Digital Bioacoustics

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Welcome to c/DigitalBioacoustics, a unique niche in the vast universe of online forums and digital communities. At its core, bioacoustics is the study of sound in and from living organisms, an intriguing intersection of biology and acoustics. Digital bioacoustics, an extension of this field, involves using technology to capture, analyze, and interpret these biological sounds. This community is dedicated to exploring these fascinating aspects of nature through a digital lens.

As you delve into c/DigitalBioacoustics, you'll notice it's not just another technical forum. This space transcends the usual drone of server rooms or the monotonous tap-tap of keyboards. Here, members engage in a unique fusion of natural wonders and technological prowess. Imagine a world where the rustling of leaves, the chirping of birds, and the mysterious calls of nocturnal creatures meet the precision of digital recording and analysis.

Within this domain, we, the participants, become both observers and participants in an intricate dance. Our mission is to unravel the mysteries of nature's soundtrack, decoding the language of the wild through the lens of science. This journey is not just about data and graphs; it's about connecting with the primal rhythm of life itself.

As you venture deeper, the poetic essence of our community unfolds. Nature's raw concert, from the powerful songs of mating calls to the subtle whispers of predator and prey, creates a tapestry of sounds. We juxtapose these organic melodies with the mechanical beeps and buzzes of our equipment, a reminder of the constant interplay between the natural world and our quest to understand it.

Our community embodies the spirit of curious scientists and nature enthusiasts alike, all drawn to the mystery and majesty of the natural world. In this symphonic melding of science and nature, we discover not just answers, but also new questions and a deeper appreciation for the complex beauty of our planet.

c/DigitalBioacoustics is more than a mere digital gathering place. It's a living, breathing symphony of stories, each note a discovery, each pause a moment of reflection. Here, we celebrate the intricate dance of nature and technology, the joy of discovery, and the enduring quest for understanding in a world filled with both harmony and dissonance.

For those brave enough to explore its depths, c/DigitalBioacoustics offers a journey like no other: a melding of science and art, a discovery of nature's secrets, and a celebration of the eternal dance between the wild and the wired.

Related communities:

https://lemmy.world/c/awwnverts
https://lemmy.world/c/bats
[email protected]
https://lemmy.world/c/birding
https://lemmy.world/c/capybara
https://lemmy.world/c/jellyfish
https://lemmy.world/c/nature
[email protected]
https://lemmy.world/c/opossums
https://lemmy.world/c/raccoons
https://lemmy.world/c/skunks
https://lemmy.world/c/whales

Please let me know if you know of any other related communities or any other links I should add.

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Bioacoustics Resources (self.digitalbioacoustics)
submitted 7 months ago* (last edited 4 months ago) by Haggunenons to c/digitalbioacoustics
 
 

A Collection of Resources related to the field of Digital Bioacoustics




SOFTWARE

Open-source Analytics

BirdVox - In-flight bird vocalization identification
VocalPy - A core package for acoustic communication research in Python
baRulho - an R package to quantify habitat-induced degradation of (animal) acoustic signals
DAS4Whales - a Python package to analyze Distributed Acoustic Sensing (DAS) data for marine bioacoustics
HARKBird - a set of scripts that use HARK for analyzing acoustic interactions among species and their surrounding acoustic environment.
OpenSoundscape (OPSO) - OpenSoundscape (OPSO) is free and open source Python utility library analyzing bioacoustic data.
Parselmouth - Parselmouth is a Python library for the Praat software.
PAMGuard - Open-source software for Passive Acoustic Monitoring
Perch - A bioacoustics research project by Google
Seewave - an R package dedicated to sound analysis and synthesis
SonoScape - SonoScape is a new software to process wav files using a full set of Acoustic Complexity metrics the (ACI metrics (ACIft, ACItf) and derivative indices: ACIft evenness, ACItf evenness, Sonic Signature Dissimilarity (SSD), Ecoacoustic Events (EE), EE Entropy, and Fractal dimensions of EE and SSD), developed under the MATLAB® platform.
warbler.py - a pipeline for segmenting, clustering and visualizing Adelaide's warbler songs
warbleR - is intended to facilitate the analysis of the structure of animal acoustic signals in R.
Whombat - an open-source web-based audio annotation tool designed to facilitate audio data labeling and annotation, with a special focus on aiding machine learning model development.

