Resarch projects

Below you will find a short description of research projects that I have conducted and been part of. Some are done and others are currently ongoing (marked with an asterix). The research involving crows were all done during my Ph.D. work (dissertion summary), and the rest post doctoral work or independent work. At the end of each section there's a reference to where the work has been published or presented.

Just a brief description of each research project is given, but if you have special interest in any topic feel free to contact me and I'll be more than happy to give you more information or take part in a discussion. Under the "LINKS" navigation link above I have listed the names and affiliation of people that have all been a significant part of the work. Righ below this paragraph there is an index that link to the various subjects that can be found further below. You can either click on the links or just scroll down the page.

I'm still however, working on improving this page, so please check back in the future, or contact me if there is something you have an interest in that has only a sketchy treatment. Thank you.

INDEX:

Hearing in Humans

Modeling of speech intelligibility in fluctuating maskers*

Orientation and Navigation in Animals

Computational model on light dependent orientation responses in animals

Software programming

Note: the links below will take you to a web page for the software and not to a description of it below like the other links

GroundCalc

Software for calculating excess attenuation due to the the acoustic ground effect incl turbulence and atmopheric attenuation.

Animal Acoustic Communication Prediction Software*

Software for predicting acoustic communication conditions for animals aiming to be a tool in conservation biology to assess the impuct of human made noise.

Sound Analysis for X-ray recordings

Software made for frame by frame analysis of sound recorded in connection with X-ray cinematography.

Acoustic Communication in Birds & Other Animals

Hearing

Effect of skull air cavities on avian hearing*

Hearing of the hooded crow

Hearing threshold

Critical ratios

Co-modulation detection differences

Acoustic brainstem responses*

Effect of AM and FM on harmonic complex detection in zebra finches

Sound production

Crows produce their call with a human like vocal register

Cardinals use their tongue to shape their song*

Cardinals use auditory feedback to control beak gape*

Bengalese finches use auditory feedback to control beak and larynx projection during song*

3D reconstruction of the songbird syrinx*

Sound production in frogs*

Sound transmission

The animal acoustic communication prediction software project*

Measurements and prediction of hooded crow calls

Elk call transmission in a North American and European habitat*

Modeling of speech intelligibility in fluctuating maskers*

This is the work I am performing during my current post doc under Dr. Joshua Bernstein at the Walter Reed National Military Medical Center in Bethesda, MD, USA. It's about understanding some of the processes behind hearing speech in noisy conditions, which especially hearing impaired has trouble with. Specifically I am working with a model of the Speech Intelligibility Index, a model that predicts how well people are going to be able to hear speech in a given noisy environment (could for instance be announcements at the train station). The model was extended to work with fluctuating maskers by Rhebergen and Versfeld (2005), which have improved speech intelligibility prediction greatly, but it still fails when the interfering masker is speech (i.e. another person that the target person talking). I have come up with a further model extention that (without giving details) is based on a picket fence effect and account for factors at the "micro level" of speech parception, namely the likelihood of perception of each phoneme of a word. So far, the model fits the real the classic data of Miller and Licklider (1950) very well.

Jensen, K. K. & Bernstein, J. (2012) Talk given at the AAS Meeting in Arizona, March 8-10, 2012.

Jensen, K. K. & Bernstein, J. Manuscript in prep.

Computational model on light dependent orientation responses in animals

The magnetic compass sense of animals is currently thought to be based on light-dependent processes like the proposed radical pair mechanism. In accordance, many animals show orientation responses that depend on light. However, the orientation responses depend on the wavelength and irradiance of monochromatic light in rather complex ways that cannot be explained directly by the radical pair mechanism.

I have constructed a radically different model that can explain a vast majority of the complex observed light-dependent responses. The model put forward an integration process consisting of simple lateral inhibition between a normal functioning, light-independent magnetic compass (e.g. magnetite based) and a vision based skylight color gradient compass that misperceives compass cues in monochromatic light.

