# Workshop on 3D mapping of habitats and biological communities with underwater photogrammetry

Loïc Van Audenhaege, Vincent Mahamadaly, David Price, Alexandre Sneessens, Hayley Cawthra, Clément Delamare, Valentin Danet, Simon Delsol, Rodolphe Devillers, Iason-Zois Gazis, et al.

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Loïc Van Audenhaege, Vincent Mahamadaly, David Price, Alexandre Sneessens, Hayley Cawthra, et al.. Workshop on 3D mapping of habitats and biological communities with underwater photogrammetry. Research Ideas and Outcomes, 2023, 9, 10.3897/rio.9.e115796. hal-04363491

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# Workshop on 3D mapping of habitats and biological communities with underwater photogrammetry

Loïc Van Audenhaege†, Vincent Mahamadaly§, David Price¶, Alexandre Sneessens¶, Hayley C. Cawthra#, Clément Delamare**, Valentin Danet«, Simon Delsol»^, Rodolphe Devillers`, Iason-Zois Gazis`, Isabel Urbina-Barreto^

† Ocean Bio Geosciences, National Oceanography Centre, Southampton, United Kingdom

§ CREOCEAN, Montpellier, France

| Instituto de Investigação em Ciências do Mar – Okeanos/IMAR, Universidade dos Açores, Horta, Portugal

¶ CREOCEAN OCEAN INDIEN, Sainte-Clotilde, Réunion

# Minerals and Energy Unit, Council for Geoscience, Cape Town, South Africa

■ Master Biodiversité et ÉcoSystèmes Tropicaux - Aquatique, Littoraux et Insulaires, Université de la Réunion, La Réunion, France

« Museum national d'Histoire naturelle, Station Marine de Dinard, CRESCO, Dinard, France

» Geo-Ocean, University Brest, CNRS, Ifremer, UMR 6538, Plouzané, France

^ UMR 9220 Entropie, Institut de Recherche pour le Développement, La Réunion, France

Espace-Dev (IRD, Univ La Réunion), Station SEAS-OI, La Réunion, France

¡ DeepSea Monitoring Group, GEOMAR Helmholtz Centre for Research, Kiel, Germany

Corresponding author: Loïc Van Audenhaege (loic.vanaudenhaege@gmail.com)

Reviewable

v 1

Received: 15 Nov 2023 | Published: 29 Nov 2023

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

## Abstract

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.

## Keywords

photogrammetry, structure-from-motion, 3D models, habitat mapping, ecology, workshop

## Date and place

Monday 8 May 2023 at the Hotel Le Récif in Saint-Gilles-les-Bains (La Réunion)

## Introduction

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 (Bayley and Mogg 2020, Pulido Mantas et al. 2023), with ~ 25% of investigations performed in the marine environment. From coastal to abyssal areas, this technique allows mapping of objects at a high level of positional accuracy (< cm) in a 3D space. This type of data is conducive for precise spatio-temporal monitoring studies (D'Urban Jackson et al. 2020, Lange and Perry 2020, Fukunaga et al. 2022). Therefore, the value of this technique has evolved considerably as its development continues and research communities continue to innovate methods to analyse these types of data, tackling a broad range of topics, from ecology to geology. The annual international GeoHab symposium covers topics ranging from marine geosciences, mapping, ecology and targeting presentation of novel data-acquisition approaches. As a result, this event gathers a broad range of stakeholders and scientists from the marine community that may empower the use of photogrammetry to forward this field of research.

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:

1. to provide GeoHab participants with knowledge on photogrammetry and to give them an overview of the potentials uses of this technique;

2. to show-case studies on marine environments from shallow waters (with aerial and underwater surveys) to the deep seas (with underwater platforms);
3. to train attendees to design and perform photogrammetry investigations that could be optionally monitored by a panel expert who ran that workshop and finally;

4. to empower the audience and, more generally the marine community, in the domain of photogrammetry and

5. to lead a hands-on session to practise photogrammetry sampling, processing with different software (e.g. Open Drone Map, ColMap, Meshroom, Agisoft Meshshape, CloudCompare) and methods for analyses (e.g. annotation on 3D mesh with 3D metrics, 3D dense cloud, digital elevation models and orthomosaics).

