Tuesday, 16 December 2014

Archaeobotany: identification of vegetal macro remains from "Battaglia excavations" in Ledro

In this post I'm going to summarize the work of identification of vegetal non-woody macro remains from the so-called “Battaglia excavations” (1937) in Ledro lake pile dwelling (Tn, Italy).
The materials are stored in the Museum of Anthropology of Padua and appear to be fairly preserved. They are in most cases charred, rarely waterlogged. For this reason the preservation status (and therefore also the morphometric variation and the color) is not uniform.
The work of identification is preliminary to future aDNA studies, in collaboration with Edmund Mach Foundation.

Some of the vegetal remains from Ledro at the Museum of Anthropology of Padua
In the autumn of 1929, when the level of Lake Ledro was appreciably lower than usual, after thousands of years a lake-settlement re-emerged into the light of day. Along the southern shores of the lake a forest of wooden piles (10.000) broke the surface, bearing all the marks of their long immersion. At first they were thought to belong to some long-forgotten sluice built to control the level of the lake, but soon they revealed to be the remains of the largest prehistoric site to have been uncovered hitherto in Italy.
Then the water-level rose once more and all was submerged, until the drought of 1936-37 lowered significantly the level of the lake and enabled further excavation to be undertaken. These are the excavations known as “Battaglia”, from the surname of the archaeological director.
These first researches, made by the University and the archaeological service of Padua, saw the continuation in years ‘50 and ‘60. In the 80s, the Natural Science Museum of Trento realized campaigns of excavations with techniques previously not available, following the stratigraphic criteria and adopting scientific naturalistic methodologies, that allowed the experts to agree in thinking 2,200 BC to 1,350 BC the dates of these pile dwelling life.

For our project (December 2014), the identification of macro remains has been accomplished to the naked eyed and with the help of a microscope for the difficult ones.
For the comparison, illustrated volumes, paper and digital atlas (such as the Digital Atlas of Economic Plants in Archaeology of the Groningen Institute of Archaeology – GIA, University of Groningen and of the Deutsches Archäologisches Institut – DAI, Berlin) have been used.

In the analysis, approximately 750 remains have been studied: 533 certain, 24 uncertain and 194 undetermined.

Summary table of the non-woody macro remains
It is possibile to observe a lot of edible plants, some of them cultivated, others wild. Among the cultivated species we can recognize wheat (Triticum monococcum/dicoccum L.) and barley (Hordeum sp. L.). Their seeds are really abundant (in some cases there are also fragments of ears) and show signs of combustion.

Charred cereals
Then there are fruits of hazels (Corylus avellana L.) and oak/holm oak (Quercus sp.), certainly used in alimentation.

Hazels fruits
There are also some fruits belonging to the family Rosaceae, but it wasn't possible to determine gender and species. The small size allow to rule out the possibility of wild apple (Malus domestica) and the spherical shape is not suited to the wild pear (Pyrus communis L.) reported by Battaglia in 1943. One of the most plausible hypothesis is that it is Sorbus sp. L.
The high presence of dogwood (
Cornus Mas L.), of which only a part seems to have been preserved at the Museum (Battaglia wrote of an entire layer composed of these seeds, while those remaining are only a hundred), does suggest its use in a massive way in the food field. One hypothesis, with archaeological and ethongraphic evidence, is that the dogwood was fermented to make a low alcohoolic drink. 
 
Dogwood seeds
In addition to fruits and seeds, in the collection we can find some galls of oak (Quercus sp. L.). The gall, or cecidia, is a malformation that may be due to several causes; these galls seem to be originated by an insect, the Cynips quercusfolii. These remains may have been gathered by the lake-dwellers to derive the tannic acid, in which are rich, a substance used in tanning.

Galls of Quercus sp. L.
Extremely fascinating are the plant remains identified as mixtures of cereals, a kind of "dumplings" made by kneading a cereal flour coarsely chopped. The morphology is rounded, the "nuggets" seem to be made by flattening the mixture on the thumb and then cooked on hot stones (another theory, proposed by botanist Della Fior in 1940, which for now is to be considered merely hypothetical not being proven by scientific analysis, is that the internal cavity is the space for a filling of some kind).

