Luis Gutiérrez

University College Dublin, School of Biology and Environmental Science, Graduate Student

Followers

Following

Co-authors

Public Views

Biological Imager with 3D expertise in macro and microscopy approaches for scientific studies, science disclosure, museum exhibitions and collection digitisation.
Address: Dublin, Dublin, Ireland

less

InterestsView All (14)

Uploads

Papers by Luis Gutiérrez

Rise of the Cybercrabs: how digital cloning in an integrated taxonomic framework can support deep-sea exploration

ABSTRACTTaxonomy has been a labour-intensive field of expertise based on hours of manual work and... more ABSTRACTTaxonomy has been a labour-intensive field of expertise based on hours of manual work and lengthy comments that are mainly bound to books and publications on a two-dimensional world. But every species described is a three-dimensional organism that needs to be seen, manipulated to be fully understood in its native shape. Nowadays, digital technology allows us to transform everyone in an avatar or a digital clone with ease, but collections do not provide many type specimens in a digital format. Here we present a simple approach used to study a specific deep-sea crabSegonzacia mesatlanticaand provide online digital taxonomy across four repository sites. This offers the possibility to describe, exchange digitally and analyse specimens in its full 3D, establish their taxonomy and share them widely on online databases as well as physically by additive manufacturing to duplicate them in collections and outreach activities. Using an integrated taxonomic approach that included the us...

Download

Simple methods for interactive 3D modeling, measurements, and digital databases of coral skeletons

Limnology and Oceanography: Methods, 2015

Coral studies rely on comparative research between several reference coral skeletons and living o... more Coral studies rely on comparative research between several reference coral skeletons and living organisms imaged on reefs. However, many of these skeletons are part of collections, making extensive comparative works difficult. Nowadays, imaging technologies and image processing approaches allow acquisition of threedimensional (3D) datasets that can be converted to virtual models. These models can be made easily accessible and shared among collaborators or researchers using the Internet. Here, we compare high cost and low cost technologies on coral skeletons as well as imaging phantoms for accurate reference. We generated 3D models that were compared. Even though CT scanning and photogrammetry are the most accurate methods the latter is far less costly. It also allows for texture mapping, an essential tool in the field, and easy dataset handling. We submitted these 3D virtual models to experts for taxonomical identification, and they identified all specimens accurately. Finally, we further discuss applicability of our approach on museum collections, living corals, and field work.

Download

Light Sheet Fluorescence Microscopy: beyond the flatlands

Light Sheet Fluorescence Microscopy (LISH-M) is a true fluorescence optical sectioning technique,... more Light Sheet Fluorescence Microscopy (LISH-M) is a true fluorescence optical sectioning technique, first described by Heinrich Siedentopf in 1902 under the name of Ultramicroscopy. Light sheet microscopy utilises a plane of light to optically section samples. This allows deep imaging within transparent tissues and whole organisms.As tissues are exposed to only a thin plane of light, photobleaching and phototoxicity are minimized compared to wide-field fluorescence, confocal, or multiphoton microscopy. Additionally, the use of a light sheet reduces drastically out-of focus light and improves the signal-to-noise ratio of the images. Light Sheet Fluorescence Microscopy combines the advantages of wide-field methods (speed, flexibility, and dynamic range) with those of a confocal arrangement (optical sectioning). The last ten years have witnessed several implementations of this technology constructed by different laboratories under various acronyms: OPFOS, SPIM, TSLIM, MISERB.... Most of ...

Assessing the Capabilities of Additive Manufacturing Technologies for Coral Studies, Education, and Monitoring

Frontiers in Marine Science

Additive manufacturing, better known as 3D printing is becoming an easily accessible method to pr... more Additive manufacturing, better known as 3D printing is becoming an easily accessible method to produce 3D objects ranging from medical devices to jet plane parts. However, this implies the creation of an accurate 3D digital model by Computer Assisted Design (CAD) or direct acquisition of a 3D model as well as a correct understanding of the various 3D printing technologies available with their pros and cons. Here, we present a method for editing and printing of 3D models of coral colonies for the generation of accurate and enhanced 3D models suitable for research and education. This is a follow-up from other papers where 3D scanning was performed on fresh coral samples from field trips and coral skeletons from museum collections using different imaging techniques (multi-image photogrammetry and Micro CT scanning). 3D scans of colonies and samples of Turbinaria sp., Leptoseris incrustans, Oulophyllia crispa, Echinopora sp., Siderastrea savignyana, and Platygira daedalea were used to produce multi-material and multi-scale 3D prints. Moreover, we studied the best practices for the 3D printing processes, and potential technologies most suitable for specific attributes in this practice. Additionally, we show the innovative application of 3D printed inert reactive corals able to indicate environmental changes, along with insights into the potential uses for the proposed method and related systems in biological fields and sharing with an online community.

