Saturday 26 December 2015

ArcheOS Hypatia 3DHOP package (call for testing)

This short post is related with the previous one (about Nexus) and it is a call for testing for the deb binary package (arm64) of 3DHOP, the software developed by the Visual Computing Lab (CNR-ISTI, Pisa - Italy) to create interactive and multi-resolution web-galleries of 3D objects.
Here below you can see just an example of a gallery related with conflict archeology (WW 1), which we are developing in these days.

Example of a 3D web-gallery with 3DHOP (work in progress)

Being a Debian Jessie derivative distro, ArcheOS Hypatia will install 3DHOP in the folder /var/www/html/3dhop-3.0.
The best way to practice with this software is to modify the code of the different examples the package comes with (they are placed in /var/www/html/3dhop-3.0/examples).
For people that wants to help ArcheOS development and test this package, I upload it here. Soon we will prepare also 32-bit packages.

I hope this package will be useful! Merry Christmas and Happy new year!


Marco Callieri (Visual Computing Lab - CNR-ISTI) notified me that Nexus and 3DHOP are under development right in these days, so there will be probably a new version in a short time. As soon as there will be changes, I will update the packages with the new functionalities.

Monday 21 December 2015

Nexus 3 videotutorial

In order to help people in testing Nexus package for ArcheOS Hypatia (see the related post), I just recorded a fast videotutorial to show how this simple tool works.
Please note that the videotutorial refers to ArcheOS Hypatia's package, where Nexus binaries are stored in /usr/bin (so that they can be start from any path in the terminal). If you compiled your Nexus version somewhere in your home folder, than probably you will have to activate the binary from that directory.
Here below is the short video; I hope it will be useful.

Soon I will upload also the new 3DHOP package for ArcheOS Hypatia, with some instruction about it.
Have a nice day! 

Wednesday 16 December 2015

ArcheOS Hypatia Nexus package (call for testing)

Hi all,
Since we are working on a project related with a 3D gallery of WW1 remains, we are using the 3DHOP application (which has been also suggested by Nicola Schiavotiello in the ArcheOS-dev Mailing List), developed by the Visual Computing Lab of the CNR-ISTI (Pisa - Italy). In order to exploit the full potential of this software it is useful to use the tool Nexus (see the related issue in ArcheOS github) , to create batched multiresolution mesh structures (to enable Level of Details  - LoD - visualization). 

An example of simple visualization in 3DHOP

For this reason, today I took the occasion to build a simple binary package (for amd64), to be tested for ArcheOS. If someone wants to help in testing the package, it can be downloaded here. Please report in the comment of this post your feedbacks. 

Thank you all!

LAST UPDATED 2016-01-29

In order to implement the two new packages in ArcheOS Hypatia in a short time, we changed the architecture field of the control file of 3DHOP deb package to let it work with all the machines, while we compiled a new i386 package for Nexus. If you want to test the new packages, here are the new files:

3DHOP (architecture all)

Nexus (architecture i386)
Nexus (architecture amd64)

Soon we will update archeos-meta in order to implement these two software.

Any help in packaging is much appreciated!

Thursday 3 December 2015

Three more animals are saved with the aid of Blender and 3D printing

Three more animals were saved thanks to a partnership between classical Veterinary Medicine and new technologies. Victoria the goose, Greenie the parrot and Beakolin the toucan were given again the possibility to feed themselves without the aid of keepers.

Ganso passa por cirurgia inédita e ganha bico artificial
Bom Dia SP (Tribuna-Globo)Ganso passa por cirurgia inédita e ganha bico artificialLink original:
Posted by Cícero Moraes on Segunda, 16 de novembro de 2015

Victoria the goose was the first of her specie to receive a 3D printed prosthetic beak. She was found by Mr. Christian Negrão of the NGO Amigos do Mar (Friends of the Sea), at Comprida Island, about 200 km from São Paulo.

Her initial conditions were quite shocking.

A considerable portion of the rhinoteca (upper beak) and gnathoteca (lower beak) were absent.

Using his dental knowledge, Dr. Paulo Miamoto initialy cast a mold of the animal.

Next, Dr. Miamoto drew several lines on the cast, in order to make it easier for the photogrammetry algorithm and took pictures of it, using the digital camera as a 3D scanner.

Then my work began.

These pictures were sent to PPT-GUI, which converted them into a pointcloud. The resulting files were imported into MeshLab and the pointcloud was converted into a 3D mesh. The file was exported to Blender as Collada (.dae).