The aspect relating to the alimentary economy is really meaningful, in particular the relationship between agricultural practices and gathering of wild vegetables. We can assume a certain balance in the use of both resources. Indeed, the environment offered many food resources that were certainly exploited by the inhabitants. The groups of herbaceous plants that characterize the wet grasslands and ruderal sites still provide an alternative and complementary source of food.

This project has been also an opportunity to make the first tests on geometric morphology techniques in archaeobotany using open-source softwares as MorphoJ. In future we will try to develop and make available these methodologies.

Saturday, 13 December 2014

Forensic Facial Reconstruction, the state of the art

As many of you know last week a team of the University of Leicester have publicly revealed to have discovered, in all likelihood, the tomb of Richard III. The results seem comforted by the analysis of mitochondrial DNA, while the discrepancy on the Y chromosome could be explained by a false paternity. The study was completed with a forensic facial reconstruction of the king, performed by the experts of the University of Dundee, led by Caroline Wilkinson, Professor of Craniofacial Identification.
Given the opportunity, I decided to publish here our state of the art on this particular field (forensic facial reconstruction applied to archeology), publishing the presentation that I gave during the study day in honor of Prof. Franco Ugo Rollo (Ascoli Piceno, November 26 2014).

You can see the presentation here below (better visualized at this link)...
 



... and here is a brief explanation of each slide:

SLIDE 1

A remember of Franco Ugo Rollo, professor at the Camerino University. It was not my fortune to know personally Prof. Rollo, but his name is surely well known also in my discipline (archeology).

SLIDE 2

"Digital faces: new technologies for the forensic facial reconstruction of the historical figures".
The presentation intend to be an overview of the digital methodologies of FFR with FLOSS, developed in the last two years on the blog ATOR with a spontaneous contribution of different authors.

SLIDE 3

The traditional work-flow involves several operations: 3D scanning the skull, preparing a replica, performing the anthropological analyses, placing the tissue depth markers, reconstructing the profile, modeling the muscles and skin, calibrating the model with the available sources and dressing it.

SLIDE 4

The same operations are necessary for the digital work-flow. Our main work has been to turn the traditional process into a digital one, using only FLOSS.

SLIDE 5

There are different technology to obtain a 3D digital copy of the original skull. The main two we are using are: SfM - IBM and X-ray CT.

SLIDE 6

IN 2009 Arc-Team perform the first test in applying SfM - IBM with FLOSS to Cultural Heritage, during its participation at the TOPOI excelent cluster of Berlin.

SLIDE 7

The test developed in a collaboration with the French researcher +Pierre Moulon (Université Paris - Est and Mikros Image; actually at Acute3D) to integrate SfM - IBM software in ArcheOS 4 (codename Caersar)

SLIDE 8

The first test (TOPOI Löwe) gave positive results

SLIDE 9

The process is mainly based on different photos with different orientations, computing the displacement of common points between images

SLIDE 10

To complete the 3D documentation of an object, the next step is the so-called mesh-editing, which can be performed in the software MeshLab (developed by the Visual Computing Lab at the ISTI - CNR of Pisa, Italy)

SLIDE 11

In order to validate the digital method of FFR, some unconventional procedures (derived from the hacker culture) have been adopted. With reverse engineering techniques, based on SfM, it has been possible to digitally replicate the process of past FFR projects and to compare the results.

SLIDE 12

The anthropological validation has been performed comparing the result of 3D models obtained with SfM - IBM and the relative results coming form 3D scan (the observed distortion remained in the range of 1 mm).

SLIDE 13

In several projects it is possible to work with DICOM data. In these cases the anthropological analysis is more accurate. (3D VS Voxel)

SLIDE 14

The main software we used for DICOM data is InVesalius, mainly developed at the Renato Archer Information of Technology Center, an institute of the Brazilian Ministry of Science and Technology.

SLIDE 15

"X-ray computed tomography (X-ray CT) is a technology that uses computer-processed X-rays to produce tomographic images (virtual 'slices') of specific areas of the scanned object, allowing the user to see inside without cutting." (Wikipedia)

SLIDE 16

Also in this case, the process was validated with unconventional procedures derived from hacker culture. With reverse engineering of CT videos it has been possible to rebuild DICOM data and the 3D model of different skulls, replicating FFR projects and comparing the results.

