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Alicona Infinite Focus metrology microscopy system for archaeological research

Lead Research Organisation: Natural History Museum
Department Name: Core Research Laboratories

Abstract

The NHM has been using an Alicona Infinite Focus G4 Microscope (IFM) for the analysis of 3D shape and form for over 15 years. The IFM differs from other digital microscopes in that it is a calibrated instrument designed primarily for the measurement of shape, dimension and surface roughness of complex objects of a variety of sizes. Unlike laser profilometry and confocal measurement systems IFM can generate image data and 3D models, and by use of an X/Y scanning stage, can build up models of larger objects. Since its measurements are traceable back to an ISO standard, the method is accurate and repeatable. Digital microscopes such as those offered by Hirox, Zeiss and Keyence do not offer this level of accuracy, although they share some of the functionality.

The IFM is most heavily used for archaeological research by NHM's Centre for Human Evolution Research (CHER) which investigates how 'modern human behaviour' can be defined, its origin(s) and the forms and expressions adopted by different species of hominins, through analyses of human-modified bones, teeth, and antlers from across Africa and Eurasia. Debates on the early appearance of cognitively complex behaviours have focused on whether they arose gradually and independently or were culturally transmitted from a single point of origin. Proposed indicators include innovations in bone and lithic technologies and the appearance of symbolically mediated behaviour represented by engraved designs and ornaments. Three key themes CHER explores are: i) Human Behaviour in 3D; ii) Documenting symbolic markings and iii) Examining tool use and development. The IFM is used to investigate bone and antler artefacts; butchery techniques; cultural modifications of human remains and cannibalistic practices. CHER have published >20 peer-reviewed papers and contributed to >30 conferences using the IFM (research which has >500 citations) and it is a vital tool in their research.

IFM has also been used to examine low relief and microfossils, has been tested on wax seals for the National Archives and historical typeface and matrices for the Type Archive (both with limited success). A novel application has been its use to create high resolution scans of coins which were 3D printed for use in outreach with visually impaired children.

The NHM's G4 has reached the end of its service life and our human remains collection cannot be moved from the London area. The G4 has been superseded by the G5+, which offers considerable improvements in sensitivity, speed and functionality. These include refinements to allow the instrument to cope with reflective and translucent surfaces. An additional rotary table (originally intended to examine the cutting surfaces of tools) allows a sample to be mounted in a "chuck" and rotated stepwise to create a full 3D model. This innovation would allow the examination and reconstruction of complex 3D shapes (e.g. shells and beads). Of particular interest is the examination of occlusal surfaces of teeth for dental microwear studies. The process is automated, so does not need the operator in attendance.

Furthermore, a simplified, portable version of the IFM is now available which could be taken into collections in other Museums or used for fieldwork to gather data on materials which could not be loaned to the NHM.

This application seeks funding to replace the G4 with the latest G5+ with the rotary table and an additional Alicona Portable RL system. This would expand the scope for novel research and increase data acquisition speeds. The combination of these instruments with the NHM's pre-existing imaging facilities (scanning electron microscopy and analytical SEM, micro-CT, laser and structured light scanning) would provide a formidable resource unparalleled in any European Gallery Library or Museum.

All instruments at the NHM are fully accessible to external researchers, visitors and industrial users.
 
