Research Ideas and Outcomes :
Workshop Report
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Corresponding author: Loïc Van Audenhaege (loic.vanaudenhaege@gmail.com)
Received: 15 Nov 2023 | Published: 29 Nov 2023
© 2023 Loïc Van Audenhaege, Vincent Mahamadaly, David Price, Alexandre Sneessens, Hayley Cawthra, Clément Delamare, Valentin Danet, Simon Delsol, Rodolphe Devillers, Iason-Zois Gazis, Isabel Urbina-Barreto
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Van Audenhaege L, Mahamadaly V, Price D, Sneessens A, Cawthra HC, Delamare C, Danet V, Delsol S, Devillers R, Gazis I-Z, Urbina-Barreto I (2023) Workshop on 3D mapping of habitats and biological communities with underwater photogrammetry. Research Ideas and Outcomes 9: e115796. https://doi.org/10.3897/rio.9.e115796
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For the past decades, photogrammetry has been increasingly used for monitoring spatial arrangement or temporal dynamics of submerged man-made structures and natural systems. As photogrammetry remains a nascent technique for data collection in the underwater environment, acquisition workflows have evolved constrained by specific methodological practicalities (e.g. euphotic environments vs. deep-sea waters). The annual GeoHab conference gathers a world-wide range of scientists interested in mapping and is, therefore, an adequate event to set up a state-of-the-art workshop on (underwater) photogrammetry. More specifically, a preliminary survey identified the overall lack of photogrammetry knowledge from the audience. A programme was conceptualised to explore within a day theoretical concepts, sampling design and practicalities and a wide range of case studies in various underwater environments. Furthermore, we provided manual training on data acquisition and processing. In overall, a post-survey demonstrated the audience’s satisfaction despite a remaining lack of confidence for implementing their own photogrammetry studies. As this workshop gathers a diversity of materials and a training relevant for a scientific audience, it sets the stage for a reproducible event and leaves room for future improvements. Finally, it provided relevant materials and discussions that enabled us to identify the aspects limiting photogrammetry methodology across scientific applications and institutes, in order to work towards standardisation.
photogrammetry, structure-from-motion, 3D models, habitat mapping, ecology, workshop
Monday 8 May 2023 at the Hotel Le Récif in Saint-Gilles-les-Bains (La Réunion)
For the past decade, with the development of acquisition platforms and computer power, publications involving photogrammetry by Structure from Motion (SfM) have increased by more than tenfold (
The “3D underwater mapping for habitats and biological communities” - GeoHab 2023 workshop took place on Monday 8 May 2023 at the Hotel Le Récif in Saint-Gilles-les-Bains (La Réunion). Throughout diverse activities, the workshop aimed:
The goal of this report is to present the conception and running of the GeoHab 2023 workshop in order to help reproduce such a workshop. The present document includes details on the participants, the type of the audience, the programme and detailed information of the content of several activities and sessions. All associated data and supplementary materials were published in an open-access Zenodo repository: 10.5281/zenodo.7934452.
The organisers comprised: Loïc Van Audenhaege (National Oceanography Centre, UK), Vincent Mahamadaly (CREOCEAN, FR), David Price (University of the Azores, PT), Alexandre Sneessens (CREOCEAN OI, FR), Isabel Urbina-Barreto (French National Institute for Sustainable Development IRD, La Réunion, FR; Fig.
The preparation of the workshop started in early February 2023 with one-hour meetings every two weeks or so.
In total, 61 people participated to the workshop (Table
List of participants to the GeoHab 2023 workshop. All participants shared consent to publish the following information.