The airways were mantained on the prosthesis that was modeled from the original beak, on appropriate scale. This was possible thanks to an addon developed by Dalai Felinto at request of Dr. Everton da Rosa, a Dentist that grant permission to use this script (under development). This addon has brought Cork inside Blender. Cork is a standalone dor complex 3D boolean operations.

The resulting model was exported as a STL and open in Slic3r, which generated G-Codes for 3D printing. This process was greatly helped by Claudio Sampaio (Patola).

The Gcode file is nothing more than a set of instructions organized as a text, which is read by the 3D printer and makes possible to materialize objects.

The 3D printed model fit perfectly the model created by Dr. Miamoto, which was also responsible by the print and finishing of the prosthesis (which received a yellow layer of dental resin, that works as both aesthetic improvement but mainly as a structural reinforcement).

With the prototype the surgical procedure was initiated. Aenesthesists Dr. Marco Antônio Ramiro de Campos and Dr. José Pedro Estrella started the operation. Next, Veterinaries Dr. Roberto Fecchio and Dr. Sergio Camargo, from University of São Paulo (USP), along with Dentist Dr. Miamoto adapted and cimented the prosthesis.

The procedure was a great success and up to date, Victoria the goose is perfectly adapted to her beak prosthesis.

Confira como é feita a cirurgia de prótese 3D
Matéria veiculada no G1: Tucano foge da eutanásia ao receber prótese inspirada em 'Lego'; vídeoLink:
Posted by Cícero Moraes on Sexta, 18 de setembro de 2015

Another case was of  Beakolin toucan, that grew with a malformation on his beak. This made it impossible for him to feed without the aid of a keeper.

The procedure was the same as described for Victoria's beak. A model was cast and digitized in 3D. A beak was modeled and wrapped around the malformation. This resulting model was 3D printed, received surface treatment and was adapted onto the animal. Shortly after the surgery, Beakolin started feeding by himself.

G1 em 1 Minuto - Bicolino
"Mãe tamo na Globo"!!! G1 em 1 Minuto apresenta o projeto que envolveu a criação de uma prótese para o tucano Bicolino durante o programa Bem Estar. 18/09/2015Conheça a história:
Posted by Cícero Moraes on Sexta, 18 de setembro de 2015

By the way... Beakolin was a national highlight in Brazil, as he was shown during G1's morning bulletin at Globo TV`s Bem Estar show.

Last but not least, there's Greenie's case. The great fear of the team was that the prosthetic beak, printed in PLA, would not resist to the mechanical effort that this species demands on its alimentary habits. The vets had to adapt the tip of the beak to relieve a bit of the load at the extremity. Thus, another animal was now independent to feed and enjoy life.

As it is a very new technique, we still do not know whether or not these prostetics will resist to constant load, but the more important is that we are always ready and alert to help these little warriors with what they need and with what is within our reach.

I can never thank enough this spectacular team, which permitted that I could be part of all this, and converted studies that were once limited to a virtual environment to a very material and life-saving reality. Thank you very much!

Friday 27 November 2015

ArcheOS 6: Hypatia!

Now we have the new codename for ArcheOS-next release!

... and the winner is:

 Hypatia !

Detail from The School of Athens, by Raffaello Sanzio (which a popular tradition identifies with Hypatia). Image under Public Domain (from wikipedi, user Yamara)

Thank you all for voting! Now we can start in fixing the package migration for ArcheOS 5 (Theodoric) to the new one, working on archeos-meta code.

Wednesday 25 November 2015

ArcheOS-next codename poll

Due to development problems, we noticed that we will need a new codename for ArcheOS-next earlier than we thought (despite what I wrote in this post). For this reason we have to stop collecting new proposal and start already with the poll, so that we will be able to complete some packages migration from ArcheOS Theodirc to the new version as soon as possible.
Up to now candidates for the ArcheOS-next codename are:

  1. Ishtar (
  2. Cleopatra (
  3. Hypatia (
  4. Lucy (
  5. Artemisia I of Caria (
  6. Hatshepsut (
  7. Zenobia (
  8. Semiramis (
  9. Zhao of Pingyang (
  10. Boudica (   

Please note that we removed the option Jeanne (d’Arc) because, as reported by our friends in France, she is now connected with a political party in France, so that choice could be misunderstood in that country.

ArcheOS new issue on GitHub repository (how to)

In order to simplify reports regarding ArcheOS from the community, I just uploaded on YouTube a short videotutorial which shows how to register a new issue on our main repository on GitHub.

Here is the video:

I am sorry for the low quality, but I think you can understand the single steps. Next time I will try to do it better :).
Have a nice day!