Title Field Casting 
Description Field Casting is a research project and exhibition, developed by Matterlurgy (Helena Hunter and Mark Peter Wright) in collaboration with curator Taru Elfving (Contemporary Art Archipelago CAA) and Archipelago Research Institute (Turku University) on the island of Seili. Matterlurgy have worked with scientists in Seili since 2019 to understand practices of fieldwork, long-term data collection and modelling of the Baltic Sea. They have focused on the scientists' practice of reading data in the ear bone (otolith) of the Baltic Herring - a fish whose changing physiology has been linked to climate change. By analysing otoliths, scientists can learn about the Herring's age, growth, temperature conditions, diet, migration pattern, maturation and about pollution. Matterlurgy are interested in how the Herring otolith becomes a kind of archive that scientists read, speculate, and make predictions about climate change. From this research, they are developing artworks for an exhibition at Titanik Gallery in Turku from late Jan - early Mar 2023. For this exhibition they will be producing a sound installation that will feature a 3D scan of the Herring otolith. Using the Alicona IFM, the NHM created 3D datasets from the otoliths supplied by the artists and then recreated them through 3D printing at a length of about 30cm, about 100x life-size. The Alicona proved to be ideal for this purpose, since the imaging capability and software enabled us to obtain high resolution 3D scans of each side of each otolith and then to seamlessly stitch the two halves together. The output could then be imported directly into the slicing software for the 3D printer. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2023 
Impact None yet, the exhibition opened on the 2nd of February. Details of the programme of events associated with the opening are here: Opening: 2 February 6-8 pm. Welcome! Fri 3.2. at 3 pm Introduction to the exhibition followed by a discussion about field research of environmental changes in the Archipelago Sea. The event is in English. Sun 19.2. at 2 pm Tour of the exhibition and discussion about art-science collaboration on the island of Seili. The event is in Finnish. 
URL https://www.titanik.fi/field-casting/
 
Description The use of the Alicona systems purchased through the AHRC CapCo grant is still at a relatively early stage. However key deliverables to date have been:
1) career development through hosting early career researchers
2) the use of the Alicona Portable RL to collect data in other collections of international importance to the NHM's research team.

Of special note is the rapid turnaround from fieldwork collecting to data acquisition through being able to take the Alicona Portable RL to directly examine newly collected materials. Previously we would have had to wait until the materials were fully catalogued before applying for a research loan from Cambridge to the NHM (something which might not have been possible). When we applied for funding to purchase two systems, this was exactly the type of research we hoped to enable.

Furthermore, the instrument has been used to support a number of UK and International Research projects, including a project which attempts to test the quality of the data outputs from Infinite Focus Microscopy (IFM) and compare it to Confocal Microscopy and other techniques for examining surface features at high resolution. This extends previous research carried out at the NHM to compare IFM (using a previous generation system) with micro-CT scanning. Thus developing a bench mark for further comparison. These types of publications are widely cited.
Exploitation Route Publications and the collaborations under development are building a community of practice amongst anthropology researchers wanting to evaluate and develop methodologies associated with the technique of Infinite Focus Microscopy. The growing number of projects and the visitors in the past (2023) year, particularly early career researchers, demonstrate the need for this facility.
Sectors Environment

Culture

Heritage

Museums and Collections

 
Description Innovation and the Economy/Societal and the Environment Tom Ranson (NHM 3D Viz lab manager) completed 3D scans of fish otoliths for artists from Matterlurgy Studio to deliver 3D prints for exhibition at Titanic gallery in Finland. The exhibition sought to highlight how scientists evaluate the health of fish stocks through the reproduction of fish otoliths (used to determine the age of fish) as greatly enlarged tactile models to help support the exhibition. Approximately 500 people attended in total. This was a mixture of a specialist audience, for example many scientists attended from the University of Turku and also artists and students from Turku Arts Academy, in addition to members of the public and international tourists. The main feedback the artists got from the Otolith 3D prints is that scaling up and making these into tactile objects allowed people to grasp more concretely how they are used by scientists to understand environmental change.
First Year Of Impact 2023
 