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When birds are placed in monochromatic light their normal preferred compass orientation can change even though they are perfectly able to see (Redstart (Phoenicurus phoenicurus))

Integration of the misperceived color compass cue and the normal magnetic compass not only explains most of the categorically different light-dependent orientation responses, but also shows a surprisingly good fit to how well the animals are oriented (r-values) under light of different wavelength and irradiance. The model parsimoniously suggests the existence of a single magnetic sense in birds (probably based on magnetic crystals).

Invited talk: Jensen, K. K. (2012) A model of multimodal integration to explain complex responses to monochromatic light. IVth European Conference on Behavioural Biology, Essen, Germany, July 19-22.

Jensen, K. K. (2010) Light-dependent orientation responses in animals can be explained by a model of compass cue integration. Journal of Theoretical Biology 262 129-141. doi:10.1016/j.jtbi.2009.09.005.

Jensen, K. K. (2000) Redstarts (Phoenicurus phoenicurus) seem able to orient by the magnetic field under red light. 28^th Göttingen Neurobiology Conference, Göttingen, Germany.

Hearing

Hearing of the hooded crow

All the hearing measurements were done by psychoacoustic measurements in a setup I build myself from scratch including building the sound proof boxes & programmed custom software to run the experiments automatically. Some info on the psychoacoustic method and a video of a crow operating the test panel can be found here.

Hearing threshold

The hearing threshold and critical ratios were estimated psycho-acoustically for captive wild-caught hooded crows by a yes/no procedure and the method of constant stimuli. Human subjects were tested in the same setup for direct comparison and to check for experimental artifacts.

The hooded crows were found to have excellent low-frequency hearing capabilities compared to other passerine birds. Their hearing sensitivity is very close to that of humans at and below 5.6 kHz (see figure below)

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Critical ratios

The distribution of the critical ratios differed from that of the average bird and humans in being rather constant with frequency and not increasing monotonically. It furthermore showed a middle region of 5–6 dB lower critical ratio values between 500 Hz and 2 kHz.

It is suggested that this improved range for hearing in noise is an adaptation to long distance communication. Human critical ratios gave the expected values and were between 3 and 6 dB lower than those of the crows (see figure below).

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Jensen, K. K. & Klokker, S. (2006) Hearing sensitivity and critical ratios of hooded crows (Corvus corone cornix). Journal of the Acoustical Society of America 119 (2) 1269 - 1276.

Co-modulation detection differences

In hearing science masking is the process or amount by which the audibility threshold of one sound is raised by the presence of another masking sound (ASA 1969). The masking sound is often referred to as the masker.

Envelope modulations have shown to be a very important factor in the effectiveness of masking noises. One example of this is in the co-modulation detection difference (CDD) where the signal is easier to detect when flanking maskers are modulated differently in envelope amplitude from the signal in comparison to when not.

One of the reasons for performing this experiment was that the natural situation in which a crow detects other crow calls share similarities to the typical CDD setup. In the natural situation a crow calls are flanked especially by low frequency noises (see fig. 1 below). The low frequency noise can be modulated in amplitude by atmospheric turbulence in one way and the crow call in another since it is inherently modulated in amplitude at the source.

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Figure 1: Average power spectrum of hooded crow calls embedded in natural noise (N=7). The part of the power spectrum showing the calls are indicated by the “calls” label in the figure. The “masking?” label is indicating possible masking from low frequency noise. Modulation of the noise by e.g. atmospheric turbulence and natural, source generated modulations of the crow calls may share properties of the typical CDD setup and cause a natural CDD effect. [Crow calls were recorded in open field habitats near Løkken, Denmark at distances above 300 m using a Sony DAT recorder (TCD-D10 Pro) and a hand held Beyer Dynamics shotgun microphone (MC737 PV)].

CDDs were measured in two wild caught hooded crows with the signal at 1.5 kHz and two maskers at 900 Hz and 2.1 kHz, respectively, presented with an overall level of 55 dB SPL (re 20 μPa).

As direct comparison three human subjects were tested in the same setup. CDDs were in this condition on average 14.8 dB for the two crow subjects and 10.8 for the human subjects (see the results presented in fig. 2 below). Although the average crow CDD was larger than the human, the number of subjects was too few to conclude any statistical difference and crow and human CDDs probably does not differ.

