Video based quantification of activity

Although not an inspiring or catchy title, our study has just been published, demonstrating that fixed-frame video capture can provide a quantitative assessment of energetics (citation below).

Summary of the study

Infrared thermal imaging is a passive imaging technique that captures the emitted radiation from an object to estimate surface temperature, often for inference of heat transfer.

Infrared thermal imaging offers the potential to detect movement without the challenges of glare, shadows, or changes in lighting associated with visual digital imaging or active infrared imaging.

In this paper, we employ a frame subtraction algorithm for extracting the pixel-by-pixel relative change in signal from a fixed focus video file, tailored for use with thermal imaging videos.  

A greyscale video of a metronome. Inanimate objects are still visible to the thermal camera due to slight differences in thermal equilibration, emissivity, and reflectivity across the different surfaces.
Same video as above, but as an “absolute difference image”, where each frame is subtracted from the previous frame and positized (i.e. the absolute value taken for each pixel difference). During zero motion, the image space is black with low variability based on sensor noise (sd number in upper left). After motion starts (~0:11), you clearly see the moving metronome as each frame difference depicts how pixels in a fixed frame differ.

By then cumulatively summing the sd for each frame across an entire video, we are able to assign quantitative activity assessments to thermal imaging data for comparison with simultaneous recordings of metabolic rates. We tested the accuracy and limits of this approach by analyzing movement of a metronome (see above) and provide an example of the approach to a study of Darwin’s finches.

Fixed frame Different Image Thermography video of a bird filmed over a long period of time within a viewing chamber. The cumulative difference image provides a slope value that corresponds to an indication of movement. Scale is relative to the degree of motion.

Simultaneous measurements of oxygen consumption (dark black lines) match up well with smoothed estimates (blue lines) of the activity score (grey lines) derived from the difference image thermography videos. Resolving fast respirometry data is difficult and best left to the experts at Sable Systems, but the average trends are informative for energy expenditure.
Correlations between 5 minute average oxygen consumption measurements and the activity values line up well at the individual level.

In principle, this “Difference Imaging Thermography” (DIT) would allow for activity data to be standardized to energetic measurements and could be applied to any radiometric imaging system.

Caveats

Fixed frame is required. Changing the reference frame or using a camera without a tripod would not work unless you do a lot of motion correction. Also, we used infrared thermal imaging because we were collecting data for a different purpose (still writing those up!), but we think that any sort of imaging should work, provided it produces a simple, ratiometric or radiometric image. Usually monochrome cameras or near infrared cameras produce a signal that is a simple greyscale image. Reflected light might interfere with the approach, so this is why we argued this might be an addition use of thermal imaging videos.

Behind the scenes

This paper took a long time to put together, but was the beginning of my lab’s journey into R, ImageJ, and open source coding. A lot has changed since I started the data analysis. Combing through 500 Gb of video files, extracting, processing, converting them into something manageable took the better part of 2 weeks on a supercomputer, until I realised that there were more efficient routes!

We have since created routines in ImageJ that help facilitate the conversions and have placed those routines in a github repository, where we will write them up as a methods paper in the future. The principles outlined in the paper are not themselves novel. Sliding average and frame subtraction routines are common in video processing software. Assessing whether the motion captured is correlated with meaningful biological information is what we hoped to capture with the study.

Citation

Tattersall, GJ, Danner, RM, Chaves, JA, and Levesque, DL. 2020. Activity analysis of thermal imaging videos using a difference imaging approach. Journal of Thermal Biology.  91 102611 https://doi.org/10.1016/j.jtherbio.2020.102611

Link to the full text here (first 50 clicks can access the paper).

Congratulations, Nick Sakich, MSc!

In a first for the lab, we just held a completely online MSc defence. Valiantly, Nick defended his MSc with grace, precision, insight, humour, and interesting anecdotes.

His thesis is entitled: “The Physiological and Behavioural Consequences of Reduced Scalation in Captive-bred Phenotypes of the Bearded Dragon (Pogona vitticeps Ahl 1926)“.

Here he is giving his presentation (sorry for the screen cap, Nick)

speaking about one of our favourite study animals:

The 3 phenotypes of captive-bred Pogona vitticeps studied in Nick’s thesis. a) wildtype, b) leatherback, and c) silkback.