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.

## Organising committee

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. 1). The organisers work in the private and public academic sectors. Their scientific background was diverse in terms of environments of interest (i.e. from coastal to deep-sea marine ecosystems) and platforms for usual data acquisition (i.e. drone, scuba and free diving and remotely operated vehicles). We believed that the workshop benefitted from the collaboration of diverse experts because it enabled a holistic approach in the photogrammetry domain highlighting the differences and similarities across scientific disciplines, thus displaying an exhaustive state-of-the-art of photogrammetry.

The preparation of the workshop started in early February 2023 with one-hour meetings every two weeks or so.

## List of participants

In total, 61 people participated to the workshop (Table 1; total number of registration = 64).

<caption>Table 1.</caption>

List of participants to the GeoHab 2023 workshop. All participants shared consent to publish the following information.

<table><tr><td>Arosio</td><td>Riccardo</td><td>Ireland</td><td>University College Cork</td></tr><tr><td>Bellec</td><td>Valérie</td><td>Norway</td><td>Geological Survey of Norway (NGU)</td></tr><tr><td>Bjarnadóttir</td><td>Lilja Rún</td><td>Norway</td><td>Geological Survey of Norway (NGU)</td></tr></table>
<table><tr><td>Boehringer</td><td>Lilian</td><td>Germany</td><td>Alfred-Wegener-Institut (AWI)</td></tr><tr><td>Brenan</td><td>Catherine</td><td>Canada</td><td>Dalhousie University</td></tr><tr><td>Broad</td><td>Emmeline</td><td>Canada</td><td>Memorial University of Newfoundland</td></tr><tr><td>Bunyan</td><td>Israel John</td><td>Madagascar</td><td>IH.SM/B.V</td></tr><tr><td>Castellan</td><td>Giorgio</td><td>Italy</td><td>Consiglio Nazionale delle Ricerche</td></tr><tr><td>Chequer</td><td>Arturo</td><td>United States</td><td>University of Florida</td></tr><tr><td>Cochrane</td><td>Guy</td><td>United States</td><td>USGS</td></tr><tr><td>Combs-Hintze</td><td>Bea</td><td>United States</td><td>University of South Florida</td></tr><tr><td>Danet</td><td>Valentin</td><td>France</td><td>Museum national d'Histoire naturelle</td></tr><tr><td>Di Giovanna</td><td>Fabio</td><td>Italy</td><td>University Federico II of Napoli</td></tr><tr><td>Dodd</td><td>Carla</td><td>South Africa</td><td>Nelson Mandela University</td></tr><tr><td>Dolan</td><td>Margaret</td><td>Norway</td><td>Geological Survey of Norway</td></tr><tr><td>Dupont</td><td>Priscilla</td><td>La Réunion (FR)</td><td>Espace-Dev, IRD</td></tr><tr><td>El-Khaled</td><td>Yusuf</td><td>Saudi Arabia</td><td>King Abdullah University of Science and Technology</td></tr><tr><td>Foglini</td><td>Federica</td><td>Italy</td><td>Consiglio Nazionale delle Ricerche</td></tr><tr><td>Galvez</td><td>Daphnie</td><td>Italy</td><td>Consiglio Nazionale delle Ricerche</td></tr><tr><td>Gazis</td><td>Iason - Zois</td><td>Germany</td><td>GEOMAR Helmholtz Centre for Ocean Research Kiel</td></tr><tr><td>Geersen</td><td>Jacob</td><td>Germany</td><td>Christian-Albrechts-University</td></tr><tr><td>Gini</td><td>Caroline</td><td>Canada</td><td>Memorial University of Newfoundland</td></tr><tr><td>Granier</td><td>Carine</td><td>France</td><td>EDF</td></tr><tr><td>Greene</td><td>Gary</td><td>United States</td><td>Circum Pacific Council (CPC)</td></tr><tr><td>Haar</td><td>Claire</td><td>Canada</td><td>Dalhousie