Monday 23 November 2015

ArcheOS-next (new release) codename

Since we started again in developing ArcheOS, we will soon need a new name for the next release (it is important also to maintain a certain continuity with what has been done for ArcheOS Theodoric).
For this new version we would like to have the name of a woman, as until now we just chose male historical figures (it should be a sort of tribute to all our female colleagues around the world).
If you want to participate in choosing the next codename for ArcheOS, just send us your ideas using one of our traditional channels (FaceBook, the development Mailing List, or ATOR itself, commenting this post). We will collect the names during this week and later we will set up a poll to choose the winner, like we did last time
The "candidates" should be female notable and historical figures, better if somehow in continuity with the old codenames we used (Akhenaton, Sargon, Xenophon, Caesar and Theodoric).
We are waiting for your proposal. Thank you very much!

The Halicarnassus relief with two "gladiatrices", thefemale counterpart of gladiators
(image from Wikipedia released under Public Domain by the user RsAzevedo)

Wednesday 28 October 2015

Australopithecus sediba

The Australopithecus sediba is another important reconstruction done for the open source exhibition "Facce. I molti volti della storia umana" [1]. In getting access to the cast and in producing the 3D model of the skull, to start the to work of the facial restitution, we have been supported by Prof. Telmo Pievani, who put us in connection with the exposition "Homo sapiens" (and with its scientific material). Once the digital model of the cranium has been produced with photographic (SfM/MVSR [2]) techniques, +Cícero Moraes could proceed with the protocol we developed about Forensic Facial Reconstruction [4] of Homini (Paleoart) with coherent anatomical deformation of a Pan troglodytes CT scan [3].
In order to go on with the free sharing and disclosure, under open licenses (Creative Commons Attribution International: CC-BY-4.0), of the material we produced during the preparation of the exhibition "Facce", I uploaded today the result of this FFR in Wikimedia Commons.
Here below is the final image, which has been developed thanks to a joned effort of Luca Bezzi (Arc-Team) and Nicola Carrara (Anthropological Museum of the University of Padua), for 3D model of the skull; +Cícero Moraes (Arc-Team) for the main work of 3D FFR modeling; Prof. Telmo Pievani (University of Padua, Biology Department), for scientific validation.

Facial Reconstruction of the Australopithecus sediba

The anatomical deformation technique, used for the facial reconstruction of the Australopithecus sediba, is well illustrated in the following video (by +Cícero Moraes):


[1] FaceBook, ATOR 1, 2, 3, 4, 5, TV7, oggiscienza, Archeomatica

[2] ATOR 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19

[3] ATOR 1, 2

[4] ATOR 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11

Sunday 18 October 2015

ArcheOS at Linux Day 2015

"Saturday, October 24 returns the main Italian event dedicated to GNU/Linux, free software, open culture and sharing: dozens of events all over Italy, hundreds of volunteers and thousands of visitors will be involved  to celebrate digital freedom!"

This incipit comes from the official website of the event and summarizes what the Linux Day has been until now. As this year there will be also an event regarding ArcheOS (presented by +Leonardo Zampi  in the city of Florence, at the organization Libera Informatica), I took the occasion to write a post with some links regarding the archaeological GNU/Linux distro, so that this material will be available for anyone who would like to show also this particular branch of the FLOSS universe.

Let's start form the official website, which has been completely renovated by +Fabrizio Furnari and +Romain Janvier, accessible at this address:

The main website

As you can read there, we have two mailing list: one for the users and the other for developers.

If you are familiar with it, you can also contact us on our IRC Channel at FreeNode (#archeos).

For those people who would like to work on the code, we use GitHub to develop the main system as well as all the related software projects (source packages, patches, small applications, GUI, etc...).

Finally (for the users), thanks to the collaboration of the University of Innsbruck (Near East and Ancient History Department), we have a wiki system in which we are slowly uploading tutorial and videotutorial. The website is available at this address:, but currently is under migration on a new server and will be not accessible for the next couple of weeks. I will keep this post update about the progress of this operation as soon as I will have news.

In the next days I hope to find the time collect more material regarding ArcheOS and to write a post about articles and presentations of the last years. Stay tuned!

Friday 16 October 2015

Slide transition speed in impress.js

One of ATOR's purposes is to serve as some kind of reminder for all the tricks and actions we find out during our hacking sessions.

Today I'm preparing a presentation  with impress.js.

After my last lecture a listener told me that the transition speed between the single slides of my presentation was to fast.
I was moving across aerial photos, zooming in and out on points of interest.