SLIDE 17

It is necessary to check and validate the protocol with a continuous methodological comparisonwith all the available resources. For this reason, we tried also the FFR of Henry the IV, a project in which Prof. Rollo was involved, rejecting (with other scholars) the attribution of the mummified head to the French king. Our test in this case is just an experiment, starting from low quality data, but it is a good example to show some benefits of digital FFR, like the possibility to quickly modify the reconstructed face (e.g. closing the mouth in order to perform superimposition with the death mask), an operation not so simple with tangible models.

SLIDE 18

Once obtained the 3D model, digital anthropological analyses do not differ from traditional ones.

SLIDE 19

In some cases, a virtual restoration of the model is necessary. The solution comes from symmetrical and boolean operations of 3D modeling software (Blender).

SLIDE 20

The whole process of 3D modeling is actually performed in the software Blender.

SLIDE 21

The first operation is to fix the 3D skull on the Frankfurt plane, which replicates the head position of a standing human figure.

SLIDE 22

Than tissue depth markers are placed. The software keeps automatically the correct normal of each marker.

SLIDE 23

In our works, for depth tissue markers, we use the tables of Degreef et alii (2006)

SLIDE 24

A second step is the profile reconstruction.

SLIDE 25

For nose shape we refer to G. Lebedinskaya method.

SLIDE 26

The validation of the method came mainly from the comparison between FFR models and the facial DICOM data of living people, a simple simple with digital techniques, using the software CloudCompaer. All this experiment were conducted ans blind test (the artist did not know the identity and the fisionomy of the people).

SLIDE 27

According to the blind test, main deviations were detected on the cheeks.

SLIDE 28

Like other 3D operations, muscles modeling has been performed in Blender.

SLIDE 29

The technique hes been continuously rationalized and optimize. For instance, once the main muscles are modeled with metaballs in Blender, the result can be reused in successive reconstructions through an anatomical deformation.

SLIDE 30

It is possible to reach more realistic results through specific modeling tools,
like the "sculpt mode" in Blender.

SLIDE 31

Also skin modeling is an operation to be performed in Blender

SLIDE 32

Again the technique has been optimized: In order to simplify and speed up the process, a neutral facial model has been  created.

SLIDE 33

The neutral model can be anatomically deformed on different skulls to meet gender and age dimorphism.

SLIDE 34

At the same time, the neutral model can be deformed to meet the anatomical criteria which determine the individual dimorphism.

SLIDE 35

After the reconstruction process, two main models are defined:  one with hair and one hairless.

SLIDE 36

Thanks to the latest developments of the software MakeHuman it is now possible to further simplify and speed up the technique. Our actual research is following this direction.

SLIDE 37

The first tests carried out in 2014 have yielded positive results, thanks to the new feature which loads base raster images. The software is also perfectly compatible with Blender.

SLIDE 38

A further development of the protocol will allow to obtain high quality forensic facial reconstructions, in less time, without the need to master the techniques of 3D modeling.

SLIDE 39

At the end of the FFR process, the final model is calibrated with historical, archaeological and medical sources.

SLIDE 40

In case of historical reconstructions, the model appearance (hairstyle and clothing) is calibrated depending on era and culture, while the physical characteristics (color of hair and eyes) are set basing on the ancestry.

SLIDE 41

The 3D printing technologies allow the materialization of the model with different levels of detail.

SLIDE 42

A case study: the forensic facial reconstruction of St. Anthony of Padua 


SLIDE 43

The 3D scan was carried out on the bronze cast performed by R. Cremesini in 1981.

SLIDE 44

The cast done by R. Cremesini is very important, because it derives from the temporary anatomical reconnection of the skull and the jaw, which were separated since the first survey of the tomb (1263). 

SLIDE 45 

3D scan has been performed with the SfM - IBM software of the archaeological GNU/Linux distribution ArcheOS.

SLIDE 46

The final model has been presented Tuesday, June 10 at the event "Scoprendo il volto di Antonio" at the Centro Culturale S. Gaetano in PAdua (Italy)  

SLIDE 47 - 50

Digital FFR allows to further define the details of the model to reach a more realistic result.

SLIDE 51

Thanks to the collaboration with the Centro de Tecnologia da Informação Renato Archer - CTI (Ministério da Ciência and Technology do Brasil) the model was printed in 3D.