University</td></tr><tr><td>Henderson</td><td>Bruce</td><td>South Africa</td><td>Wreckless Marine</td></tr><tr><td>Henderson</td><td>Ben</td><td>South Africa</td><td>Wreckless Marine</td></tr><tr><td>Ierodiaconou</td><td>Daniel</td><td>Australia</td><td>Deakin University</td></tr><tr><td>Ingleton</td><td>Timothy</td><td>Australia</td><td>NSW Dept. Planning & Environment</td></tr><tr><td>Johnson</td><td>Alysha</td><td>Australia</td><td>University of Wollongong</td></tr><tr><td>Judah</td><td>Aaron B.</td><td>Canada</td><td>Dalhousie University</td></tr><tr><td>Koskikala</td><td>Joni</td><td>Finland</td><td>Parks and Wildlife Finland</td></tr><tr><td>Kotilainen</td><td>Aarno</td><td>Finland</td><td>Geological Survey of Finland</td></tr><tr><td>Le Bas</td><td>Tim</td><td>United Kingdom</td><td>National Oceanography Centre</td></tr><tr><td>Lecours</td><td>Vincent</td><td>Canada</td><td>Université du Québec, Chicoutimi (UQAC)</td></tr><tr><td>Lisniowski</td><td>Maria Aline</td><td>Brazil</td><td>Geological Survey of Brazil</td></tr><tr><td>Mackay</td><td>Kevin</td><td>New Zealand</td><td>NIWA</td></tr><tr><td>MacKay</td><td>Fiona</td><td>South Africa</td><td>Oceanographic Research Institute</td></tr><tr><td>MacMillan-Kenny</td><td>Zachary</td><td>Canada</td><td>Memorial University of Newfoundland</td></tr></table>
<table><tr><td>Madricardo</td><td>Fantina</td><td>Italy</td><td>Consiglio Nazionale delle Ricerche</td></tr><tr><td>Marticorena</td><td>Julien</td><td>France</td><td>ABYSSA</td></tr><tr><td>Misiuk</td><td>Benjamin</td><td>Canada</td><td>Dalhousie University</td></tr><tr><td>Mitondrasoa</td><td>Yves Amoros</td><td>Madagascar</td><td>Institut Halieutique et des Sciences Marines</td></tr><tr><td>Moschino</td><td>Vanessa</td><td>Italy</td><td>Consiglio Nazionale delle Ricerche</td></tr><tr><td>Mouquet</td><td>Pascal</td><td>La Réunion (FR)</td><td>SEAS-OI - IRD</td></tr><tr><td>Nattkemper</td><td>Tim</td><td>Germany</td><td>Bielefeld University</td></tr><tr><td>Parnum</td><td>Iain</td><td>Australia</td><td>Curtin University</td></tr><tr><td>Pearman</td><td>T.</td><td>United Kingdom</td><td>National Oceanography Centre</td></tr><tr><td>Pinel</td><td>Romain</td><td>La Réunion (FR)</td><td>Geolab</td></tr><tr><td>Remia</td><td>Alessandro</td><td>Italy</td><td>Consiglio Nazionale delle Ricerche</td></tr><tr><td>Requi-Le Noheh</td><td>Maya</td><td>Mayotte (FR)</td><td>Parc naturel marin de Mayotte PNMM</td></tr><tr><td>Schneider von Deimling</td><td>Jens</td><td>Germany</td><td>Christian-Albrechts-University</td></tr><tr><td>Sklar</td><td>Emily</td><td>Canada</td><td>Dalhousie University</td></tr><tr><td>Strong</td><td>James Asa</td><td>United Kingdom</td><td>National Oceanography Centre</td></tr><tr><td>Thamsanqa</td><td>Wanda</td><td>South Africa</td><td>SAIAB (South African Institute for Aquatic Biodiversity)</td></tr><tr><td>Thorsnes</td><td>Terje</td><td>Norway</td><td>Geological Survey of Norway</td></tr><tr><td>van Zyl</td><td>Frederik Wilhelm</td><td>South Africa</td><td>Council for Geoscience</td></tr><tr><td>Vandenbossche</td><td>Philippe</td><td>Australia</td><td>CSIRO</td></tr><tr><td>Watson</td><td>Sally</td><td>New Zealand</td><td>NIWA/University of Auckland</td></tr><tr><td>Whitford</td><td>Grant</td><td>South Africa</td><td>Wreckless Marine</td></tr><tr><td>Young</td><td>Mary</td><td>Australia</td><td>Deakin University</td></tr></table>