Open-source Soundscape

AviaNZ - Abundance estimation. The AviaNZ project is a collaboration between mathematicians, data scientists, and conservation biologists, to enable acoustic recordings of birdsong to be turned into reliable estimates of abundance
soundscape_IR- a python-based toolbox of soundscape information retrieval, aiming to assist in the analysis of soundscape recordings. The toolbox is primarily desgined for: (1) visualization of soundscape dynamics and (2) audio source separation.

Open-Source Machine Learning

AVES - (Animal Vocalization Encoder based on Self-Supervision) is a self-supervised, transformer-based audio representation model for encoding animal vocalizations ("BERT for animals")
BioLingual - Transferable Models for bioacoustics with Human Language Supervision. An audio-text model for bioacoustics based on contrastive language-audio pretraining.
soundclim - This repository compiles scripts and modules to search for soundmarks in audio recordings using machine learning.

Open-Source Database Access

rfishbase - interactive and programmatic access to the FishBase repository

Closed-source

Arbimon- Upload and analyze an unlimited amount of audio from your AudioMoth, Song Meter, or other recording device, with our free cloud-based analytical tool.
Avisoft-SASLab Pro - versatile sound analysis, editing, classification and synthesis tool.
Beluga and ARTwarp - MATLAB sound analysis tools
Kaleidoscope - versatile bioacoustics sound analysis tool, available in Pro and Lite, Kaleidoscope helps you more quickly identify species and report on findings.
Raven Pro - Raven Pro is a software program for the acquisition, visualization, measurement, and analysis of sounds. Raven Pro provides a powerful, user-friendly research and teaching tool for scientists working with acoustic signals. Raven Pro’s highly configurable views provide unparalleled flexibility in data display.
Raven Lite - Raven Lite is a free software program that lets users record, save, and visualize sounds as spectrograms and waveforms. Raven Lite is intended for students, educators, and hobbyists, and can be used for learning about sounds, as an aid in birdsong recognition, and in musical instruction.
SigPro - SigPro generates various noise sources or sine waves and plays WAV files at the desired sound pressure levels. Up to 8 independent sources can be generated real time of either pure tones, white, pink, red, full or 1/3 octave band-limited noise. WAV files of any sample rate can be looped to the desired length.

Hardware(Underwater)

Haiku Box - Device for identifying and being notified of different bird species. AURAL-M2The AURAL-M2 ( Autonomous Underwater Recorder for Acoustic Listening) is an underwater recorder used for any application that requires continuous underwater sound recording
HydroMoth - HydroMoth is a variant of the standard AudioMoth specifically designed to be deployed in the underwater case.
SoundTrap 300 series - The SoundTrap 300 series are compact self-contained underwater sound recorders for ocean acoustic research.

Hardware(Terrestrial)

AudioMoth - a low-cost, full-spectrum acoustic logger, based on the Gecko processor range from Silicon Labs. Just like its namesake the moth, AudioMoth can listen at audible frequencies, well into ultrasonic frequencies. It is capable of recording uncompressed audio to microSD card at rates from 8,000 to 384,000 samples per second and can be converted into a full-spectrum USB microphone.
Birdbuddy - AI-powered Smart Bird Feeder. Capture their photos and organize them in a beautiful collection.
Frontierlabs Bar-LT - The BAR-LT is a professional 2 channel audio recorder designed specifically for long term autonomous field deployments.
Wildlife Acoustics Song Meter Line - Passive Acoustic Monitoring Devices

DATASETS

Animal Kingdom - A Large and Diverse Dataset for Animal Behavior Understanding
AnuraSet - A large-scale acoustic multi-label dataset for neotropical anuran call classification in passive acoustic monitoring
AnimalSpeaks - over a million audio-caption pairs holding information on species, vocalization context, and animal behavior
BEANS: Benchmark of Animal Sounds - The Benchmark of Animal Sounds
Egyptian fruit bat calls Prat Et. al. 2017 - An annotated dataset of Egyptian fruit bat vocalizations across varying contexts and during vocal ontogeny
HubBugDB - HumBugDB: A Large-scale Acoustic Mosquito wingbeat Dataset
Ushichka - Bat echolocation data, a multichannel audio-video dataset consisting of between 12-22 microphones and three thermal cameras.
Watkins Marine Mammal Sound Database
Xeno-Canto - Massive bird database, over 10,000 species.