Description 3-Dimensional methodology testing 
Organisation Catalan Institute of Human Paleoecology and Social Evolution
Country Spain 
Sector Academic/University 
PI Contribution With Lloyd Courtenay (University of Bordeaux), Dr Lucile Crété and Dr Silvia Bello (NHM) are testing different 3-Dimensional methodologies to study the topographic texture of bone and teeth surfaces at a microscopic scale. This is a combination of the 3D project and the GroundTruth project, directed by Lloyd. This collaboration is also developed with Noé Valtierra (IPHES, Spain) With Francesco d'Errico (University of Bordeaux), we are currently collaborating on the analysis of four fish bones from Tabun cave (Israel), which are the oldest fish bones used as tools. With Francesco and Lloyd Courtenay, Silvia is also working on Palaeolithic (dating between Ëœ 25 to 19 ka) engraved artefact from Ishango (Democratic Republic of Congo).
Collaborator Contribution Noé Valtierra: Silvia and Lucile hosted Noé (PhD student from the Catalan Institute of Human Paleoecology and Social Evolution, IPHES, Tarragona) from September to December on a 3-month internship. Noé was trained to use the Alicona 3D microscope housed at the Natural History Museum as part of his PhD, and to qualify for an international PhD. Noé's PhD research evaluates the effect of cleaning treatments on archaeological bone material and the impact that these may have on subsequent analytical studies. Using the Alicona, he could evaluate at a microscopic level how cleaning processes can alter bone surfaces. Additionally, he worked with the Alicona microscope at the NHM as part of the GROUND TRUTH project (directed by Lloyd Courtenay) to assess how the Alicona equipment compares with other microscopes for topographic micro-wear analysis.
Impact None to date
Start Year 2023
 
Description 3-Dimensional methodology testing 
Organisation University of Bordeaux
Country France 
Sector Academic/University 
PI Contribution With Lloyd Courtenay (University of Bordeaux), Dr Lucile Crété and Dr Silvia Bello (NHM) are testing different 3-Dimensional methodologies to study the topographic texture of bone and teeth surfaces at a microscopic scale. This is a combination of the 3D project and the GroundTruth project, directed by Lloyd. This collaboration is also developed with Noé Valtierra (IPHES, Spain) With Francesco d'Errico (University of Bordeaux), we are currently collaborating on the analysis of four fish bones from Tabun cave (Israel), which are the oldest fish bones used as tools. With Francesco and Lloyd Courtenay, Silvia is also working on Palaeolithic (dating between Ëœ 25 to 19 ka) engraved artefact from Ishango (Democratic Republic of Congo).
Collaborator Contribution Noé Valtierra: Silvia and Lucile hosted Noé (PhD student from the Catalan Institute of Human Paleoecology and Social Evolution, IPHES, Tarragona) from September to December on a 3-month internship. Noé was trained to use the Alicona 3D microscope housed at the Natural History Museum as part of his PhD, and to qualify for an international PhD. Noé's PhD research evaluates the effect of cleaning treatments on archaeological bone material and the impact that these may have on subsequent analytical studies. Using the Alicona, he could evaluate at a microscopic level how cleaning processes can alter bone surfaces. Additionally, he worked with the Alicona microscope at the NHM as part of the GROUND TRUTH project (directed by Lloyd Courtenay) to assess how the Alicona equipment compares with other microscopes for topographic micro-wear analysis.
Impact None to date
Start Year 2023
 
Description Anthropological material from Hacettepe University 
Organisation Hacettepe University
Country Turkey 
Sector Academic/University 
PI Contribution Silvia Bello and Lucile Crété were invited to participate to the World Neolithic Congress, and in particular to contribute to the session on mortuary practices and funerary treatment of the dead. This was the opportunity to present the work conducted over the past years on cut marks using the Alicona focus variation microscope. • Bello, S.M. (Podium) The archaeology of death: a review of the taphonomic traits associated with the manipulation and butchery of human bodies. • Crété, L., Parfitt, S.A., & Bello. S.M. (Poster) Non-masticatory striations on human posterior teeth from the British Neolithic: evidence of post-mortem treatment of the dead?
Collaborator Contribution Following the Congress, Lucile was invited to visit colleague Prof Yilmaz Erdal at Hacettepe University to look at anthropological material. During this visit, Lucile made molds of selected bone surfaces bearing cut-marks that are currently being scanned using the Alicona G5+. She also gave a talk entitled 'Bones, teeth and scratches: Inferring behaviours from ancient remains using 3D imaging', which was attended by around 40 students and research staff. This visit allowed preliminary data collection for a future study led by Prof Erdal, Silvia Bello, and Lucile Crété, and to discuss future collaboration on collections from Neolithic Anatolia.
Impact None to date
Start Year 2024
 