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).

## Preliminary survey

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.
<figure><img src="image_2.png" /><figcaption>Figure 1. doi</figcaption></figure>

Organising committee (from left to right): Loïc Van Audenhaege, Vincent Mahamadaly, Isabel Urbina-Barreto, Alexandre Sneessens, David Price and Rodolphe Devillers (GeoHab conference co-organiser with Hayley Cawthra taking the picture).

## Methods

A Google form was set up to collect answers from each participant to the seven following questions:

1. What is your current position?*¹

2. What field of research do you consider yourself involved in?*¹

3. What ecosystem(s) does your work relate to?*²

4. How long have you used photogrammetric models for?*¹

5. What aspects of photogrammetry do you particularly intend to focus on during the workshop?*²

6. Any additional comment?*³

7. What platform do you usually use to perform photogrammetry?*²

N.B. All questions required an answer from the survey participant.

## Results

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), with a relative balance between early-career scientists (BSc/ MSc, PhD and post-docs; 44.5%) and permanent researchers (35.2%). Still, 9.3% of participants were engineers.

<figure><img src="image_3.png" /><figcaption>Figure 2. doi</figcaption></figure>

Pie chart of the answers to Question 1 of the preliminary survey: 'What is your current position?'

## 2. What field of research do you consider yourself involved in?

Geologists, biologists/ecologists and mappers predominated (90%; Fig. 3) in roughly equal proportions, reflecting the general GeoHab conference's focus. The rest was mostly made of subgroups of one to two people (e.g. marine energy, computer sciences).

<figure><img src="image_4.png" /><figcaption>Figure 3. doi</figcaption></figure>

Pie chart of the answers to Question 2 of the preliminary survey: 'What field of research do you consider yourself involved in?'

## 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). A large share of attendees were identified as having experience in the sublittoral ecosystem (0-200 m depth). Still, the deep-sea realm was well represented with 44.4% working in bathyal and with 18.5% working in abyssal waters. Seventeen responders (31.5%) work on both sublittoral and bathyal environments.

## 4. How long have you used photogrammetric models for?

Half of the participants had no experience at all with 3D photogrammetry (Fig. 5). Still, 35.2% had less than two years of experience with photogrammetry. This overall 'lack of
experience' demonstrates the relevance of this workshop as photogrammetry has become more relevant over the past decade (Pulido Mantas et al. 2023).

<figure><img src="image_5.png" /><figcaption>Figure 4. doi</figcaption></figure>

Poll of the answers to Question 3 of the preliminary survey: 'What ecosystem(s) does your work relate to?'

<figure><img src="image_6.png" /><figcaption>Figure 5. doi</figcaption></figure>

Pie chart of the answers to Question 4 of the preliminary survey: 'How long have you used photogrammetric models for?'

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).

6. Any additional comment?

From a selection of comments:

* "Suggestions on best software (affordability vs. quality) would be very helpful, also if we came away with generic workflows".

* "How to make the most of available data that was gathered without using any controlling methods (e.g. laser pointers, stabilisation)"?

* "How can we get an orthophoto from georeferenced images" (x2)?

* "I am interested in QPS SfM or QGIS Plugins".

* "I am interested to know more about using AI or programming for post-processing and analyses" (x2).
* "would be interested in 'filling the gap' nearshore between where multibeam stops and terrestrial mapping starts".

* "Calibration/bundle adjustment and georectification".