Systema Naturae - massive searchable collection of many different kinds of datasets across many different types of animals

Libraries

BirdNET - BirdNET is a research platform that aims at recognizing birds by sound at scale.
Discovery of Sound in the Sea - Well-organized examples of different kinds of sounds of marine animals
FishSounds Library - a comprehensive, global inventory of fish sound production research. Information can be searched by fish taxa, by sound characteristics, or by reference.
Macaulay Library - it features 150,000 recordings of 9,000 species, including three-quarters of all known birds to science.
MNHN - Large collection of birds sounds from Muséum National d'Histoire naturelle
MorphoSource - Find, view, and download 3D data representing the world's natural history, cultural heritage, and scientific collections.

Citizen Scientist Programs

Observations.be - the largest nature platform in the Netherlands and Belgium.
Happywhale - Happywhale engages citizen scientists to identify individual marine mammals, for fun and for science
eBird - eBird is among the world’s largest biodiversity-related science projects, with more than 100 million bird sightings contributed annually by eBirders around the world
Flukebook - Flukebook applies computer vision algorithms and deep learning to identify and track individual whales and dolphins across hundreds of thousands of photos. We help researchers collaborate with each other and citizen scientists contribute to the effort. A.I. scales and speeds research and conservation.

Live-streamed bioacoustics

Streaming audio from the ALOHA Cabled Observatory
Locus Sonus
Rainforest Connection Apple App

Live-streamed other

Smithsonian’s Naked Mole Rat cam

Online Forums

Bioacoustics Stack Exchange - Bioacoustics Stack Exchange is a question and answer site for people interested in the studies of non-human animal sounds and the impacts of sounds on animals. It only takes a minute to sign up.
Earth Species Project Discord - Join the dynamic and growing online conversation around interspecies communication!

Conferences

Detection, Classification, Localisation and Density Estimation (DCLDE) of marine mammals - Spring 2024 in Rotterdam, Netherlands
5th World Ecoacoustics Congress - July 8-12 in Madrid, Spain
The African Bioacoustics Community - Fall 2024 in Cape Town, SA
IBAC - 2025 in Denmark

Organizations

The African Bioacoustics Community - Bioacoustic research from Africa and by African scientists is not well represented in the global field and thus the African Bioacoustics Community strives to shine a light on the achievements of bioacoustics research in Africa.
BDFFP - The Biological Dynamics of Forest Fragments Project
Earth Species Project - Earth Species Project is a non-profit dedicated to using artificial intelligence to decode non-human communication.
IBAC - The International Bioacoustics Society
Rainforest Connection - Rainforest Connection (RFCx) builds and deploys scalable, open acoustic monitoring systems that can halt illegal logging and poaching, and can enable biodiversity measurement and monitoring.
Robots4Whales - We monitor the presence of marine mammals from ocean-going robots using the sounds the animals make.

I'm sure there is so much that I have missed, so if you know of anything that belongs in here, please let me know and I'll get it added!

Edits:

02/07/24 - Haiku Box, Birdvox
02/05/24 - VocalPy
11/07/23 - BioLingual, AnimalSpeaks
11/09/23 - Discovery of Sound in the Sea, Macaulay Library
11/12/23 - Smithsonian's Naked Mole Rat cam, observations.be
11/25/23 - FishSounds Library

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cross-posted from: https://lemmy.ml/post/16392398

Barn Owl Sounds & What Each Call Means

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I've got another study on owl hearing for those of you who have enjoyed some of my past articles. This one looks at the ability of birds to regrow the tiny hairs responsible for mechanoelectrical transduction of soundwaves to nerve impulses and its contribution to preventing age related hearing loss.

cross-posted from: https://lemmy.world/post/16024126

This summary is of "Barn owls have ageless ears," by Bianca Krumm, Georg Klump, Christine Köppl, and Ulrike Langemann (2017). This is my best interpretation of their study and findings. I'm not a scientist, just a hobbyist, so feel free to browse the source provided and correct me if I've gotten anything incorrect.

Time for another look at another amazing bit of owl research!

In this paper, the researchers looked into owls as creatures with amazing hearing, to see how their hearing changes with age. I will go over some of their testing and findings to try to break down what they did and what was learned. As always, this is not my area of expertise, so if you do understand this well and are curious, please take a look at the full paper and fill me in on what I misunderstood.

The National Council on Aging says that 1/3 of people ages 65-74 and 1/2 of those 75 and older suffer from hearing loss. Mammals as a whole suffer from presbycusis, age related hearing loss due to changes in the inner ear structures. Birds, while having different, but functionally similar ear structures, do not seem to suffer from these effects.

Mammalian presbycusis is associated with progressive damage to the loss of hair cells inside the corti, an organ of the cochlea, the spiral shaped part of your inner ear. This is a very small structure, so I’ve included a picture of the cochlea, a picture of the tiny hairs we’ll be discussing, and a 3D printed cochlea to give a size perspective. I then also have a Barn Owl cochlea picture.