Description Catalan Institute - Spain 
Organisation Catalan Institute of Human Paleoecology and Social Evolution
Country Spain 
Sector Academic/University 
PI Contribution Silvia and Lucile hosted Noé Valtierra (PhD student from the Catalan Institute of Human Paleoecology and Social Evolution, IPHES, Tarragona) from September to December on a 3-month internship. Noé was trained to use the Alicona 3D microscope housed at the Natural History Museum as part of his PhD, and to qualify for an international PhD.
Collaborator Contribution Noé's PhD research evaluates the effect of cleaning treatments on archaeological bone material and the impact that these may have on subsequent analytical studies. Using the Alicona, he could evaluate at a microscopic level how cleaning processes can alter bone surfaces. Additionally, he worked with the Alicona microscope at the NHM as part of the GROUND TRUTH project (directed by Lloyd Courtenay) to assess how the Alicona equipment compares with other microscopes for topographic micro-wear analysis.
Impact None to date
Start Year 2023
 
Description Hebrew University of Jerusalem 
Organisation Hebrew University of Jerusalem
Country Israel 
Sector Academic/University 
PI Contribution Dr Lucile Crété (NHM) hosted Anaelle (PhD student from the Hebrew University of Jerusalem, Israel) in May-June 2023 to complete the data collection initially started in November 2022 during Lucile's visit to Jerusalem. This is part of the ongoing collaboration between Dr Silvia Bello (NHM) and Prof Rivka Rabinovich, fully funded by an Israeli National Research grant, which focuses on the faunal material from Kebara and Amud, two major cave sites in Israel containing Middle Palaeolithic archaeological layers dated to 70,000-50,000 years ago. In November 2022, Dr Lucile Crété (NHM) was invited to travel to Israel to continue an ongoing collaboration between Dr Silvia Bello and Prof Rivka Rabinovich, fully funded by an Israeli National Research grant. This project, initially started a few years ago before the pandemic, focuses on the faunal material from two major cave sites in Israel, Kebara and Amud, which contain Middle Palaeolithic archaeological layers dated to 70,000-50,000 years ago. Both sites were occupied intensively, as seen from the densities of lithic artefacts and bones, ashes derived from fireplaces and repetitive patterns of use of space throughout the time of occupation, as well as from the presence of Neanderthal burials. This study aims to explore the behaviours and technologies related to the procurement of animal resources and their ensuing treatment and disposal by the Neanderthal occupants of Kebara and Amud. By combining quantitative methods with analysis of the surface modifications (e.g., cut marks, striations, etc.), we aim to define and reconstruct the butchery practices applied at both sites. We will attempt to identify the parallel processes of decision-making from these faunal assemblages and the relation between environment and human behaviour at these sites. Our visit to the Institute of Archaeology at The Hebrew University of Jerusalem this year allowed us to work on the Amud collections with our Israeli collaborators to scan identified cutmarks on the remains, and allow future measurements and analyses of these marks. For this occasion, the Portable Alicona RL was for the first time transported by our team abroad for data collection, and proved to be a very useful tool to collect preliminary data. Further collaboration with our Israeli colleagues is planned for 2023 to complete data collection on the rest of the studied specimens.
Collaborator Contribution This year, Lucile and Anaelle successfully completed the data collection on the assemblage, using both the Alicona G5+ and the Portable Alicona. The data is currently being analysed and a resulting paper is in progress, led by Anaelle and Lucile.
Impact None to date
Start Year 2022
 