Thus is it concluded that the CDD does occur in hooded crows and that it is not different from that observed in humans. It is therefore possible that hooded crows take advantage of this ability when they are trying to hear out faint crow call by far away senders. A reduction in threshold of 14.8 dB is very significant as will certainly prove handy in a natural detection situation in a noisy environment.

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Figure 2: Individual thresholds and co-modulation detection differences (CDD) for the two crows (SP and CO) and for the three human subjects (KKJ, CB, and SK). The signal to be detected was a 20 Hz wide noise centered at 1.5 kHz (3 dB BW). The signal was masked by two similar flanking noises centered at 0.9 and 2.1 kHz respectively with an overall level of 50 dB SPL (re 20 mPa). A 400 Hz low pass Gaussian noise was added at a power spectrum level of 28 dB SPL (re 20 mPa2) to mask potentially disturbing combination tones. “Correlated” indicates thresholds when the signal and the two maskers were modulated coherently and “Uncorrelated” when the signal and maskers were modulated incoherently. The CDD is the threshold differences between the uncorrelated and correlated thresholds. Error bars are standard deviations.

Jensen, K. K. (2007) Co-modulation detection differences in the hooded crow (Corvus corone cornix), with direct comparison to human subjects. Journal of the Acoustical Society of America 121 (3) 1783 - 1789.

Acoustic brainstem responses*

Acoustic brainstem responses (ABR) is a technique where electrodes are placed certain places on the scalp of animals (or humans) and the electric responses of neural auditory pathways and brain nuclei to played back sounds can be registered. Beth Brittan-Powell, Robert Dooling, Ole Næsbye Larsen, and I studied the ABR in the hooded crow for comparison to the hearing tested by behavioral means (see above).

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A hooded crow is taken out of the test chamber (left). The setup is being put together (right). A loudspeaker is playing back short pulses of sound (left). A set of three electrodes connected to an amplifier (right) and a Tucker-Davis III system (not visible) are placed different places on the scalp of a deeply sedated crow that is laid on some acoustic foam close to the electrode amplifier. When playing back sounds from the loudspeaker we can register how the crow brain response to the sounds. This is a fast way to assess the hearing abilities of animals, which usually are done by tedious and time consuming behavioral test (see above).

The acoustic brainstem response (ABR) in the hooded crow showed an interesting pattern (see figure below). In comparison to the behavioural hearing threshold (green trace; THR) the ABR threshold (red trace; ABR) showed an apparent cut-off in sensitivity around 2 kHz towards lower frequencies.

This cut-off occur just as it enters the region of low critical ratios (CR) (> 500 Hz to < 2 kHz; blue trace; CR). Actually, simple subtraction of the critical ratios from the behavioral hearing threshold (THR - CR + 45 dB) nearly reproduces the ABR threshold (see figure below). Thus the ABR mirrors apparently not only the behavioral threshold, but a combination of that and the critical ratios.

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Brittan-Powell, E., Jensen, K. K., Dooling, R. & Larsen, N. Manuscript in prep.

Effect of AM and FM on harmonic complex detection in zebra finches

Phenomena like for instance detection of harmonic complexes (Buus 1985) but perhaps especially co-modulation masking release (CMR) in both birds and humans point to some degree of integration of information between auditory filters (see e.g. Klump & Langemann 1995; Verhey, Pressnitzer, et al. 2003; Hofer & Klump 2003).

In CMR it is seemingly the coherent envelope modulations across maskers that enable correlation of information in different auditory filters and allow them to integrate across filters. Based upon this I speculated that the modulations coherent across frequencies of crow calls might allow auditory filters to integrate signal information and thus facilitate detection of the calls.

During a stay in Professor Robert J. Dooling's lab I used zebra finches as an initial model. Like crows, zebra finches also use broad band harmonic calls. The birds were tested with harmonic complexes with a fundamental frequency (F0) of 500 Hz and with all the harmonics up to 5 kHz which is comparable to natural zebra finch calls (see e.g. Lohr, Wright, et al. 2003).