After some groping in the dark I found the solution on github.

It's very easy:

Look for your impress.js file, open it with an editor and look for the tag "transitionDuration".
You will find it among the defauld config values, it's expressed in milliseconds. 6000 means 6 seconds of transition time.

Consider that this option defines an equal transition time for the whole presentation.
It's also possible to set different speed for every single slide transition.

Tuesday 13 October 2015

Homo georgicus

One of the main attractions of the open source exhibition "Facce. I molti volti della storia umana"[1] is the facial reconstruction of four of the five individuals found in the Dmanisi (Georgia) excavation [2] and currently known as Homo georgicus. This project was possible thanks to the kindness of Prof. David Lordkipanidze (of the Georgian National Museum) and to the precious help of our friend Dr. Zviad Sherazadishvili.
The particular feature that characterized the facial reconstructions of the specimens of H. gerogicus is that each skull has some peculiarities that make it unique compared to the other subjects of the same species so far recognized. Moreover these differences are due both to sex, both to age and both to individual physiognomy. Indeed the five skulls of Dmanisi represent a wide range of variables, with at least a female specimen, two males with different individual characteristics (one with a pronounced undershot), an old subject and a young one (unfortunately impossible to reconstruct due to the missing facial part of the cranium).
The forensic reconstruction, performed with the anatomical deformation methodology [3], amplifies these differences, giving a face to our ancestors and simplifying at the same time the perception of the peculiarities which characterize the four specimens, at least for those people who are not familiar with anthropology and osteometry (like most of the visitors of the exposition). 
According to the main purpose of the open source exhibition (sharing as open data all the material we produced), today I am uploading the result of these reconstructions on Wikimedia Commons with a CC-BY license. Here below you can see the four images developed, like always, with a team work. This time the equipe was composed by Nicola Carrara (Anthropological Museum of the University of Padua) and Luca Bezzi (Arc-Team), for the 3D scan with SfM and MVSR techniques [4]; Cícero Moraes (Arc-Team), for the facial reconstruction with Blender; Telmo Pievani for the final validation (University of Padua, Biology Department).

The first  male subject

The old subject

The female subject

The second male subject (with pronounced undershot)


[1] FaceBook, ATOR 1, 2, 3, 4, 5
[2] ATOR 1

[3] ATOR 1, 2
[4] ATOR 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19

Sunday 27 September 2015

ArcheoFOSS VI, proceedings of the workshop now available as Open Access

This is just another fast post to notify that we are going on in spreading all the proceedings of the workshop ArcheoFOSS as Open Access. This time, thanks to the effort of Francesca Cantone (University of Federico II - Napoli), we released the publication of the sixth meeting, which took place in Napoli in 2011. The doc is in PDF and it is available under a Creative Commons license at this link.
Here below is the front cover of the printed version, which can be ordered at this page.

© 2015 - Scienze e Lettere dal 1919 S.r.l.

Wednesday 19 August 2015

ArcheoFOSS I, proceedings of the workshop now available as Open Access

Hi all,
this fast post is to notify that are finally available as Open Access the proceedings of the first workshop "Open Source, Free Software e Open Format nei processi di ricerca archeologici" (en: "Open Source, Free Software and Open Format in archaeological reasearch precesses"), which in the later editions will be known as ArcheoFOSS. The event took place in Grosseto in May 2006.
Since Open Access in archeology has always been one of the main topics of this workshop, some days ago we started a discussion on the official mailing list to try to free some of the proceedings which are actually available just as printed publications. The first result has been the release of the articles collected in the first edition, thanks to the kindness of Giancarlo Macchi Janica. Currently we are working on the other two workshops which are not yet available: ArcheoFOSS V (held in Foggia in 2010) and ArcheoFOSS VI (held in Neaples in 2011). 
The image below shows the front cover of the digital publication of the proceedings of the first edition, while here you can read the official announcement about the Open Access publication (pdf here).

Front cover of proceedings of the first workshop "Open Source, Free Software e Open Format nei processi di ricerca archeologici"
A special thanks also to +Stefano Costa for uploading everything on ArcheoFOSS website.