SLIDE 52

One of the materialized models was repainted by the Brazilian Mari Bueno,
specialized in religious art.


SLIDE 53

Thank you for your attention!


 

Wednesday, 3 December 2014

Space archaeology

Per aspera ad astra

When you start a new research you know where your path begins, but you do not know where it will end (and where it will take you). 
As many of you knows, we work also with 3D printing of archaeological objects: here (1 and 2) is the two post +Leonardo Zampi wrote about the Taung Project and here is a post regarding some Augmented Reality applications, in one of which a 3D printed skull was used (look the first video).
Most of these experiments are connected with the open source exhibition "Facce. I molti volti della storia umana" (please, do not forget our crowdsourcing campaign: send us your images!). For this event, whose English title is "Faces. The many aspects of human history", we planned to used 3D printed objects for different Augmented Reality applications and to expand the accessibility to the digital exhibit for the visitors (reducing the restrictions connected with disability). This post reports an preliminary overview of the event (done during the European Academic Heritage Day 2013), in which are presented the main topics of the exhibition, the problems and the solutions we planned to apply (sorry, the slides are in Italian; I will translated the text ASAP).
Today, working on a new research for this exposition, I tested different possibilities to reconstruct a 3D from a unique image. Normally our (Arc-Team) work-flow starts with a 3D model obtained from Structure from Motion and Image-Based Modeling (using different software) or from x-ray Computer Tomography (like for the paleoart or mummiology projects), but in archeology can happen to use Single View Reconstruction techniques when there are no other solutions. This post of +Cícero Moraes is a good example of a reconstruction in Blender based on perspective and vanishing points. Of course this technique is optimized for architectural documentation of structures, but is almost unusable for more irregular objects. 
To avoid this problem I studied different possibilities and I decided to use the same software, Blender, but in a different way. I looked in internet for an archaeological picture that could meet my requirements: not too simple, but with a correct light exposition. My problem in finding a good base image comes from the fact that the archaeological artifact photography has codified rules and normally the light source is located in the upper-left corner, otherwise bas-relief (convex) would appear as counter-relief (concave) and vice versa (due to the Hollow-Face optical illusion).
After a while I found this image, which has an almost correct light exposition (sorry, I do not know anymore the source of the photo and I did not find informations about the author).

The base image
I modified the picture with GIMP, in order to obtain a grayscale photo, than I imported it in Blender.

The grayscale image
There I used the "displace" modifier and I automatically obtained a fast 3D of the object (of course nothing comparable with SfM and IBM technique, but enough for my SVR needs).

The displace modifier
After some additional smoothing operation in Blender (you can directly use the related modifier), the model was ready to be saved as an stl file, loaded in Cura and printed in 3D.

The stl file in Cura
At this point I was ready to adapt the entire process to my needs in order to work for the exhibition "Facce", but here is were my research took a complete different way.
On my desk was lying a local newspaper in which was a photo of the Italian astronaut Samantha Cristoforetti, who is actually on board the International Space Station (ISS). Dr. Cristoforetti was born in Milano, but her family is originally form a town (Malé) very close to the one in which I live (Cles) and this is the reason why local press is following her scientific mission very closely. Reading the article I was thinking that it would be nice to print in 3D something that could be a tribute to her work and to the whole mission: something related with space exploration and archeology. Suddenly in my mind appeared a black and white picture, which probably most of you know and that dates back to July 20 1969, so I decided to test the process on this image and see the result.
I searched on the NASA website regarding the Apollo 11 mission and I found what I was looking for: the photo of the first footprints on the moon. I turned the picture into a grayscale image and I repeat the protocol of Single View Reconstruction with this data

The grayscale image
The video below shows all the work-flow and is a new videotutorial for the Digital Archaeological Documentation Project.



Of course the result has no metric, nor topographic value and it is more an artistic reconstruction than a 3D documentation, but this time it was just for fun and for a tribute to woman's contribution in space exploration. BTW on board the ISS astronauts are currently testing 3D printing in space (Made in Space).
If you want to print directly the .stl file I did, you can download it at this link. Otherwise in this post you can find all you need to do the process by yourself.
Have fun! 