Many thanks to the examining committee:

External Examiner, Dr. Chris Oufiero, Towson University
Chair, Dr. Cheryl McCormick
Committee Member, Dr. Jeff Stuart
Committee Member, Dr. Robert Carlone
Supervisor, Dr. Glenn Tattersall

Virtual congratulations to Nick are insufficient expression of gratitude for his hard work and devotion to his research. When and if we can safely congregate in small groups, we will celebrate appropriately! I really owe Nick my thanks for joining my lab. He has helped educate me through his efforts. It cannot be fun wrapping up one’s MSc during a pandemic, and Nick did a brilliant job.

A few highlights from Nick’s presentation below.

Thanks as well to A&A Dragons for their support over the years.

Massassauga Rattlesnake Overwintering Lifezone

Congratulations to lab member, Anne Yagi on publishing a life’s work of research on the overwintering lifezone of the Eastern Massassauga rattlesnake! The final proofs have been sent back to the publisher and we are anxiously awaiting it to make it to press:

Summary of the study here, with links to the paper below.

Temperate snakes occupy overwintering sites for most of their annual life cycle. Microhabitat characteristics of the hibernaculum are largely undescribed yet are paramount in ensuring snake overwintering survival.

We hypothesized that snakes survive hibernation within a vertical subterranean space that we termed a “life zone”, that is aerobic, flood, and frost-free throughout winter and did this by studying an isolated, endangered population of Massasaugas (Sistrurus catenatus) inhabiting an anthropogenically-altered peatland and monitored the subterranean habitat during a period of environmental stochasticity.

Lifezone concept (Credit: A Yagi)

Initial radio telemetry confirmed that snakes moved between altered and natural habitats during the active season and showed hibernation site fidelity to either habitat. We used a grid of groundwater wells, and frost tubes installed in each hibernation area to measure lifezone characteristics over 11 consecutive winters.

The lifezone within the impacted area was periodically reduced to zero during a flood-freeze cycle, while the lifezone in the natural area was maintained.

Sample figure from the paper showing year by year changes in the winter lifezone size (cm = depth or size underground that remains frost and flood free). Mined sites refer to an anthropogenically disturbed site where surface peat extraction had historically occurred. Unmined site is a peat bog. Flood events refer to a period of time when large regions of the site experienced sustained surface flooding.

Soil-depth and flood status best predicted lifezone size. Thermal buffering and groundwater dissolved oxygen increased with lifezone size, and annual Massasauga encounters were significantly correlated with lifezone size.

This analysis suggests a population decline occurred when lifezone size was reduced by flooding. Our data give support to the importance and maintenance of a lifezone for successful snake hibernation.

Our methods apply to subterranean hibernation habitats that are at risk of environmental stochasticity, causing flooding, freezing, or hypoxia, and speak to the issues regarding management of sensitive watersheds inhabitated by species-at-risk.


Snake well installation in the field to test the overwintering lifezone.

Citation

Yagi, A, Planck, RJ, Yagi, KT, and Tattersall GJ. 2020. A long-term study on Massasaugas (Sistrurus catenatus) inhabiting a partially-mined peatland: presenting a standardized method to characterize snake overwintering habitat. Journal of Herpetology. 54: 235-244. https://journalofherpetology.org/doi/full/10.1670/18-143

For further information, please see 8Trees.ca.

Avian Thermal Biology Visitor

The lab will be hosting a PhD student from Spain for the next 3 months.

Núria Playà Montmany from the University of Extremadura has just arrived (I’m a few days late, she arrived in late January!). I met Núria last summer defending her poster at the SEB meeting in Sevilla. She will be becoming a thermal imaging expert while she is here!

With overlapping interests in avian physiology and the lab’s interests in thermal biology and studying animal responses to climate change, we hope to have a productive visit. Here is a link to Núria’s blog:

https://birdsfacingclimatechange.wordpress.com/author/nuriaplaya/

Welcome to the lab, Núria! Let’s hope you have a good few months working with us.

Visitor to the Lab

It has been a busy January, and so my updates are out of date! From Jan 10th to the 24th, I hosted Dr. Agnes Jullian Vinet in the lab, mostly to learn thermal imaging for future human thermogenesis research.

