A new member of the morphometrics jungle to better monitor vulnerable lagoons
Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aurelia spp.)
Recommendation: posted 03 December 2020, validated 19 December 2020
In the recent years, morphometrics, the quantitative description of shape and its covariation  gained considerable momentum in evolutionary ecology. Using the form of organisms to describe, classify and try to understand their diversity can be traced back at least to Aristotle. More recently, two successive revolutions rejuvenated this idea [1–3]: first, a proper mathematical refoundation of the theory of shape, then a technical revolution in the apparatus able to acquire raw data. By using a feature extraction method and planning its massive use on data acquired by aerial drones, the study by Lacaux and colleagues  retraces this curse of events.
The radial symmetry of Aurelia spp. jelly fish, a common species complex, is affected by stress and more largely by environmental variations, such as pollution exposition. Aurelia spp. normally present four gonads so that the proportion of non-tetramerous individuals in a population has been proposed as a biomarker [5,6].
In this study, the authors implemented the Hough transform to largely automate the detection of the gonads in Aurelia spp. Such use of the Hough transform, a long-used approach to identify shapes through edge detection, is new to morphometrics. Here, the Aurelia spp. gonads are identified as ellipses from which aspect descriptors can be derived, and primarily counted and thus can be used to quantify the proportion of individuals presenting body plans disorders.
The sample sizes studied here were too low to allow finer-grained ecophysiological investigations. That being said, the proof-of-concept is convincing and this paper paths the way for an operational and innovative approach to the ecological monitoring of sensible aquatic ecosystems.
 Kendall, D. G. (1989). A survey of the statistical theory of shape. Statistical Science, 87-99. doi: https://doi.org/10.1214/ss/1177012589
 Rohlf, F. J., and Marcus, L. F. (1993). A revolution morphometrics. Trends in ecology & evolution, 8(4), 129-132. doi: https://doi.org/10.1016/0169-5347(93)90024-J
 Adams, D. C., Rohlf, F. J., and Slice, D. E. (2004). Geometric morphometrics: ten years of progress following the ‘revolution’. Italian Journal of Zoology, 71(1), 5-16. doi: https://doi.org/10.1080/11250000409356545
 Lacaux, C., Desolneux, A., Gadreaud, J., Martin-Garin, B. and Thiéry, A. (2020) Hough transform implementation to evaluate the morphological variability of the moon jellyfish (Aurelia spp.). bioRxiv, 2020.03.11.986984, ver. 3 peer-reviewed and recommended by Peer Community in Ecology. doi: https://doi.org/10.1101/2020.03.11.986984
 Gershwin, L. A. (1999). Clonal and population variation in jellyfish symmetry. Journal of the Marine Biological Association of the United Kingdom, 79(6), 993-1000. doi: https://doi.org/10.1017/S0025315499001228
 Gadreaud, J., Martin-Garin, B., Artells, E., Levard, C., Auffan, M., Barkate, A.-L. and Thiéry, A. (2017) The moon jellyfish as a new bioindicator: impact of silver nanoparticles on the morphogenesis. In: Mariottini GL, editor. Jellyfish: ecology, distribution patterns and human interactions. Nova Science Publishers; 2017. pp. 277–292.
Vincent Bonhomme (2020) A new member of the morphometrics jungle to better monitor vulnerable lagoons. Peer Community in Ecology, 100066. 10.24072/pci.ecology.100066
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
Evaluation round #1
DOI or URL of the preprint: https://www.biorxiv.org/content/10.1101/2020.03.11.986984v1
Author's Reply, 27 Nov 2020
Decision by Vincent Bonhomme, posted 27 Apr 2020
Dear Justine Gadreaud and colleagues,
The first round of revision is now over. It took some time given the lockdown and reviewers availabilities. Based on their reviews and my own, I think this preprint deserves a revision and I hope this will help.
Reviewer 1 asked for a larger dataset and for measurement error. Reviewer 2 also asked these points to be discussed. I agree with all their remarks and I also add my own comments. That being said, I think we could ultimately recommend your work, providing you answer and/or discuss these requests.
I wish you all the best,
My own comments (Vincent Bonhomme)
56: I grown there, and I would have removed "often"
About the use of Matlab: perhaps you could point to open-source alternatives. eg R + magick package that binds to eponym library?
Tab2: You can perhaps remove the N= and n=
174: wonder -> tested, at least past tense everywhere? Also turns like "we continue the study" or "our interest grew" tell your story but can be made more formal.
181+185: "does not make sense" + "bilateral runs test for randomness". I'm not sure to perfectly understand and perhaps this could be made clearer with one more sentence
Overall I think that the balance could be changed a bit towards the method versus the case study you used. With such sample sizes, I'm not sure it is worth discussing so much? I have the feeling this is the main blocking point for Reviewer 1.
Also the method is well described but I think a raw output of the Hough transform on a jellyfish picture would help (eg around lines 91+)
244: "have limits" I have got the same problems myself, segmenting overlapping objects. I'm sot sure it is really limiting, I'd say it's just painful to detect and filter out such overalapping structures. Sometimes I think we could even use them but, given the number of jellyfishes during a bloom, I think the filtering is the way to go.
264: "distinguish the jellyfishes with 4 gonads and the jellyfishes with 5 gonads": if the idea is to discriminant between tetramerous and non-tetramerous why dont just use the number of detected gonads? The test you have made sounds more like a biological investigation in the how and why (as stated in lines 276+) rather than just the non-tetramerous proportion (that seems to have merits by itself) you introduced in Table 1. I think the best option would be to separate what Hough trasnforms brings here: i) first count the number of gonads, ii) allow to test biological hypotheses as you also got informative descriptors besides the number of gonads.
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