Description Late Palaeolithic Art Network in the Eurasian Region (PArtNER) 
Organisation Sapienza University of Rome
Country Italy 
Sector Academic/University 
PI Contribution Silvia helped develop a European Post-doctoral grant application (HORIZON Unit Grant) titled 'Late Palaeolithic Art Network in the Eurasian Region (PArtNER)' to host Dario Sigari at the NHM to conduct 3D analysis of Palaeolithic engraved artefacts from two key Palaeolithic art sites, Polesini Cave (in Italy) and Ovular Shelter (Azerbaijan). The project is Coordinated by Dr Marina Galinaro (Università degli Studi di Roma La Sapienza, Rome) and if granted, will start in Spring 2024. Silvia and Lucile started a collaboration with Elena Varotto and Francesco Maria Galassi (FAPAB Research Centre, Avola, Sicily, Italy) studying modifications of human remains buried at the Eneolithic site (4600-4300 BC) of Calaforno (Ragusa). Silvia and Simon started a collaboration with Sahra Talamo and Andrea Picin (University of Bologna) to develop analyses of Upper Palaeolithic sites in Poland. Silvia, Simon, Sahra and Selina Brace (aDNA Lab, at the NHM) are also developing an AHRC Curiosity Grant proposal to work on burial practices and genetic ancestry during the Upper Palaeolithic.
Collaborator Contribution Still in development
Impact None to date
Start Year 2023
 
Description Late Palaeolithic Art Network in the Eurasian Region (PArtNER) 
Organisation University of Bologna
Country Italy 
Sector Academic/University 
PI Contribution Silvia helped develop a European Post-doctoral grant application (HORIZON Unit Grant) titled 'Late Palaeolithic Art Network in the Eurasian Region (PArtNER)' to host Dario Sigari at the NHM to conduct 3D analysis of Palaeolithic engraved artefacts from two key Palaeolithic art sites, Polesini Cave (in Italy) and Ovular Shelter (Azerbaijan). The project is Coordinated by Dr Marina Galinaro (Università degli Studi di Roma La Sapienza, Rome) and if granted, will start in Spring 2024. Silvia and Lucile started a collaboration with Elena Varotto and Francesco Maria Galassi (FAPAB Research Centre, Avola, Sicily, Italy) studying modifications of human remains buried at the Eneolithic site (4600-4300 BC) of Calaforno (Ragusa). Silvia and Simon started a collaboration with Sahra Talamo and Andrea Picin (University of Bologna) to develop analyses of Upper Palaeolithic sites in Poland. Silvia, Simon, Sahra and Selina Brace (aDNA Lab, at the NHM) are also developing an AHRC Curiosity Grant proposal to work on burial practices and genetic ancestry during the Upper Palaeolithic.
Collaborator Contribution Still in development
Impact None to date
Start Year 2023
 