In the proceedings you can also find some articles written by Arc-Team members, regarding:
1. One of the first release of ArcheOS (v.1.6): here in Academia and here in ResearchGate (by +Alessandro Bezzi, +Luca Bezzi, +Denis Francisci, +Rupert Gietl)
2.  The use of +GRASS GIS in archaeology: Academia / ResearchGate (by Michael Burton, +Alessandro Bezzi, +Luca Bezzi, +Denis Francisci, +Rupert Gietl+Markus Neteler)
3. The use of FLOSS in a case of study in archaeology: Academia / ResearchGate (by +Luca Bezzi, Stefano Boaro, Giovanni Leonardi, +damiano lotto)

Thursday 13 August 2015

Homo floresiensis

"Homo floresiensis ("Flores Man"; nicknamed "hobbit" and "Flo") is widely believed to be an extinct species in the genus Homo. The remains of an individual that would have stood about 3.5 feet (1.1 m) in height were discovered in 2003 on the island of Flores in Indonesia. Partial skeletons of nine individuals have been recovered, including one complete skull, referred to as LB1"

This is the incipit of the Wikipedia page dedicate to the Homo floresiensis. I started the post with this sentence because today I will share the result of our research about Archaeological Foresic Facial Reconstruction (AFFR) of the individual LB1 of this species, performed for the open source exhibition "Facce. I molti volti della storia umana". If you are a regular reader of tis blog, you will know that we attempted already a facial reconstruction of the "hobbit", as he was one oh the Hominini we worked on for the Brazilian exposition "Faces de Evolução" (curated by Prof. Dr. Moacir Elias Santos of the Archaeological Museum of Ponta Grossa and Prof. Esp. Vivian Tedardi of Rosicrucian and Egyptian Museum in Brazil). Like it happened for the Taung Child (Australopithecus africanus), also in this case we developed a new model (v 2.0), after a first reconstruction, simply based on a an anatomical study and on basic paleo-artistic techniques.
Here below you can see the image of the first reconstructive model (H. floresiensis v. 1.0), while here you can read the old ATOR post about this first attempt.

Homo floresiensis version 1.0

After the first model, we changed completely our approach to paleo-art, as we developed the new technique based on the anatomical deformation of Pan troglodytes or Homo sapiens ct x-ray scan (depending of the kind of hominid to be reconstructed). The result of this new approach is the H. floresiensis new model (v. 2.0) we release today and that you can see in the image below.

Homo floresiensis version 2.0

Also in this case, the model is the result of a team work. Here below are the credits:

1. 3D scan of the cast: Moacir Elias Santos (Archaeological Museum of Ponta Grossa)
2. 3D modeling (skull restoration, anatomical study, CT deformation): +Cícero Moraes (Arc-Team) with the precious contribute of Prof. Peter Brown (New England University in Armidale, Australia)
3. scientific validation: Prof. Telmo Pievani (University of Padua, Department of Biology), Dott. Nicola Carrara(Anthropological Museum of the University of Padua), Prof. Peter Brown (New England University in Armidale, Australia)
The image of the new model of Homo floresiensis has just been added on Wikimedia Commons and it is avalible for any use under the CC-BY license (which we use normally for the material we share through ATOR).
Have a nice day!

Wednesday 29 July 2015

When Veterinary Medicine and 3D printing meet each other

TV story with English subtitle

The Brazilian Team of Forensic Anthropology and Forensic Dentistry (Ebrafol) was founded in 2014. Comprising a number of liberal professionals, mostly belonging to the field of Dentistry, it always sought a shortcut using the know-how of its members and considering the necessity of the Brazilian population for relevant applications. Even before the Ebrafol started, we (me and Dr. Paulo Miamoto) had already worked a handful of partnerships and they would contemplate not only the human population but also other animals.

TV Story with English subtitle
In the second half of 2013 we have met the Veterinarian Dr. Roberto Fecchio. He was well known for his mastery in saving the lives of many animals and bringing dignity and quality of life to them. Rebuilt beaks, perfectly fitting prosthesis, and implanted well treated teeth. And I mean animals ranging from a small rodent to a scary feline, whether a Guinea pig or a lion, there would be Dr. Fecchio and his staff, caring for and rehabilitating them.
When I meet Dr. Fecchio (at center) at Sao Paulo University (USP)

It seems a short period, but since 2013 a lot has happened. In the meantime, regarding skills in computer graphics applied to human and animal health, our knowledge advanced quite a bit. Since 2013, Dr. Fecchio would motivate us to develop 3D-printed prosthetic beaks, but at that time we just did not have the necessary know-how to actually model them, nor the equipment to print them.

The red-footed tortoise (Chelonoidis carbonaria) "Fred" in the surgery home

That changed a few weeks ago. Dr. Paulo Miamoto purchased a 3D printer. The goal was to explore it for scientific studies and commercial printing. All was very new, interesting and unknown.

Wealthy tortoise scanned (wireframe) and Fred inside it.