The whole complex was either (a) un-modulated, (b) amplitude modulated (modulation frequency = 75 Hz; modulation index = 0.75), (c) frequency modulated (modulation frequency = 75 Hz; frequency deviation = 100 Hz * harmonic number such that the fundamental would be modulated by ±50 Hz, the second harmonic by ±100 Hz, etc., as would be the case if the fundamental of a harmonic sound would modulate in frequency, or finally (d) both amplitude and frequency modulated.

The modulations were approximated those measured in hooded crow calls. The results pointed to a possible effect of frequency modulations on detectability, but apparently none of amplitude modulations. However, the design turned out to be inappropriate and the results are only weakly indicative. A re-designed experimental series, preferably on crows, is necessary to confirm the effect.

See chapter 6 in: Jensen, K. K. (2005) Acoustic communication in the hooded crow (Corvus corone cornix). Ph.D. Thesis, University of Southern Denmark.

Effect of skull air cavities on avian hearing (supported by a grant from Oticon)*

Through careful dissections I discovered that the skull of most birds (left panel in figure below) have an intricate system of interconnected air cavities and tubes that communicates with the ears (colored structures in right figure below). The existance of the inter-aural canal (pink) has been known for years, but the complex system illustrated below has to my knowledge never been described.

It seems likely that such a system of air cavities and tubes in such close communication with the ears and inter-aural canal will affect the hearing of the bird somehow. Perhaps it can enhance the important effect the inter-aural canal is already known to have on the birds' ability to hear the direction of the incoming sounds.

Ole Naesbye Larsen, Jacob Christensen-Dalsgaard, Rod Suthers, Neville Fletcher, and I are therefore studying the possible acoustic effect of this system. We have made laser vibrometric measurements of the ear drums before and after blocking parts of the air cavity system to test if the directional sensitivity and sensitivity in general of the ears would be affected by the air cavity system.

The figure show a 3D reconstruction of the system which has been created out from micro-CT scans of zebra finch heads. From those scans we are also working on making a 3D print in plastic of the system to provide a enlarged model that can be taken apart and makes it easy to make further acoustic measurements. We are furthermore working on a theoretical physical model of the sytem as well, which is performed by renowned physicist Professor Neville Fletcher.

Jensen, K. K., Christensen-Dalsgaard, C., Suthers, R. A., & Larsen, O. N. (2010) A newly discovered superoantero-orbital sinus connecting to the interaural canal may play a role in zebra finch hearing. 9th International Congress of Neuroethology, Salamanca, Spain, August 2nd - August 7th.

Sound production

Crows produce their call with a human like vocal register

Dr. Ole Næsbye Larsen (University of Southern Denmark, DK), Dr. Brenton Cooper, Dr. Franz Goller (both at University of Utah, US) and I have worked on the dynamics of the crow syrinx during phonation. Crows has a special modulated, complex broad band call which has caught my interest both in the matter of how they generate such calls, and what, if any, the functional significance of it is (see below).

This was studied by coupling a high-speed camera to clinically used angioscopes that fit down the narrow song bird trachea, a technique that Drs. Ole Næsbye Larsen and Franz Goller developed (Goller & Larsen, 1997). Together we refined the technique by applying laser light illumination and gamma correction of the video recordings making high-speed recordings up to 1000 fps possible for the first time in the study of song bird vocal production dynamics.

We found that they use a vocal register similar to one in humans often referred to as pulsed phonation and vocal fry. We furthermore found indirect evidence of the use of such a vocal register in other song birds during low frequency phonations suggesting that birds use this type of phonation in their lowest frequency range of their vocalizations as is the case in humans. To the right you can find a movie illustrating the sound production in crows and other songbirds.

Jensen, K. K., Cooper, B. G., Larsen, O. N., & Goller, F. (2007) Songbirds use pulse tone register in two voices to generate low-frequency sound. Proceedings of the Royal Society B, 274 (1626) 2703 - 2710.