Download

Applications for advanced 3D imaging, modelling, and printing techniques for the biological sciences

2016 22nd International Conference on Virtual System & Multimedia (VSMM), 2016

Many zoological activities, including scientific expeditions, or in educational settings, necessi... more Many zoological activities, including scientific expeditions, or in educational settings, necessitate disruptive removal of specimens from their natural environment. The Anthropogenic Effect theory present by Courchamp clearly indicates the unsustainability of current practices, with dramatic changes necessary for the wellbeing and sustainability of our ecosystems. For both public, and academic, education and research, there is a clear link between increasing rarity and access limitation for certain specimens, leading to the decrease in both public awareness and capability for education and research. From this research's prospective, an idealized situation is where fully digital specimens can be created to represent 3D geometry, visual textures, mechanical properties and specimen functionality, allowing for exact replicas to be generated from this digital specimen when required. Combining this with the use of virtual reality, augmented reality, and mixed reality can satisfy the educational and research needs but also the sustainability of our ecosystems. The aim of this paper is to explore the potential use of combinations of emerging technologies such as 3D scanning alongside various 3D printing and virtual reality techniques to fulfil the goals outlined previously. Examination of the 3D modelling process and how these models can be enhanced for educational proposes will be presented with a focus on corallites and crab specimens. The methods presented are fully translatable with the results showing the true potential of these techniques for education, research and conservation. A futuristic outlook is presented on the potential applications, including education, museum displays, conservation, and scientific analyses, with discussion on the implications for global conversation and sustainability of ecosystems.

2 Headed Coral SLR Scale2cm

C-Di Photogrammetry on Mushroom coral (Scale bar 2cm)123D Scale2cm

C-Oc Photogrammetry on Tubular coral (Scale bar 2cm)

End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites

PloS one, 2016

Download

The Tara Oceans Expedition

infocus Magazine, Mar 6, 2014

Download

Applications for advanced 3D imaging, modelling, and printing techniques for the biological sciences

by Colin Keogh and Luis Gutiérrez

3D Printing Solutions for Coral Studies, Education and Monitoring

by Luis Gutiérrez and Colin Keogh

Since the early adoptions of 3DP (3DP) technologies in the late 80's, and more significantly by ... more Since the early adoptions of 3DP (3DP) technologies in the late 80's, and more significantly by the rep rap movement in 2005, 3DP has become extremely accessible. There are many different new and exciting methods of 3DP but it the increase in accessibility, through low cost and easy to use formats that has seen 3DP’s diffusion across nearly all sectors. There have been astonishing results in medicine, engineering, product design and art, paleontology, archaeology, biomolecular sciences, and even fashion. The methods focused primarily on in this paper are Stereolithography (SLA) and Fused Deposition Modelling (FDM). However, no matter the method the critical factor for all is extremely high quality Computer aided design (CAD) models to drive the printing process. The ultimate goal of this paper is for the nondestructive testing, replication, and analyses of corals and corallites. As part of this there is a strong focus on Micro CT scanning and Multi-image Photogrammetry for extremely high resolution CAD model generation. Skeletons and fresh samples from corals and corallites were imaged using these techniques and subsequently 3D printed. Color, size, and post processing methods were varied to optimize contrast and differentiation of structures on the replicated samples. The use of reactive-sensory materials, as well as multimaterial printing is explored, especially on photo and thermo reactive in aquarium maintenance and coral studies. Overall there are numerous applications for this use of 3DP including education, museums displays, conservation, and scientific analyses, all with destruction of the corals.