Upon learning about the 3D printer, Dr. Fecchio, always at the forefront, proposed that we participated in a project with him, from Santos-SP, and other team, from Brasília-DF. The case was about a poor tortoise, who had been the victim of a bushfire in the Brazilian plains. The flames injured her hoof and she lost a considerable part of its structure. Luckily the animal was rescued and taken barely alive to the hands of Dr. Rodrigo Rabello, whom with the aid of his brother Dr. Matheus Rabello, successfully treated and healed two pneumonia episodes and other diseases caused by the animal’s deficient immune system.

System of matching

Although the tortoise regained stable health, she tortoise found herself in big trouble. She had no hoof as the bony plates that were left fell off and gave her a shelled egg-like aspect, with only a thin membrane which could be perforated quite easily.

Hoof exploded

That’s when Dr. Fecchio stepped in, proposing the partnership and finding himself quite content with everybody’s agreement to participate in this project.

I figured the reconstruction of the hoof could be made using a simple methodology. First we would do a 3D scan of the tortoise who had lost the hoof. The technique used is called photogrammetry. Roughly, we took several pictures of the animal, sent them to a computational algorithm and it reconstructed the 3D volume. Then we did the same with a healthy tortoise hoof. This way, we digitized the 3D volumes of the tortoise without a hoof and the healthy hoof. Then, we would just have to proceed with Boolean calculations and, a structure that fits the sick animal is obtained.

Printed part

Of course we had a lot of problems in the process. The hoof had to be printed in 4 parts because we did not know if Dr. Paulo’s printer would finish the job in time. That’s why we divided it into four pieces, so that we could hire companies or people who offered this service in case we had any problems with 3D printing. Fortunately, 3D prints were successful, although this process wasn’t quite quick. It took five days of almost uninterrupted printing for the hoof to get ready. After that, we had an unpleasant surprise upon cleaning the support material created by the printer. In the joint areas it was very difficult to remove it. Thanks to the help of Dr. Paulo Esteves, an experienced Dentist, cleaning the support material was possible and everything went smoothly well.

Te team after surgery (I'm on the grayscale photo)

The surgery was covered by the largest Brazilian TV station, Rede Globo. The procedure was a success and at the end Fred the tortoise, received a new hoof and it wasn’t necessary to screw it to bony parts of her body, as a photogrammetry provided a high precision scanning of the area and made possible a very nice adaptation of the prosthesis.

Steps of surgery - toucan

Meanwhile, another case had been handled by the team. Zeca, The toucan, broke his beak when he hit a window. A homologous prosthesis was installed using a cadaver beak adapted to the fracture, which is a common practice in veterinary medicine. Unfortunately, Zeca’s “new” beak could not stand a very high load and broke. Upon seeing that the toucan had lost his beak, Dr. Fecchio proposed reviving the first project that we developed together, back in the pre-Ebrafol period, i.e., to create digitized beak prosthesis. Inspired by the successful surgery, we got back in track and to our complete joy, everything worked out and Zeca is fully adapted to his new beak!

Our team is very happy and honored for all that has happened. Besides the feeling of nobility and accomplishment, we are also proud of accomplishing everything using free and open software. Photogrammetry was done with PPT-GUI, and 3D modeling was done in Blender. We used Cork for Boolean calculations and sliced the mesh for printing with Slic3r.

We barely enjoyed the taste of success and we are already engaged in a new project. Soon we'll post more news, see you!


Dr. Everton da Rosa, which made possible my trip to Brasilia to meet the Rabello doctors and participate in Fantástico, Brazil’s most popular Sunday TV show. Claudio Marques Sampaio (patola) to help us with 3D printing. Denise Oltramari, which provided us with one of the tortoises she takes care of for photogrammetry. Dr. Gilbert Bernstein to develope the powefull Cork, the boolean standalone used to create the prosthesis. Daniel Ludwig and Lis Caroline for the aid in the process of photography (photogrammetry). Giovanna Leite Soares and Dr. Paulo Miamoto, who assisted us with translations into English. To all the news crews that documented this project while respecting the scientific aspects and highlighting the importance of such initiatives for the sake of animals.

