch/categorizing_soundscapes/tree/main

Furthermore, not ours but maybe also interesting:
https://github.com/earthspecies/aves (and maybe other packages from ESP? https://github.com/earthspecies)
https://github.com/earthspecies/cocktail-party-problem
https://git-dev.cs.dal.ca/meridian/NARW_detection_tool
https://bitbucket.org/CLO-BRP/manta-wiki/wiki/Home
https://github.com/schonkopf/soundscape_IR
https://github.com/kitzeslab/opensoundscape

Thank you!