Download

End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites

Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion pe... more Coral reefs hosts nearly 25% of all marine species and provide food sources for half a billion people worldwide while only a very small percentage have been surveyed. Advances in technology and processing along with affordable underwater cameras and Internet availability gives us the possibility to provide tools and softwares to survey entire coral reefs. Holistic ecological analyses of corals require not only the community view (10s to 100s of meters), but also the single colony analysis as well as corallite identification. As corals are three-dimensional, classical approaches to determine percent cover and structural complexity across spatial scales are inefficient, time-consuming and limited to experts. Here we propose an end-to-end approach to estimate these parameters using low-cost equipment (GoPro, Canon) and freeware (123D Catch, Meshmixer and Netfabb), allowing every community to participate in surveys and monitoring of their coral ecosystem. We demonstrate our approach on 9 species of underwater colonies in ranging size and morphology. 3D models of underwater colonies, fresh samples and bleached skeletons with high quality texture mapping and detailed topographic morphology were produced, and Surface Area and Volume measurements (parameters widely used for ecological and coral health studies) were calculated and analysed. Moreover, we integrated collected sample models with micro-photogrammetry models of individual corallites to aid identification and colony and polyp scale analysis.

Simple methods for interactive 3D modeling, measurements, and digital databases of coral skeletons

by Luis Gutierrez Heredia, Luis Gutiérrez, and Catherine D'Helft

Coral studies rely on comparative research between several reference coral skeletons and living o... more Coral studies rely on comparative research between several reference coral skeletons and living organisms imaged on reefs. However, many of these skeletons are part of collections, making extensive comparative works difficult. Nowadays, imaging technologies and image processing approaches allow acquisition of three-dimensional (3D) datasets that can be converted to virtual models. These models can be made easily accessible and shared among collaborators or researchers using the Internet. Here, we compare high cost and low cost technologies on coral skeletons as well as imaging phantoms for accurate reference. We generated 3D models that were compared. Even though CT scanning and photogrammetry are the most accurate methods the latter is far less costly. It also allows for texture mapping, an essential tool in the field, and easy dataset handling. We submitted these 3D virtual models to experts for taxonomical identification, and they identified all specimens accurately. Finally, we further discuss applicability of our approach on museum collections, living corals, and field work.

Download

Rise of the Cybercrabs: how digital cloning in an integrated taxonomic framework can support deep-sea exploration

Download

Simple methods for interactive 3D modeling, measurements, and digital databases of coral skeletons

Limnology and Oceanography: Methods, 2015

Download

Light Sheet Fluorescence Microscopy: beyond the flatlands

Assessing the Capabilities of Additive Manufacturing Technologies for Coral Studies, Education, and Monitoring

Frontiers in Marine Science

Download

Applications for advanced 3D imaging, modelling, and printing techniques for the biological sciences

2016 22nd International Conference on Virtual System & Multimedia (VSMM), 2016

2 Headed Coral SLR Scale2cm

C-Di Photogrammetry on Mushroom coral (Scale bar 2cm)123D Scale2cm

C-Oc Photogrammetry on Tubular coral (Scale bar 2cm)

End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites

PloS one, 2016

Download

The Tara Oceans Expedition

infocus Magazine, Mar 6, 2014

Download

Applications for advanced 3D imaging, modelling, and printing techniques for the biological sciences

by Colin Keogh and Luis Gutiérrez

3D Printing Solutions for Coral Studies, Education and Monitoring

by Luis Gutiérrez and Colin Keogh

Download

End to End Digitisation and Analysis of Three-Dimensional Coral Models, from Communities to Corallites

Simple methods for interactive 3D modeling, measurements, and digital databases of coral skeletons

by Luis Gutierrez Heredia, Luis Gutiérrez, and Catherine D'Helft

Coral studies rely on comparative research between several reference coral skeletons and living o... more Coral studies rely on comparative research between several reference coral skeletons and living organisms imaged on reefs. However, many of these skeletons are part of collections, making extensive comparative works difficult. Nowadays, imaging technologies and image processing approaches allow acquisition of three-dimensional (3D) datasets that can be converted to virtual models. These models can be made easily accessible and shared among collaborators or researchers using the Internet. Here, we compare high cost and low cost technologies on coral skeletons as well as imaging phantoms for accurate reference. We generated 3D models that were compared. Even though CT scanning and photogrammetry are the most accurate methods the latter is far less costly. It also allows for texture mapping, an essential tool in the field, and easy dataset handling. We submitted these 3D virtual models to experts for taxonomical identification, and they identified all specimens accurately. Finally, we further discuss applicability of our approach on museum collections, living corals, and field work.

Download

Luis Gutiérrez

Uploads

Papers by Luis Gutiérrez

Log In