Tuesday 28 July 2015

The meaning of an "open source exhibition"

As many of you know, since more than one year we are working on the exhibition "Facce. I molti volti della storia umana". Now that the exhibition was inaugurated and our work is completed, it is time to share with open licenses (CC-BY) what we produced. 
It will be a long process, as the materials are different (images, photos, video, 3D models), nevertheless we have to start uploading the documents. Thanks to a short discussion with +Maurizio Napolitano (Fondazione Bruno Kessler) and +Rodrigo Padula (Grupo Wikimedia Brasileiro de Educação e Pesquisa), both expert in open data, I think that the best solution will be to upload the data directly in ATOR, where I can cite all the people who participated in the "production process", from 3D scan to facial reconstruction, till scientific validation.
IMHO the best image to start with is the one of the Taung Child, for different reason: it has been the first attempt performed by our team in order to reconstruct the face of an hominid; it summarizes our concept of Open Research; it has been one of the ideas that gave birth to exhibition "Facce", as Dr. Nicola Carrara conceived it; it is the first project in which Arc-Team, the Anthropological Museum of the University of Padua and Antrocom worked together; last but not least, it is a perfect example of what we mean of open data. Indeed the first reconstruction we produced (version 1.0), which actually is already part of the related article in Wikipedia, has been modified after the development (and the validation) of a new technique of paleo-art, based on the anatomical deformation of a CT scan of a Pan troglodytes. For this reason now we have a new and more accurate reconstruction, which can be considered a version 2.0 of the same model. 
The open data we intend to share here in ATOR are meant to be open not only in the direction of free access for everyone, but also (most important) under the temporal dimension: they should just represent a step of a continuous evolution of the research, in which all the reconstructions can be considerate simply as the latest release of a model (exactly like in software development, with new versions and forks). For this reason we choose the Creative Commons Attribution license, in order to allow derived works and projects.
The two images below can explain better this concept: the first one represent the Taung Child reconstruction in his first version (based on an anatomical study of primates), while the second one is derived by the anatomical deformation of Pan troglodytes CT scan.

The first version of the reconstruction of the Taung Child

The second version of the Taung Child
Both of the models are the result of a team work, although most of the process (and in particular the most important and delicate phases) has been performed by the 3D artist  +Cícero Moraes. Here below I want to cite the credits for this reconstruction (following the same order of the work-flow):

1. 3D scan of the cast: Luca Bezzi (Arc-Team) and +Moreno Tiziani (Antrocom)
2. 3D modeling (skull restoration, anatomical study, CT deformation): +Cícero Moraes (Arc-Team)
3. scientific validation: Prof. Telmo Pievani (University of Padua, Department of Biology) and Dott. Nicola Carrara(Anthropological Museum of the University of Padua)


The Anthropological Museum of the University of Pauda, for providing the cast of the fossil.
The KUPRI, Primate Research Institute Kyoto University, for sharing the CT scans of different primates.
Dr. Claudio Paluani (University of Padua), who, during the lesson "Digital bones" at the Botanical Garden of the University of Padua, had the same idea we had about the validation of the methodology of anatomical deformation through the modification of two CT scans of living primates. This fact convinced us to perform the test, after seeing that more people reached the same conclusion about the validation problem.

Monday 27 July 2015

Documentation of a bas-relief on a cliff : the workflow

This summer, between May and June, we worked for a joint mission, led by the University of Innsbruck (Institut für Alte Geschichte und Altorientalistik) and the Cultural Heritage, Handcrafts and Tourism Organization of Iran. The project was held in Firuzabad, in the Pars Province of Iran. We will write more details about this work in the next post. By now I just want to use some material we collected to illustrate the work-flow in data acquiring during an archaeological documentation of a bas-relief on a cliff.
The video below shows the overall process.

You can see the initial preparation phase (1), during which we placed the Ground Control Point (GCP) to perform normal 2D vertical photo-mapping and to rectify and georeference the 3D point-cloud. Than (2) we collected pictures with three different flights of our DIY drone, in order to use them with different open source SfM/MVSR software (PPT, openMVG and MicMac), to reach the best possible result: a couple of flights with parallel camera, to have a good superimposition of the whole bas-relief, and a higher acquisition to cover the upper details. In the meantime (3) another operator (+Rupert Gietl) was collecting pictures from the ground, to register also the lower perspective. Later (4), I prepared the total station and collected the GCP, thanks to some fixed points we placed the day befor (0) with our GPS. Finally +Rupert Gietl  took the last (very close) details photos, using a ladder.
The entire process lasted more or less four hours, but we needed some more time the day before to place the fixed GCP down in the valley (in international Geographic Coordinates System). A good part of the work involved just the logistics or the approach to the site, and has been slowed by the transportation of the necessary equipment (ladder, total station and drone) through a couple of passages where it was necessary to climb some rocks.
It is interesting to note that it would not have been possible to accomplish this mission with a commercial drone, due to the embargo rules (which are currently under revision), while with a DIY hexacopter it has been simple to disassemble the components which were not allowed (like the FPV system ore the GPS controlled flight).
I hope this post was useful, have a nice day!