Larsen ON, Jensen K. K. and Goller F (2006): Pulse register phonation in crows revealed with high-speed video endoscopy. Proceedings of the 5^th International Conference on Voice Physiology and Biomechanics, Tokyo, Japan p. 127-128.

Larsen, O. N., Jensen, K. K., & Goller, F. (2004) High-speed video recording of labial movement during bird phonation. 7^th congress of the international society for neuroethology (ICN), Nyborg, Denmark.

Cardinals use their tongue to shape their song*

Here we have used X-ray cinematography to film cardinals while singing with a metal marker in their tongue. With motion analysis software we have measured the use of the tongue during song in relation to the vocalizations produced.

Suthers, R.A. & Jensen, K. K. Manuscript in prep.

Cardinals use auditory feedback to control beak gape*

X-ray cinematography was used to film cardinals during song. The cardinals were either singing in normal air or in heliox (20% oxygen and 80% helium). The speed of sound is higher in heliox which changes the resonance properties of the vocal tract upwards in frequency (Mickey Mouse voice). With motion analysis software we measured the movement of different parts of the vocal tract to see if the birds were using auditory feedback to configure the vocal tract like humans does. It turned out that they appeared to lower the beak gape when singing in heliox compared to air which suggest that they are in fact actively using auditory feedback during song. Songbirds are important models for human vocal learning and the observation that songbirds use auditory feedback to control the vocal tract is therefore and important one.

Jensen, K. K. & Suthers, R. A. (2008) Real-time compensation for formant changes by beak gape in a songbird. Acoustic Communication by Animals, Corvallis, Oregon, USA.

Jensen, K. K. & Suthers, R. A. Manuscript in prep

Bengalese finches use auditory feedback to control beak and larynx projection during song*

This work was mainly conducted by Dr. Charlotte Cure. In the experiments bengalese finches were deafened and their responses seem to confirm that songbirds depend on real time auditory feedback to control the configuration of their vocal tracts during song (see above).

Cure, C., Jensen, K. K. & Suthers, R. A. Manuscript in prep

3D reconstruction of the songbird syrinx*

Songbirds are important animal models for human vocal learning. The vocal apparatus is the ultimate target for learned vocalizations and therefore knowledge about the songbird vocal apparatus, the syrinx, is important.

We reconstructed in 3D the brown thrasher (Toxostoma rufum) syrinx from both histological sections and micro-CT scannings of brown thrasher syringes. The 3D reconstruction allowed deductions about the biomechanical function of some of the muscles and the small cartilageous bones.

Jensen, K. K., Zollinger, S., Childress, S., Larsen, O. N., & Suthers, R. A. (2008) Anatomy and vibratory dynamics in the songbird syrinx. Acoustic Communication by Animals, Corvallis, Oregon, USA.

Jensen, K. K., Zollinger, S., Childress, S., Larsen, O. N., & Suthers, R. A. Manuscript in prep.

Sound production in frogs*

To be described...

Sound transmission

The animal acoustic communication prediction software project*

This is a project that aims at developing software that can be used as a tool in animal conservation to assess the potential impact of (usually) generated noise on wildlife acoustic communication. Acoustic communication is essential in many animals for upholding their territory and attracting mates. Without it or if it is significantly disturbed by noise animals are likely to be impacted. The software integrates data and knowledge of animal hearing and vocal production with physical models on sound propagation to estimate the distance over which the animals are able to communicate with each other under normal circumstances and how noise will impact and diminish communication.

The web page for the project with possibility to download the software can be found here.

Software beta version presented in a talk by Ole Næsbye Larsen titled "Environmental Acoustics -Basic Principles" given at the XXIII Meeting of the International Bioacoustics Council, La Rochelle, France, 13-09-2011.

Measurements and prediction of hooded crow calls

The environment that birds and other animals live in is just as important in shaping their vocal behavior as is for instance sound production constraints, hearing abilities, and predator or sexual selection. Many animals have large territories between which they for instance communicate with neighbors or they forage in large flocks spread over a large area.