<figure><img src="image_7.png" /><figcaption>Figure 6. doi</figcaption></figure>

Poll of the answers to Question 5 of the preliminary survey: 'What aspects of photogrammetry do you particularly intend to focus on during the workshop?'

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. 7).

<figure><img src="image_8.png" /><figcaption>Figure 7. doi</figcaption></figure>

Pie chart of the answers to Question 7 of the preliminary survey: 'What platforms do you usually use to perform photogrammetry'?
## Workshop activities

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 theoretical 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. 8). Second, various presentations focused on sampling/survey designs, including what optical camera parameters should be considered or, depending on the sampled environment and acquisition platform, what practical constraints and limiting factors need to be considered. Legislation for drone acquisition was also discussed and underlined the specific regulation for each country. Third, the participants attended a hands-on session aiming to teach them image acquisition to live model reconstruction while leaving room for more specific questions at the same time.

<figure><img src="image_9.png" /><figcaption>Figure 8. doi</figcaption></figure>

Detailed programme of the "3D underwater mapping for habitats and biological communities" GeoHab 2023 workshop (Morning session).
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. 9). For this session, additional speakers from academia were invited as guest speakers (Simon Delsol, lason-Zois Gazis and Valentin Danet). The day ended with a feedback panel discussion.

<figure><img src="image_10.png" /><figcaption>Figure 9. doi</figcaption></figure>

Detailed programme of the “3D underwater mapping for habitats and biological communities” GeoHab 2023 workshop (Afternoon session).

## Presentations

Presentations during the workshop allowed participants to discover a wide range of acquisition platforms (e.g. aerial to underwater; Fig. 10). Objects imaged varied from man-made structures, geomorphological facies and different biological scales of interest (e.g. from sessile individuals to communities). Applications ranged from the use of photogrammetry to investigate spatial organisation and to monitor temporal dynamics of man-made structures or biological communities and to raise awareness of local population regarding their marine ecosystems. All presentations emphasised the importance of photogrammetry that provides centimetric-resolution of investigations needed for various
ecological applications, such as growth monitoring in natural conditions or after
disturbance, characterisation of topographically complex habitat and species co-existence
to investigate niche partitioning.

<figure><img src="image_11.png" /><figcaption>Figure 10. doi</figcaption></figure>

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 vehicle *Victor6000* - Lucky Strike vent field, -1665 m (2020) © MoMARSAT 2020, IFREMER. All pictures have been reused under CC by 4.0.
## Hands-on

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. 8):

* Isabel Urbina-Barreto, Simon Delsol and Clément Delamare;

* Vincent Mahamadaly & Alexandre Sneessens;

* Loïc Van Audenhaege & David Price.

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 11, 12). Some stands proposed extra activities, such as mini ROV piloting in the hotel swimming pool and visualisation of a shipwreck using virtual headsets.

<figure><img src="image_12.png" /><figcaption>Figure 11. doi</figcaption></figure>

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.

As an example, for reproducibility purposes, the hands-on activities of Loïc Van Audenhaege and David Price is presented below:

1. Prior to the hands-on, a scene was created. Sand and fragments of different shapes were collected. After the workshop, fragments were put back in their original locations to comply with the environmental regulations;
2. Attendees first collected 42 images with a camera and from different angles of view and zooms of the scene. We advised that the stand leader checks carefully that shading on the scene is limited by the light position and participant standing location;

3. While images were being copied on the processing computer, participants could have an extra activity (e.g. piloting of mini ROV) and participate in discussions;

4. Participants then attended the processing of a 3D mesh on Agisoft displayed on a projector: feature extraction, image matching, sparse cloud computation, mesh creation, texturing and scaling. For each of the steps, the output was checked and explained (e.g. camera optimisation: check of features matched and discarded in different pairs of images). For pointcloud, mesh and textures, a file .txt, .obj and .jpg + .mtl were respectively extracted and their content and structure was displayed with notepad. The resolution of the final model was also investigated (e.g. number of vertices per m²). By zooming in and out on specific areas, we provided an idea on the resolution of the output (i.e. how many details were captured);