These tiny hairs are responsible for mechanoelectrical transduction of sound. That is a process that turns vibrational energy from sound waves into an electrical signal in the nerves of the cochlea which your brain can interpret as sound. Click this link for a brief article on mechanoelectrical transduction.

Humans and most mammals have partial regeneration of the hair cells of the inner ear, but they cannot replace these sound sensing hairs in the cochlea. Some other vertebrates, birds in particular, have been studied for some time as they can regenerate their basilar papillae, the structure in birds that serves the same purpose as the corti do in mammals.

Prior studies of the basilar papillae have shown amazing regenerative properties of the sensory hairs. Many species have been looked at showing a lack of age-related damage, and even in experiments where chemicals were applied directly to damage the hair cells experienced very quick recovery and growth of new hairs. As long as the hair growing cells themselves are not damaged, the hairs can grow back when damaged from age or by physical trauma.

Most hearing loss in mammals occurs at higher frequencies. Prior studies of their range of sounds they can hear had shown Barn Owls are able to hear sounds between 200 Hz – 12 kHz. The higher 12kHz is higher than most other birds can hear, so the Barn Owl became a great candidate species to study presbycusis. The Barn Owl’s has a specialized cochlea with one of the longest basilar papilla of any bird. Low frequency hearing appears to be similar to many other birds, but there were numerous differences to the inner ear to better process mid to high frequencies.

I was happy to learn we had names and backstories to our test subjects this time! They were all Common Barn Owls, Tyto alba, the most widespread owl in the world. The group of young owl, aged >2 years, consisted of Ugle, Sova, Grün, and Rot, and the old owls, aged 13 and 17, were Bart and Lisa, along with a third owl, Weiss. Most of them were hatched at German universities, but I’m thinking Bart and Lisa may have come from somewhere else, as I imagine this can only be a Simpsons reference as they were born in the 90s.

Experiments were conducted in two sound-deadened chambers. In the chambers, there was a starting perch and a target perch on the opposing side. A speaker was placed directly behind the target perch. There was a video camera to monitor the birds’ activity, and an automatic feeder near the target perch.

The owls were trained to sit on the starting perch facing the target. After a random time of 1-30 seconds, the owl was played a test signal over the speaker. Test frequencies of frequencies of 0.5, 1, 2, 4, 6.3, 8, 10, and 12 kHz were used. The owl knew a sound indicated a tasty snack was available and would fly over to get its reward. After the test signal was played, if the owl flew to the target immediately (within 5 or 10 seconds) it was taken as the owl had heard the auditory signal. In total, 99% of trials had a positive response occurring within 5 seconds upon hearing the test sound. “Catch trials” were done in 20-30% of all trials where no tone was played to ensure there was no movement to the target perch when no sound was played. If there were more than 20% false flights to the target perch, that trial was excluded from the results. Results were also excluded if the 2 loudest sounds did not receive strikes in 80% of the times they were played. I imagine this was to rule out the owl either being too eager to land at the “food perch” or if the owl was in a bad mood and didn’t want to fly to the target perch.

The results showed that neither age or physical damage to the hairs themselves much affected the regeneration process. The one owl, Weiss, was observed over a period of 21 years (at 2, 17, 23 years old) and only lost the smallest bit of hearing at the very high frequency range.

Both age ranges had the best hearing between 2 and 8 kHz. At 0.5, 1.0, and 6.3 kHZ the hearing ability of the older owls was slightly better than the younger group. At the other remaining frequencies, the younger group did better, but not by enough to be statistically significant.

The line for Konishi in the above graph are results obtained from a test in the 1970’s in Japan that was done to replicate the results of owls being able to hunt in total darkness using sound that I wrote about in the summary of Payne’s testing, which can be found here. Results were comparable, but that was only testing of a single owl, and it was a different species of Barn Owl than the ones in this experiment.

Here is the lifetime data for Weiss. Initial testing was done at 18-22 months old, when owl hearing finished developing. He was tasted again in these 2 rounds of experiments at ages 17 and 23. While there was some loss of very high frequency hearing over time, at the 12 kHZ range. The other frequencies showed slight deterioration, but only by a few decibels, so they interpreted that as a change in hearing more than actual deterioration.

The change was even less significant between ages 17-23, with some frequency responses seeming to have improved a tiny bit. As most wild Barn Owls do not live more than 3 or 4 years, this shows that over even an owl’s maximum expectant lifespan, there is no significant deterioration of hearing quality in a way that would negatively impact them.