Sunday, 30 November 2014

The reconstruction of an Egyptian mummy in Latvia

Final facial reconstruction of the mummy


Sveiki mani draugi!

Or "hello my friends" in Latvian. Latvia is a country in the Baltic region of Northern Europe, one of the three Baltic states. It is bordered by Estonia, Lithuania, Russia, Belarus and by a maritime border to the west with Sweden. Latvia has 1,997,500 inhabitants and a territory of 64,589 km².

TV story in a Latvian channel
It was precisely from this country, specifically from Riga, the capital, that I received a message via Facebook Messenger few weeks ago. The initial contact was made by the expert in stereoscopic technologies Artūrs Šlosbergs. He told me of a project involving the facial reconstruction of a mummy belonging to the Art Museum Riga Bourse collection.


First presentation of the 3D application with real-time manipulation via Kinect and stereoscopic view (3D glasses).
The project had two great challenges. 1) The mummy did not have richly segmented tomography, but only with some x-ray and CT with a few cuts in the body. 2) The project was to be finished soon as possible (it's my friends, this does not happen only in Brazil, like I thought).

Steps of facial and body reconstruction, starting from skull modeling and then the body's adequacy initially configured in MakeHuman and subsequently imported into Blender

As I worked on something similar in Tothmea project (an Egyptian mummy), where we reconstructed her skull joining data from multiple materials (CT-Scan, X-ray and photogrammetry) we could rebuild considerable part of the structure needed to make the reconstruction. It is clear that the volume of the skull of the last mummy is an approximation, but this was done using accurate data.

Bone structure previously configured in software MakeHuman
But the challenge did not stop there. Modeling the skull was only the first part. They would need a full body character to be animated via Kinect. Who works with modeling and animation knows that a full-length setup for this to be articulated is not a trivial task. Fortunately I had with me the MakeHuman, a free software to create "human beings parametrically." And among the many interesting features, it is possible to select a predefined rig system for the type of animation you need, be it for a movie or even a game, as was our case.

Adaptation of the mesh created in MakeHuman to the skull and the face drawn with the technique Manchester + Lebedinskaya.
To adapt the character to the game room they put me in touch with the game developer Jānis Lācis, and he guided me to know what we would need to change, since the deadline was short.

I also met Mr. Dmitrijs Ščegoļevs owner of PARUS studio Ltd., the company that hired me for this work. I must say that everything was very peaceful, the staff of Latvia is very objective and worked almost without sleep to make the application was finished. Even though I was weakened by a terrible sinusitis, the time zone and an excess of commitments could more or less follow them and end the task when the time was almost expiring.

Priest (mummy) properly linked and already with their costumes, compatible with the historical period from observations of archaeologist Dr. Moacir Elias dos Santos (thanks!). GLSL within Blender.
In addition to being kind people, Latvians are good at press office. Quickly the news of the reconstructed mummy took the headlines of some news sites.

Link: http://www.lgblog.lv/2014/11/21/dodies-virtuala-celojuma-pa-noslepumaino-valsti-nilas-ieleja-ar-lg-electronics/

Link: http://m.la.lv/izstade-tutanhamona-dzintars-vares-digitali-pieskarties-eksponatiem/

 TV story: http://ltv.lsm.lv/lv/raksts/14.11.2014-kulturas-zinjas.id38844/

 Link: http://www.lnmm.lv/lv/lnmm/info/learn/programs/pasakumi/varti-uz-egjipti/

Finally, I can only say I am very happy and pleased to have participated in this project. Thank you very much PARUS Studio, and thank you also to Professor Dr. Moacir Elias Santos for providential help regarding the clothing of the mummy.

A big hug to everyone and see you soon!

Friday, 28 November 2014

Member of Arc-Team receives an honorary title in Brazil

Small press conference. Below left Councilman Fernando Brandão and right Councilman Fernando Assumption.


Dear friends,

It is with great joy that I share with you the honorary title I received from the City Council of Sinop-MT in Brazil. This is an honorific title known as "Comenda Colonizador Enio Pipino," (Commendatory) that is offered the personalities that stand out in various ways, in my case was in relation to computer graphics work exercised with Blender and free software.