Description Making a point: early wood technologies of the British Isles 
Organisation University of Reading
Department Department of Archaeology
Country United Kingdom 
Sector Academic/University 
PI Contribution Joint project funded by University of Reading and Natural History Museum Partnership Project Members: Silvia Bello, Simon Parfitt and Lucile Crété (CHER, NHM), and Annemieke Milks (Department of Archaeology, University of Reading).
Collaborator Contribution We recorded and analysed in three dimensions the Clacton spear point, discovered in Clacton-on-Sea in 1911, using a variety of state-of-the-art imaging techniques, and interpret the internal and external features to better understand the object's 'biography'. Over a two-week period, the team undertook standard microscopy, 3D microscopy using the Alicona G5+, micro-Computed Tomography (HMX-ST 225 CT system), and 3D scanning (Artec Space Spider). We also created CT scans and a model of the earliest cast made, which helps to track the post-excavation alterations and modifications due to drying out of the wood. Initial results indicate, based on the internal features and differential density properties of the wood, that the hominins who made the Clacton spear point were aware of the wood's material properties, and shaped the spears by modifying the softer (less dense) side of the wood branch (figure 3e). Superficial analysis using the Alicona, also demonstrate how the wood knots were flattened and small wood flakes removed to shape the wood into a smooth artefact (Figure 2b-d). The analysis and images are currently being prepared to submit as a journal article in summer 2025.
Impact We recorded and analysed in three dimensions the Clacton spear point, discovered in Clacton-on-Sea in 1911, using a variety of state-of-the-art imaging techniques, and interpret the internal and external features to better understand the object's 'biography'. Over a two-week period, the team undertook standard microscopy, 3D microscopy using the Alicona G5+, micro-Computed Tomography (HMX-ST 225 CT system), and 3D scanning (Artec Space Spider). We also created CT scans and a model of the earliest cast made, which helps to track the post-excavation alterations and modifications due to drying out of the wood. Initial results indicate, based on the internal features and differential density properties of the wood, that the hominins who made the Clacton spear point were aware of the wood's material properties, and shaped the spears by modifying the softer (less dense) side of the wood branch (figure 3e). Superficial analysis using the Alicona, also demonstrate how the wood knots were flattened and small wood flakes removed to shape the wood into a smooth artefact (Figure 2b-d). The analysis and images are currently being prepared to submit as a journal article in summer 2025.
Start Year 2024
 
Description Modified faunal remains - Malta 
Organisation University of Malta
Country Malta 
Sector Academic/University 
PI Contribution Silvia and Simon Parfitt (NHM) recently started a collaboration with Eleanor Scerry (University of Malta) to analyse modified faunal remains from periods stretching from the Holocene to the Pleistocene.
Collaborator Contribution Still in development
Impact Still in development
Start Year 2023
 
Description Shanidar Cave 
Organisation University of Cambridge
Country United Kingdom 
Sector Academic/University 
PI Contribution Shanidar Cave (Iraq) Lucile was invited by Prof. Graeme Barker (Cambridge University) to join the 2023 field season at Shanidar Cave (Iraq) last May. This Palaeolithic site was originally excavated in the 1950s-1960s, and is considered one of the most important sites in the Middle East due to the large number of Neanderthal individuals found in the Middle Palaeolithic layers, interpreted as burials. Recent re-excavations have been focusing on improving the dating and understanding of the site, and on identifying further evidence of Neanderthal occupation. Lucile previously participated in the excavations in 2016, and returned this year to take part in the excavation and finds recording of Middle Palaeolithic layers containing traces of Neanderthal occupation, including evidence of fire and butchered fauna. Data collection Following her participation in the 2023 field season at Shanidar Cave (Iraq), Lucile was invited by Dr Emma Pomeroy to the Department of Archaeology at the University of Cambridge to start a potential collaboration involving the use of the Alicona microscope to study the Neanderthal dental remains recently found at Shanidar Cave. Lucile brought the Portable Alicona to Cambridge on this occasion, to collect preliminary data on the teeth to be further analysed in 2024. Following her participation in the annual excavations at Shanidar Cave in 2024, Lucile Crété was invited by the project research team to come to Cambridge University in January 2025 to assess bone surface alterations on excavated material, and scan some of the remains using the Portable Alicona RL for further analysis. During this visit, Lucile was invited to give a talk at the PalMeso seminars organised by the McDonald Institute of Archaeology, where she presented a summary of the work carried out at the NHM with Silvia Bello and Simon Parfitt using 3D imaging techniques such as the Alicona InfiteFocus microscope.
Collaborator Contribution Still in development
Impact None to date
Start Year 2023
 
Description Upper Palaeolithic engraved stone tool 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Silvia Bello initiated a new collaboration with Nick Barton (University of Oxford) to study an Upper Palaeolithic engraved stone tool. For this analysis, she produced 3D images using the Alicona G5+ of the engraved lithic artefacts. The goal is to find the most suitable method to reproduce and measure incision made on lithic tools.
Collaborator Contribution Provided samples for analysis
Impact None to date
Start Year 2024