Arosio |
Riccardo |
Ireland |
University College Cork |
Bellec |
Valérie |
Norway |
Geological Survey of Norway (NGU) |
Bjarnadóttir |
Lilja Rún |
Norway |
Geological Survey of Norway (NGU) |
Boehringer |
Lilian |
Germany |
Alfred-Wegener-Institut (AWI) |
Brenan |
Catherine |
Canada |
Dalhousie University |
Broad |
Emmeline |
Canada |
Memorial University of Newfoundland |
Bunyan |
Israel John |
Madagascar |
IH.SM/B.V |
Castellan |
Giorgio |
Italy |
Consiglio Nazionale delle Ricerche |
Chequer |
Arturo |
United States |
University of Florida |
Cochrane |
Guy |
United States |
USGS |
Combs-Hintze |
Bea |
United States |
University of South Florida |
Danet |
Valentin |
France |
Museum national d'Histoire naturelle |
Di Giovanna |
Fabio |
Italy |
University Federico II of Napoli |
Dodd |
Carla |
South Africa |
Nelson Mandela University |
Dolan |
Margaret |
Norway |
Geological Survey of Norway |
Dupont |
Priscilla |
La Réunion (FR) |
Espace-Dev, IRD |
El-Khaled |
Yusuf |
Saudi Arabia |
King Abdullah University of Science and Technology |
Foglini |
Federica |
Italy |
Consiglio Nazionale delle Ricerche |
Galvez |
Daphnie |
Italy |
Consiglio Nazionale delle Ricerche |
Gazis |
Iason - Zois |
Germany |
GEOMAR Helmholtz Centre for Ocean Research Kiel |
Geersen |
Jacob |
Germany |
Christian-Albrechts-University |
Gini |
Caroline |
Canada |
Memorial University of Newfoundland |
Granier |
Carine |
France |
EDF |
Greene |
Gary |
United States |
Circum Pacific Council (CPC) |
Haar |
Claire |
Canada |
Dalhousie University |
Henderson |
Bruce |
South Africa |
Wreckless Marine |
Henderson |
Ben |
South Africa |
Wreckless Marine |
Ierodiaconou |
Daniel |
Australia |
Deakin University |
Ingleton |
Timothy |
Australia |
NSW Dept. Planning & Environment |
Johnson |
Alysha |
Australia |
University of Wollongong |
Judah |
Aaron B. |
Canada |
Dalhousie University |
Koskikala |
Joni |
Finland |
Parks and Wildlife Finland |
Kotilainen |
Aarno |
Finland |
Geological Survey of Finland |
Le Bas |
Tim |
United Kingdom |
National Oceanography Centre |
Lecours |
Vincent |
Canada |
Université du Québec, Chicoutimi (UQAC) |
Lisniowski |
Maria Aline |
Brazil |
Geological Survey of Brazil |
Mackay |
Kevin |
New Zealand |
NIWA |
MacKay |
Fiona |
South Africa |
Oceanographic Research Institute |
MacMillan-Kenny |
Zachary |
Canada |
Memorial University of Newfoundland |
Madricardo |
Fantina |
Italy |
Consiglio Nazionale delle Ricerche |
Marticorena |
Julien |
France |
ABYSSA |
Misiuk |
Benjamin |
Canada |
Dalhousie University |
Mitondrasoa |
Yves Amoros |
Madagascar |
Institut Halieutique et des Sciences Marines |
Moschino |
Vanessa |
Italy |
Consiglio Nazionale delle Ricerche |
Mouquet |
Pascal |
La Réunion (FR) |
SEAS-OI - IRD |
Nattkemper |
Tim |
Germany |
Bielefeld University |
Parnum |
Iain |
Australia |
Curtin University |
Pearman |
T. |
United Kingdom |
National Oceanography Centre |
Pinel |
Romain |
La Réunion (FR) |
Geolab |
Remia |
Alessandro |
Italy |
Consiglio Nazionale delle Ricerche |
Requi-Le Noheh |
Maya |
Mayotte (FR) |
Parc naturel marin de Mayotte PNMM |
Schneider von Deimling |
Jens |
Germany |
Christian-Albrechts-University |
Sklar |
Emily |
Canada |
Dalhousie University |
Strong |
James Asa |
United Kingdom |
National Oceanography Centre |
Thamsanqa |
Wanda |
South Africa |
SAIAB (South African Institute for Aquatic Biodiversity) |
Thorsnes |
Terje |
Norway |
Geological Survey of Norway |
van Zyl |
Frederik Wilhelm |
South Africa |
Council for Geoscience |
Vandenbossche |
Philippe |
Australia |
CSIRO |
Watson |
Sally |
New Zealand |
NIWA/University of Auckland |
Whitford |
Grant |
South Africa |
Wreckless Marine |
Young |
Mary |
Australia |
Deakin University |
Although all five continents were represented, participant origins were relatively uneven, with Europe (48.4%), North America (20.3%), Africa (15.6%), Oceania (12.5%), South America (1.6%) and Asia (1.6%). For future similar events, it could be helpful to consider a hybrid format and recording activities that could encourage attendance from zones with a large time difference (e.g. Oceania, America and Asia).
A preliminary survey aimed to collect information about participants to better understand their experience level and diversity. That helped adapt and define the content of the workshop. The reader will be assisted in determining how similar that audience was to their audience in order to determine whether our workshop is applicable to their particular situation.
A Google form was set up to collect answers from each participant to the seven following questions:
N.B. All questions required an answer from the survey participant.
All participants consented to share their answers anonymously. The total answer rate was 84.4% (54 participants out of the 64 registered).
1. What is your current position?
Most of attendees belonged to academia (~ 80%; Fig.
2. What field of research do you consider yourself involved in?
Geologists, biologists/ecologists and mappers predominated (90%; Fig.
3. What ecosystem(s) does your work relate to?
Most of the attendees’ work focuses on the marine environment (from the littoral to the deep sea; Fig.