Dr. Vinet was a welcome visitor, enduring the dark, but not so cold, Canadian winter with us! Thanks to Stephen Cheung’s lab, Gary Hodges and Leed McNab for helping to host Agnes.

Hopefully we can return the favour and visit her lab next summer!

Problems with assumptions in macroecology

Thanks to some very kind and smart colleagues, we have an editorial published in Ecology and Evolution!

https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.5721

Here is the citation:

Justin G. Boyles, Danielle L. Levesque, Julia Nowack, Michał S. Wojciechowski, Clare Stawski, Andrea Fuller, Ben Smit, and Glenn J. Tattersall 2019. An oversimplification of physiological principles leads to flawed macroecological analyses. https://doi.org/10.1002/ece3.5721

Take home message? Few endotherms are homeothermic, so they do not conform to assumptions of the Scholander-Irving model. Taking predictions from the SI model based on a broad range of lab studies can lead to huge errors in predictions. A re-assessment of macroecological predictions using this approach is warranted.

Demonstration of the inherent limitations of using body temperature (Tb) and the lower critical temperature (Tlc) of the thermal neutral zone to calculate thermal conductance (C) when Tb and Tlc are poorly defined.

Bridgeman now the Master

When he left the lab to write up his thesis, he was but the learner…now, HE is the Master.

Congratulations, Justin Bridgeman for a successful defence! Justin’s thesis earlier today was on “Behavioural thermoregulation and escape behaviour in the round goby”.

Thanks to the selfless efforts of the committee members (Dr. Gaynor Spencer, Dr. Liette Vasseur, and Dr. Patricia Wright), external examiner (Dr. Dennis Higgs, U Windsor), and committee chair (Dr. Cheryl McCormick).

Thank to all the lab mates for supporting Justin and welcoming him back for his brief visit.

All the best in the future Justin! We look forward to the manuscripts…and for a place to crash when we visit you in Halifax! 😉

Toucans of the atlantic

Earlier this summer, I was lucky enough to visit the Isle of May, Scotland to fulfill a long-time ambition to collect thermal image data on puffins in the wild. Ever since we published our work on the toucan in 2009, I have wanted to study the puffins, examining evidence for elevated capacity to control or distribute body heat through their uniquely colourful bill. Living in a cool climate with a large radiator like their bill presents a unique opportunity to test our hypotheses. In spring of 2018 I managed to visit the Elliston, Newfoundland puffin colony to start this project, but the distance to view a little too far to obtain high quality results.

Well, the short story is that they do show an extraordinary capacity to do so! Here is just a sample image (from the 200 Gb of videos):

Active and basking Atlantic puffins show capacity for intense heat transfer to the bill. The one above has recently landed back at the colony, presumably foraging although in this case, there is no evidence of food. Other images show cool bills, as we have seen in many other bird species, demonstrating the vasomotor control over blood flow to the bill is a fairly generalised phenomenon.
Infrared thermal video of an Atlantic puffin in May 2018 – early arrival at nest and investigating burrows.
Atlantic puffin in the rain.

If I only had the time to conduct the data analysis, I could put some numbers on these values. I certainly have my work cut out for me, examining those returning from the water with food vs. those basking and resting. I have a few other thoughts about these data that I hope to extract.

Many thanks must go to the town of Elliston, Newfoundland and the Atlantic puffin colony there, the Centre for Ecology and Hydrology (UK), the Isle of May (Scotland) Scientists, and especially Mark Newell for hosting me at the Isle of May, and Mike Harris for introducing us. Sorry it took so long to post this.

Further Reading

Tattersall, GJ, Arnaout, B, and Symonds, MRE.  2017.  The evolution of the avian bill as a thermoregulatory organ. Biological Reviews 92: 1630-1656. doi:10.1111/brv.12299

Greenberg, R, Cadena, V, Danner, RM, and Tattersall GJ. 2012. Heat loss may explain bill size differences between birds occupying different habitats. PLoS One, 7: e40933. 

Symonds, MRE and Tattersall, GJ. 2010. Geographical variation in bill size across bird species provides evidence for Allen’s rule.American Naturalist. 176: 188-197.

Tattersall, GJ, Andrade, DV, and Abe, AS. 2009. Heat exchange from the toucan bill reveals a controllable vascular thermal radiator.Science, 325: 468-470.