Typical age-related hearing loss in mammals leads to a threshold (range of volumes and frequencies they can hear) increase of 20-40 decibels, while even over the course of a very long-lived owl’s life, the increase was only 4-10 decibels. While many owls die early, this shows it is not due to hearing degradation related issues. While the majority do not live longer than 3-4 years, it is not rare to find ones 10-20 years of age.

While younger owls were as a group more sensitive to sound that the old owls, it was by less than 3 decibels different in threshold. Overall statistical testing showed no significant difference in hearing ability between the two groups.

Other experiments over the years have shown pigeons, chickens, finches, budgies, European starlings, quails, and more have all been able to regrow hairs of the basilar papilla removed chemically in about 4-6 weeks with no significant loss in original hearing ability. Physical damage to the hairs by acoustic trauma (hitting them with high pressure sound waves to break them by vibration) yielded very similar regrowth and regaining of hearing to a remarkable degree.

The ability to regrow these hairs seems to be key to this amazing ability of birds as had been previously hypothesized due to testing on some of those other birds. Further study of this process will hopefully help us to find treatments to help us in the future to treat this widespread issue of humankind. While most of us will eventually suffer from some extent of hearing loss, it is something most birds will never have to deal with, no matter how long they live. Hopefully in the future, we will learn their secret and share in the joy of a long life full of vibrant sound.

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African savannah elephants (Loxodonta africana) are the world's largest living land-based animals, reaching a height between 10 and 13 feet (roughly 3 to 4 meters) and weighing between 4 to 7 tons. One in particular, Doma, is the most dominant male in his group. Yet he seems to have developed this superiority as much through charisma and kindness as from sheer girth. All the other elephants in his herd run to him at the first sign of trouble; during calmer times, they willingly present him with their rumps in a seeming sign of submission...

Via @jeffw

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cross-posted from: https://lemmy.world/post/15757735

I was reading more about owl vocalizations and had a hard time making much of the actual research paper as I don't know much about statistics or acoustics. I think I got the jist of it, but this is probably more informative for you than it is for me, so I thought I'd share the post with you.

I'm sure things like this are being used in projects like BirdNET-Pi and in ongoing research.

Post based on: The assessment of biases in the acoustic discrimination of individuals Pavel Linhart (2017)

Owl live lives that are largely based on sound. This lets them have an almost omniscient view of the world around them. Being able to hear their world from a distance lets them stay in one location, allowing them to stay safely hidden while not having to fly around expending crucial energy to monitor their territories.

Pavel Linhart of the University of South Bohemia has studied many animal vocalizations to try and understand all the things they are able to communicate. Sound samples of animals are recorded, analyzed, and characteristics are removed with an algorithm to determine the contents of the animal’s message. These messages can contain body size, emotional states, and the identity of individuals among other things. Little Owls made a great species for Linhart to study. They live close together, do not migrate, and stay in a relatively small range, making them easy to work with.

The sounds are looked at by duration, frequency, and “colorations,” which seem to be small changes to basic calls. These differences can be analyzed and used to help determine both the number of individuals in a population, but also who those individuals are, with the goal being to allow individual monitoring through sound, basically being able to see the sounds of owl (or other animals) the way the owls themselves do; to know who is where and doing what.

One of the key takeaways from his research is that variations between individuals grow along with the density of the owl population. The conclusion drawn is there are benefits from having uniquely distinct sound signatures for individuals. Owls can communicate their presence to others and be identified as known owls, saving them the energy of investigating potential intruders to their territory. Owl calls do not change much over time, so even if they only encounter each other once a year for mating season, they can identify each other over great distance, year after year. There is also benefit to researchers, as it brings them closer to being able to use those same sounds to monitor individual animals using recorded sound.

To demonstrate some of the variations between individuals, Linhart has also published a Little Owl Match Game. There are 16 “cards,” each containing a recording of a Little Owl (and some simulated owls) for you to try to successfully match the calls as if you where the algorithm trying to match the sound to a known individual. You can play the game here.

In a related story, researcher Karla Bloem was studying Great Horned Owl calls when she met Baroque music specialist Marjon Savelsberg, who fell in love with the sounds of owl calls and became a virtual assistant volunteering to try to pick out individual owls by their vocalizations.

Her musical training made her very successful to pick out these individual variations between individual calls. She is now using her abilities to work with Eurasian Eagle Owls in her native Netherlands.

Savelsberg with a baby Eagle Owl

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