Small songbirds communicate typically between territories over moderate distances of perhaps 50 - 150 m, and larger birds or smaller mammals communicate typically over rather long distances of perhaps 500 - 1000 m, which obviously attenuates the sounds quite a bit. In addition to this, the receiving animal has to detect the vocal signals in the ever present noise resulting from other birds or animals, the wind whistling in the trees, or as it is nowadays, urban and traffic noise.

Crows are excellent examples of animals coping with communication over longer distances. Together with Dr. Ole Næsbye Larsen (University of Southern Denmark, DK) and Prof. Keith Attenborough (University of Hull, UK) I have thus studied the physical aspects of sound propagation over open field habitats and its impact on hooded crow long distance communication. The study is the first to introduce the powerful tool of sound propagation modeling developed by acoustic engineers to animal communication. This was done as a very fruitful, interdisciplinary study with the acknowledged physical and engineering acoustician Prof. Keith Attenborough.

Together we continue to fuse hearing science and neurobiology with acoustic modeling to explore and develop modeling techniques as tools for studying and evaluating animal communication. This includes for instance tools for evaluating the impact of human noise on animal communication.

The crow study involves field measurements of sound propagation, sound propagation modeling, and estimation of hooded crow active space found to be approximately 1 km.

One interesting finding and demonstration of the power of sound propagation modeling was the estimation of the general, inter-territorial "sound window".

A sound window is defined as the optimal propagated frequency range across a habitat or distance and constitutes a "window" within which acoustic communication is most favorable.

The crow sound window, which we call the "active matrix", was evaluated by the model by taking a number of sender and receiver heights and separations representing typical crow inter-territorial communication.

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The results indicated that crow hearing is specially adapted for long distance communication by showing a special sensitivity and ability of hearing in noise strongly overlapping the calculated sound window (see figure).

Jensen, K. K., Larsen, O. N., & Attenborough, K. (2008) Measurements and predictions of hooded crow (Corvus corone cornix) call propagation over open field habitats. Journal of the Acoustical Society of America, 123 (1) 507 - 518.

Jensen, K. K., Larsen, O. N. & Attenborough, K. (2007) Modeling and measuring sound propagation of hooded crow calls in open field habitats. International Ethology Conference, Halifax, Nova Scotia, Canada.

Deer call transmission in a North American and European habitat*

The North American Elk or Wapiti (Cervus canadensis) is closely related to the European Red Deer (Cervus elaphus) but they have radically different calls. The call of the Elk is a very high pitched, almost pure tone call with a F0 between 1-2 kHz whereas the Red Deer call is of a more typical low pitched, roaring quality that one would expect from a 200 Kg heavy animal. Why did the North American Elk develop such a radically different call?

To investigate if the acoustic properties of typical North american and European habitats could play a role in shaping the call differences we conducted sound propagation experiments at typical Elk habitats at a location in North America in the Rocky Mountains and at typical Red Deer habitats at a locations in Denmark, Europe. We also measured the acoustic impedance of the soil at the different locations and used the parameters as input into in a sound propagation model for comparison with the sound propagation data

The differences in the acoustic properties of the North American and European habitats were too small to have played any role in shaping the call differences. However, independent of habitat there was an optimal sound transmission channel around 1-2 kHz and it is possible that the Elk has adapted to this channel by focusing all the energy of its call within this channel and thereby being able to reach recievers further away than otherwise possible.

Riede, T., Jensen, K. K., Larsen, O. N., Attenborough, K., & Shahram, T. (2010) Habitat acoustics of Rocky Mountain elk in Colorado and European Red deed in Denmark. The 90th Annual Meeting of the American Society of Mammalogists, Laramie, USA, June 11th - June 15th.

Riede, T., Jensen, K. K., Larsen, O. N., Attenborough, K., & Shahram, T. (2010) Habitat acoustics of Rocky Mountain elk in Colorado and European Red deed in Denmark. Rocky Mountain National Park 2010 Research Conference, Estes park, Colorado, USA. March 30th - March 31st.

Larsen, O. N., Riede, T., Attenborough, K., & Shahram, T., Jensen, K. K. (xxxx) Manuscript in prep.

*Ongoing projects