4. How long have you used photogrammetric models for?
Half of the participants had no experience at all with 3D photogrammetry (Fig.
5. What aspects of photogrammetry do you particularly intend to focus on during the workshop?
Answers from participants showed a relatively balanced interest amongst data collection, model computation and result extraction (Fig.
6. Any additional comment?
From a selection of comments:
Comments highlighted that the workshop duration was not sufficient to approach deeply enough all aspects of photogrammetry. However, those comments provided valuable information for modulating the hands-on session and the panel discussion (e.g. first comment on standardisation of photogrammetry and selection of software).
7. What platforms do you usually use to perform photogrammetry?
A balance predominated amongst the use of drones (33.3%), scuba diving (29.6%) and the use of underwater platforms, such as remotely operated vehicles (20.4 to 24.1%), towed cameras (40.7%), and, surprisingly, the more recent technologies of autonomous underwater vehicles (33.3%; Fig.
The programme was intended to cover multiple aspects of photogrammetry by SfM considering a meaningful progression amongst the different workshop sessions.
The first session of the morning focused on the theorical principles, presenting the mathematical rationale behind photogrammetry, the algorithms involved and the types of files that can be extracted to be displayed in a virtual environment (Fig.
The afternoon consisted of case studies presentations which were focused on describing various applications from various environments as proofs of concept for the variety of research contexts in which photogrammetry can be used (Fig.
Presentations during the workshop allowed participants to discover a wide range of acquisition platforms (e.g. aerial to underwater; Fig.
Diversity of photogrammetry models, acquisition methods and applications presented during the workshop. (A) 3D model of Xestospongia testudinaria from scuba diving - Mozambique (2020) © Creocean; (B) Acropora sp coral nubbin 3D model for temporal survey. © Urbina-Barreto I. Future Maore Reefs project - French National Institute for Sustainable Development (IRD); (C) Coral reef model in Mayotte underwater photogrammetry, artistic and awareness actions. © Urbina-Barreto I. Future Maore Reefs project & Simon R. CORAUX project. French National Institute for Sustainable Development (IRD) & OFB Natural Marine Parc of Mayotte; (D) 3D model of the seabed geomorphology at the Dellec shoreline in the French Brittany using the Poseidon floating platform © TELEMAC project; (E) coral reef photograph acquired with an unmanned aerial vehicle - Belizes © National Oceanography Centre; (F) 3D model of Antonio Lorenzo wreck from scuba diving - La Reunion (2017) © Geolab – Comité de plongée Réunion; (G) Inspection of submerged structures for coastal road construction - Reunion Island. © Urbina-Barreto I. PhD thesis (2020); (H) 3D model of a cold-water coral reef imaged with the remotely operated vehicle Isis - Whittard Canyon, -850 m (2015) © JC125, National Oceanography Centre (I) 3D model of the > 10 m-high Capelinhos vent edifice with the remotely operated vehcle Victor6000 - Lucky Strike vent field, -1665 m (2020) © MoMARSAT 2020, IFREMER. All pictures have been reused under CC by 4.0.
Ranked preference between three hands-on was requested to each participant during the pre-event online survey. Based on their preferences, we assigned them to a hands-on stand that was run by one person or a group (Fig.
The activities of the hands-on stand were defined by the stand leader(s). However, we encouraged the stand leaders to coordinate themselves to offer a similar content structure despite featuring different environment and acquisition platforms. Content similarities included display of image acquisition, mesh acquisition and manipulation of the mesh (e.g. Figs
3D model of a scene rebuilt by the participant during the hands-on session of L. Van Audenhaege (n = 42 images) and displayed on Meshlab. Note the small vignettes on the upper part to automatically scale the model in Agisoft. Note also a 3D map of La Réunion topography on the lower right part of the picture.
3D model of a scene rebuilt by the participant during the hands-on session of I. Urbina-Barreto, S. Delsol and C. Delamare (n = 54 images). Hands-on was divided in image acquisition (coordinator: Delamare C.), processing with Agisoft Metashape and Open Drone Map and computation of ecological analyses (Urbina-Barreto I.) and examples of point cloud comparison (Delsol S.).
As an example, for reproducibility purposes, the hands-on activities of Loïc Van Audenhaege and David Price is presented below:
We briefly displayed other tools of Cloudcompare, such as the ICP and point-to-point registration algorithm to overlay models together. Although time did not allow it, we intended to load the 3D model on Meshroom and Codemap to display alternative and opensource photogrammetry software. Originally, we also intended to load data in Meshlab. This software includes algorithms that Cloudcompare does not hold, such as for remeshing algorithms to lower mesh resolution and fasten the display of results.
Due to time constraint, the panel discussion only lasted 40 minutes:
A post-event feedback survey was conducted to allow participants to provide feedback on the workshop and identify aspects that were satisfactory from those that could have been improved.