5. Once the model was exported in .obj, we loaded it on CloudCompare. We first taught participants how to navigate throughout a 3D model in the CloudCompare virtual environment. The mesh was subsampled in a pointcloud from which the normals were extracted and orientated. Slope, orientation and roughness were computed with different kernel radii to highlight the importance of defining a set of Kernel radius number(s) as it will ultimately constrain the scales of investigation for testing particular hypotheses. Statistics (e.g. histograms) of those descriptors were displayed. The output was saved as a .txt file to demonstrate the ease of using that workflow in R for multivariate analyses;

6. Throughout the hands-on, questions were freely asked by the participants who showed interest. Answering actually took most of the time needed to run the hands-on which encouraged us to provide a dynamic hands-on (in the future?). Interesting questions came up, such as what the regular time of processing is, what software do you advise etc.

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.

## Panel discussion

Due to time constraint, the panel discussion only lasted 40 minutes:

* What (developing) technologies could complement underwater photogrammetry to acquire high-resolution mapping? Sonar, Lidar and the hyperspectral camera in development were mentioned;
* Practical aspects of scale integration of photogrammetry were discussed, notably with sonar dataset acquired at much lower resolution;

* The differences between using SfM and colour band ratios to calculate bathymetry.

<figure><img src="image_13.png" /><figcaption>Figure 12. doi</figcaption></figure>

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.).

## Feedback survey

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.

## Methods

A Google form was set up to collect answers from each participant on the seven following questions:

1. Now that you know better photogrammetry, do you think it could be a valuable tool for your work (if you were using photogrammetry before, please answer N/A)?*¹

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)?*¹
3. Do you think that some aspects photogrammetry remained unclear or should have deserved more time?*¹

4. Feel free to comment your answer.*³

5. Do you think that some aspects of photogrammetry were too extensively detailed?*¹

6. Feel free to comment your answer.*³

7. On a scale from 1 (dissatisfied) to 5 (highly satisfied) by 3 (neutral), how clear were the presentations?*¹

8. Do you think of anything that could improve the presentations?*³

9. On a scale from 1 (dissatisfied) to 5 (highly satisfied) by 3 (neutral), how satisfied were you with the hands on?*¹

10. How would you improve the hands on?*³

11. On a scale from 1 (dissatisfied) to 5 (highly satisfied) by 3 (neutral), how satisfied are you with that workshop?*¹

12. Do you think of anything missing or that could be improved for that workshop?*³

N.B. All questions required an answer from the survey participants.

## Results

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. 13). From those 15 participants, 13 considered photogrammetry to have potential for their own work after the workshop.

<figure><img src="image_14.png" /><figcaption>Figure 13. doi</figcaption></figure>

Answers to Question 1 of the feedback survey: '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)?'

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. 14). This reflects the difficulty to adapt the workshop for beginners when working with time constraints. While we intended to provide an overview of the overall workflow, there remains space for them to play with their own data to empower them even more. Still, one participant attempted a reconstruction by his/her own after the workshop.

<figure><img src="image_15.png" /><figcaption>Figure 14. doi</figcaption></figure>

Answers to Question 2 of the feedback survey: '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)?'

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. 15). Five attendees found that all aspects were clear enough.

<figure><img src="image_16.png" /><figcaption>Figure 15. doi</figcaption></figure>

Answers to Question 3 of the feedback survey: 'Do you think that some aspects of photogrammetry remained unclear or should have deserved more time'?

4. Feel free to comment on your answer.

* "A handout for the software usage (a "cheat sheet") for a simple case";

* "Data quantity, best practice for handling large datasets";

* "Practical acquisition and processing of ROV data";

* "Short time frame and high number of people";

* "The hands-on session covered aspects that remained difficult to understand only with presentations".
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. 16).

<figure><img src="image_17.png" /><figcaption>Figure 16. doi</figcaption></figure>

Answers to Question 5 of the feedback survey: 'Do you think that some aspects of photogrammetry were too extensively detailed'?