 [Subtitled in English] Clipping of TV stories presented during the vote to show the to show the projection of computer graphics work around the world

On November 10, 2014, during the 38th Session of the City Council, the Legislative Decree No. 022/2014 Project was presented under prot. No 808/2014, authored by councilors Fernando Brandão and Dalton Martini, whose main body describes the following:

Decree Law copy signed by the councilors.

"The City Council of Sinop - State of Mato Grosso, in exercise of its statutory duties approved and the President promulgate the following Legislative Decree:

Art. 1. Is granted the Commendation Colonizador Enio Pipino the Lord Cicero André da Costa Moraes - in recognition of the Municipal Legislature for its outstanding performance in computer graphics, helping to project Sinop around the country including at the international level."


Note newspaper with the title "Nerd Commendatory" describing the vote and talking about a creation of a scientif center based on free software

The project was approved unanimously in single vote.

It is important to document that thanks to this commendation the Jamerson Mileski Journal reporter Capital proposed the creation of a science institute devoted to the use of free software, and Councilman Fernando Brandão answered and will lead to the plenary at an early date.

Blog post of Councilman Fernando Brandão about the honorary title and the future project to establish a scientific research center focused to free software
This is the second honorary title issued by the City Council in two years. First it was a Motion of Applause also offered me due to the projection that the computer graphics work achieved at national and international level.

Aerial photo of Sinop city

We of Arc-Team are glad and honored to realize that the authorities and representatives of the population are becoming more interested in free technologies, which above all contemplate the society widely.

We leave here our thanks to City Council of Sinop!

Sunday, 23 November 2014

A study day in honor of Prof. Franco Ugo Rollo

Next week, on November 26, will be held a study day in honor of Prof. Franco Ugo Rollo, the famous anthropologist at the University of Camerino who sadly left us this year.
I have been invited to participate in the event, which will take place in Ascoli Piceno and Monsampolo del Tronto, where the Professor analyzed the mummy which are now exposed in the Museum of the Crypt of the S. Mary Church.
During the first session in Ascoli (in the morning) Prof. Gino Fornaciari (University of Pisa) will give a presentation titled "Fra principi e mummie: le origini della paleopatologia moderna" (en: "Between princes and mummies: the origin of modern palaeopathology". Later, Marco Samadelli, of EURAC, will speak about "Life Traces. Alla ricerca della vita nel microcosmo: batteri psicrofili e psicrotolleranti nella mummia dei ghiacci" (en: "Life Traces. Searching the life into the microcosm: psychrophilic  and psicrotollerant bacteria in the ice mummy"). Before the lunch break I will talk about "Volti in byte: le tecnologie digitali per la ricostruzione dei volti del passato" (en "Faces in bytes: new digital technologies for the forensic facial reconstruction of historical figures").
The second session will take place in Monsampolo, with a guided tour in the Museum of the St. Mary's crypt.
The event is organized by the University of Camerino (Scuola di Bioscienze e Medicina Veterinaria; Scuola di Scienze e Tecnologie, Corso di Laurea in Tecnologie e diagnostica per la conservazione e il restauro) and the municipalities of Ascoli Piceno and Monsampolo del Tronto. 

IMHO the study day promises to be interesting and it is worth to attend for people living in the nearby. For more information I publish here the official poster:

The poster of the event

Friday, 21 November 2014

Arc-Team: Conflict Archaeology of the First World War on the Carnic ridge and in the Sexten Dolomites

With the centenary years 2014–2018, a hitherto relatively unknown branch of archaeological research, the so-called conflict archaeology, is coming into the limelight. Since  excavation work is able to supply only very selective assertions on account of the enormous extent of the mountain front, the overriding objective of monument conservation in the years to come must focus on taking stock of all material remains from the WWI era.




As a result of the developments in satellite geodesy and 3D documentation, it is now possible to approach this task on a wide scale and comparatively economically. The data collected form the basis of targeted protection measures and provide for future reference numerous new methods of presentation which fulfil the requirements of nature and monument preservation as well as the growing interest of demographic groups.

The article is illustrating the latest research results of Arc-Team and is written in German Language by Rupert Gietl. 
It was published inside the volume:
Das Pustertal und der Krieg 1914–1918 (TAP-Forschungen, Bd. 2) by the 
Tyrol Archive for Photography (TAP)

Download the article


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