A Google form was set up to collect answers from each participant on the seven following questions:
N.B. All questions required an answer from the survey participants.
All feedback participants consented to share their answers anonymously. The answer rate was of 34.4% (22 participants out of the 64 registered).
1. Now that you know photogrammetry better, do you think it could be a valuable tool for your work (if you were using photogrammetry before, please answer N/A)?
From the 22 participants that answered the survey, 15 did not use photogrammetry prior to this survey (Fig.
2. Do you now feel confident enough to be able to run a 3D reconstruction on your own (if you were using photogrammetry before, please answer N/A)?
Despite the workshop, 10 beginners out of 16 still required supervision for photogrammetry (Fig.
3. Do you think that some aspects of photogrammetry remained unclear or should have deserved more time?
A majority of 10 responders pointed out the need to investigate more the software from pre-processing to post-processing (Fig.
4. Feel free to comment on your answer.
5. Do you think that some aspects of photogrammetry were too extensively detailed?
Overall, 17 participants considered that no aspect was too extensively detailed (Fig.
6. Feel free to comment your answer.
7. On a scale from 1 (dissatisfied) to 5 (highly satisfied) by 3 (neutral), how clear were the presentations?
With a weighted average score of 4.41/5, the audience was satisfied about the presentation clarity (Fig.
8. Do you think of anything that could improve the presentations?
9. On a scale from 1 (dissatisfied) to 5 (highly satisfied) by 3 (neutral), how satisfied were you with the hands-on?
With a weighted average score of 4.23/5, the audience was satisfied with the hands-on activities (Fig.
10. How would you improve the hands-on activities?
11. On a scale from 1 (dissatisfied) to 5 (highly satisfied) by 3 (neutral), how satisfied are you with that workshop?
With a weighted average score of 4.55/5, the audience was generally very satisfied of the workshop in overall (Fig.
12. Do you think of anything missing or that could be improved for that workshop?
This report outlined the architecture and organisation (contents and manpower) of a one-day photogrammetry workshop delivered to a scientific audience with no prior knowledge about this technique. In addition, it uses semi-quantitative approach, based on surveys to assess the relevance and the impact of the workshop. This report could help plan future photogrammetry workshops targeting a scientific community. We stress the need to survey participants prior to the event to better capture participants’ experience and needs. Activities included theoretical lessons on data acquisition followed by practical hands-on and case studies presentations. Despite the difficulty to empower attendees with high confidence on the use of photogrammetry, the workshop helped attendees to identify the potential for photogrammetry use for their own case studies. Despite logistical constraints (e.g. time and room layout), the audience was satisfied, demonstrating the success of this workshop. Future offering of such a workshop could be held in a hybrid in-person/online format and could include additional days to allow participants to attend all hands-on sessions, to lead a real field photogrammetry sampling, to practise more with the different photogrammetric software or even to give them the opportunity to play with their data in groups from beginners to more advanced users. Finally, this report not only sets the stage for a photogrammetry training, it also provides details on a wide diversity of workflows and applications that could help to identify current limits, future needs and ways for standardising photogrammetry in the future.
The material is provided in open-access at 10.5281/zenodo.7934452. It contains samples of presentation and images acquired during the hands-on.
The authors would like to thank Veronique Rousseau for offering help on the logistical aspects of the workshop. They warmly thank the Hotel Le Récif for offering a swimming pool for the mini ROV demonstration and their compliance with logistical request. The organising committee would like to thank Romain Pinel who kindly offered his help for facilitating the workshop. Finally, we are grateful to the participants of this workshop who contributed in great number to the surveys of this report.
LVA’s participation was funded by the H2020 EU project iAtlantic (no. 818123). IUB was funded by Future Maore Reefs project: Plan Relance France, French Office for Biodiversity and French National Institute for Sustainable Development. DP is funded by the PO2020 project DeepWalls (ACORES-01-0145-FEDER-000124) and attendance to GeoHab was supported by MAF WORLD (COST (European Cooperation in Science and Technology): CA 20102), Deepwalls (ACORES-01-0145-FEDER-000124) and by Fundação para a Ciência e a Tecnologia (FCT) through the strategic project (UID/05634/2020) granted to OKEANOS.
All participants consented to share their details in Table
All participants consented to share anonymously their answers to pre- and post-surveys.
DP, IUB, MV, SA and LVA conceived the programme of this workshop. RD and HCC provided the logistical support and infrastructure. SD, CD, DP, IUB, MV, SA and LVA conceived the hands-on. SD, DP, GIZ, VD, IUB, MV, SA and LVA conceived the presentations of the workshop. DP, IUB, MV, SA and LVA conceived the pre- and post-workshop survey. LVA wrote the manuscript. All authors reviewed the manuscript.
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