6. Feel free to comment your answer.

* "The level of detail was good".

* "This workshop provided a great overview of photogrammetry applications".

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. 17).

<figure><img src="image_18.png" /><figcaption>Figure 17. doi</figcaption></figure>

Answers to Question 7 of the feedback survey: 'On a scale from 1 (dissatisfied) to 5 (highly satisfied) by 3 (neutral), how clear were the presentations'?

8. Do you think of anything that could improve the presentations?

* "More time for interaction between speaker and the attendees was needed";

* "Difficulty to see and hear";

* "Presentations on software".

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. 18).

<figure><img src="image_19.png" /><figcaption>Figure 18. doi</figcaption></figure>

Answers to Question 9 of the feedback survey: 'On a scale from 1 (dissatisfied) to 5 (highly satisfied) by 3 (neutral), how satisfied were you with the hands-on?'

## 10. How would you improve the hands-on activities?

* Give the option for attendees to discuss with the stand mentor what they want to practise;

* Smaller groups and not having groups in the same room were recommended several times;

* Providing more details on software functionalities during the hands-on session was recommended twice. More time for the hands-on and the possibility to attend different stands was also raised.

## 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. 19).

<figure><img src="image_20.png" /><figcaption>Figure 19. doi</figcaption></figure>

Answers to Question 11 of the feedback survey: 'On a scale from 1 (dissatisfied) to 5 (highly satisfied) by 3 (neutral), how satisfied are you with that workshop?'
12. Do you think of anything missing or that could be improved for that workshop?

* A cookbook was recommended;

* Possibility to participate to all group activities was also recommended;

* Giving the possibility for participants to bring their own data was suggested in order to discuss photogrammetry under various case studies and practicalities and help the audience to deal with their data at the same time;

* For a next edition, longer discussion panel (e.g. 2 hours) is suggested to better identify the needs and the challenges that the growing photogrammetry community will likely face in the future (e.g. data publication standardisation, novel acquisition technologies, generalisation of open-source photogrammetry software).

## Conclusion

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.

## Supplementary material

The material is provided in open-access at 10.5281/zenodo.7934452. It contains samples of presentation and images acquired during the hands-on.

## Acknowledgements

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.

Ethics and security

All participants consented to share their details in Table 1.

All participants consented to share anonymously their answers to pre- and post-surveys.

Author contributions

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.

Conflicts of interest

The authors have declared that no competing interests exist.

References

*   Bayley DI, Mogg AM (2020) A protocol for the large-scale analysis of reefs using Structure from Motion photogrammetry. Methods in Ecology and Evolution 11 (11): 1410-1420. https://doi.org/10.1111/2041-210x.13476

* D'Urban Jackson T, Williams G, Walker-Springett G, Davies A (2020) Three-dimensional digital mapping of ecosystems: a new era in spatial ecology. Proceedings of the Royal Society B: Biological Sciences 287 (1920). https://doi.org/10.1098/rspb.2019.2383

* Fukunaga A, Pascoe K, Pugh A, Kosaki R, Burns JR (2022) Underwater Photogrammetry Captures the Initial Recovery of a Coral Reef at Lalo Atoll. Diversity 14 (1). https://doi.org/10.3390/d14010039
* Lange I, Perry C (2020) A quick, easy and non-invasive method to quantify coral growth rates using photogrammetry and 3D model comparisons. Methods in Ecology and Evolution 11 (6): 714-726. https://doi.org/10.1111/2041-210x.13388

* Pulido Mantas T, Roveta C, Calcinai B, di Camillo CG, Gambardella C, Gregorin C, Coppari M, Marrocco T, Puce S, Riccardi A, Cerrano C (2023) Photogrammetry, from the Land to the Sea and Beyond: A Unifying Approach to Study Terrestrial and Marine Environments. Journal of Marine Science and Engineering 11 (4). https://doi.org/10.3390/jmse11040759

Endnotes

<footnote>*1 Only one answer possible</footnote>

<footnote>*2 Multiple answers possible</footnote>

<footnote>*3 Free answer</footnote>