Thursday 2 July 2015

The archaeometric excavation

Last year, on November 28, Arc-Team joined the conference "Lo scavo archeometrcio: scienza e tecnologia applicate allo scavo archeologico" (en: "The archaeometrcic excavation: science and technology applied to the archaeological excavation"), which was held in Rovereto (Italy) at the Museo Civico.
During the meeting we gave a presentation titled "Professional archaeology. Innovations and best practice with free technology. Toward an Open Research." Today I uploaded on our server the slides, so that we can share this work (like always under Creative Commons Attribution - CC BY).
As usual the presentation has been done with impress.js through the Graphical User Interface Strut (both GPL licensed) and it is optimized for Firefox or Iceweasel (better visualized here).

Here is a little explanation regarding the single slides:

A fast presentation regarding Arc-Team.
An animation representing the importance of geocoding in archaeology (from space to site).

Differential GPS and Total Station: the main tools needed by archaeologists on the field (to georeference every single element of the archaeological record).

Some examples of geocoding in archaeology: everyday work, project in extreme conditions and missions abroad...

... survay and excavations

In survay projects the geocoding tolerance for archaeology is higher, so that we are testing alternative solutions to build a low-cost and open source GPS with centimetric accuracy, using the software RTKLIB (or its port in Android)

All the recorded data (in 2D and 3D) can be imported into an open source GIS.

For aerial archaeology it since 2008 we are working with open source DIY UAV, like the UAVP or the KKcopter (in the slide).

Our last UAV prototype and an example of 3D pointcloud form aerial pictures.

Since 2014 we are testing DIY camera (using the filter of Public Lab) for NDVI and NGB pictures in archaeological remote sensing.

Just removing the IR filter, a normal camera can be used for endoscopic prospections in low light conditions.

In the field of geophysical prospections we use a DIY  machine for Electrical Resistivity Imaging. The data can be visualized in a GIS (e.g. GRASS GIS in the slide), using the east and north and the resistivity values.

Some geoarchaeological analyses can be performed directly on the field, like the settlement test (using the soil triangle) for the texture or the lithologic recognition for the skeleton.

Also some basic analytical chemistry can help during the excavation (giving indications on the ancient use of the soil), to verify the presence/absence of phosphates or of organic remains.

Other preliminary laboratory (flotation and sieving) analyses can prepare the samples for further investigation. Also in this case we use a DIY machine.

Colorimetry can be performed in many ways. Currently we are testing different options, like the open source spectrometer of Public Lab.

For some laboratory geoarchaeological analysis (e.g. microscopic morphology) we use normal optic microscopes, while for more advanced studies we externalize the service (e.g. SEM or energy dispersive x-ray spectroscopy)

Currently we are testing the potentialities of the FLOSS MorphoJ to speed up the process in carpological remains recognition

To document archaeozoological remains in the field, we use the standard digital documentation techniques (in 2 and 3D), with FLOSS (e.g. bidimensional photomapping with the Aramus method or 3D recording through SfM and MVSR)

In the evolutionary anthropology field we developed a new technique (anatomical deformation) thanks to the FLOSS Blender

The same software (Blender) is used in the process of archaeological forensic facial reconstruction

Open source GIS (e.g. GRASS) are the main software we use to process and manage the recorded data

Thanks to open source UAV and Blender we experimented new ways to disclose archaeological data in a four-dimensional way (x,y,z,t)

A more detailed explanation of the entire presentation will come soon with the related article. For the topics which were already discussed in AOTR, I suggest to read the related post (see the above bibliography). For the latest experiment (e.g. near infrared, NDVI and NGB; Electrical Resistivity Imaging; Sedimentation test; litologic recognition on the field; flotation and sieving; colorimetry; microscopic morphology; MorphoJ;), we will try to write something as soon as possible.


Lo scavo archeologico professionale, innovazioni e best practice mediante metodologie aperte e Open research (here on Research Gate and here in Academia)

Webography (from ATOR):

3D and 4D GIS

SfM and MVSR

Aerial 3D documentation

Archaeological endoscopy



Evolutionary anthropology
Anatomical Deformation Technique (ADT): validation; ADT Paranthropus boisei; ADT Homo rodhesiensis;

Archaeological Forensic Facial Reconstruction (AFFR); Digital AFFR: technique validation; AFFR: state of the arts; AFFR: poster;

Archaeological dissemination
Caldonazzo Castle 4D (case of study);
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