What is the Aves 3D website?
How can I access database content?
Why do I have to register (free) to download 3D models and other database content?
Why are not all bone models on Aves 3D available for download?
Why are there no scale bars on the interactive 3D models?
Why are there no (pneumatic) foramina visible on the models?
Why do the interactive 3D models not work on an iPad or iPhone?
How can I contribute to the Aves 3D database?
What research projects is Aves 3D currently undertaking?
How are scans made?
Aves 3D is an online database with three-dimensional digital models of the many different bones that make up the skeleton of birds. The models available on Aves 3D are created through non-contact laser surface scanning of skeletons, which provides accurate digital models of the bones; these scans can be used for a variety of educational and research purposes. Scanning is done by students and researchers of the Claessens laboratory at the College of the Holy Cross, as well as on location at the Harvard Museum of Comparative Zoology, the Peabody Museum of Natural History at Yale University, and other institutions. The Aves 3D database project is funded by the National Science Foundation, and is a collaboration between the College of the Holy Cross, Harvard Museum of Comparative Zoology, and Peabody Museum of Natural History. We have tried to make the Aves 3D website useful and appealing for a broad community of users, and we hope that it will provide resources for students, educators, scientists and anyone interested in, or looking to learn more about birds, skeletal anatomy, and biology.
Visitors to the Aves 3D website can view all database content and manipulate interactive three-dimensional models of scanned bones and skeletons in their web browser. To access 3D digital models for download, registration is required. Registration is free. A link to the Aves 3D Registration page can be found in the top, as well as a link to the Login page for returning registered users. Visitors to the Aves 3D website can use and interact with the database in a variety of ways. Visitors can search or browse the Aves 3D database using a bird’s common and scientific name, specific skeletal element, or via a diagram of evolutionary relationships. Interactive 3D (Java applet-based) models of bones can be manipulated in a web browser without the need for additional plug-ins or specialized software. In addition, museum specimen and scan data, downloadable full resolution 3D models, photographs of the skeletal specimens, and links to related information are available. Researchers can use the digital models available on Aves 3D for a wide variety of scientific research, including comparative and functional morphological studies, phylogenetic systematics, and taxonomic identification. The full resolution 3D digital models are in a format ready for a wide range of computational applications, without the need for time-consuming laser surface scanning or specialist equipment. The 3D models also provide a method of digital curation of rare or fragile specimens, as well as rapid global dissemination of biological data. Finally, we hope that the Aves 3D site provides a portal where one can enjoy the beauty and complexity of avian morphology and biology. We are continually expanding database holdings, and are working on a set of lesson plans and analytical tools.
Free registration and login is required for downloading digital 3D models and other database content. Registration includes formal acceptance of the Aves 3D User Agreement. Registration allows us to monitor database use, which is important for database development. Data on specimen access and downloads provides invaluable information to our contributing institutions regarding the use of their collections. Aves 3D allows greater access to museum collections for the public, educational and research communities, in a format ready for a wide range of computational applications, while at the same time limiting the physical handling of specimens.
The ultimate goal of the Aves 3D database is to make most elements in the database available for immediate download, but there are several reasons why some elements may not (yet) be available. In some cases, especially with very rare specimens, the institutions that have allowed us to generate 3D scans would like to maintain control over the number of times, and purposes for which, a model is distributed. This is accomplished by requiring individual authorization for each download. Also, the generation of 3D models is a slow and time-consuming process. Since most 3D models are generated with specific research questions in mind, the researchers responsible for scan generation may request that we do not make the models that they generated available for free download until their research projects have been finalized. By monitoring requests for access for specific elements, museums and researchers have control over the distribution of their models, which helps to avoid copyright violations or research conflicts. If a model is not available online for free download, we advise you to contact the detailing the requested use of the model.
There are no scale bars on the interactive models. We would like to have scale bars on the interactive models, but placing scale bars on the models is more complicated than it seems, and we have not yet found an ideal solution. Some of the hurdles to placing scale bars in the models are that (1) if we place a static scale bar on the Wirefusion frame, it will not respond to changes when zooming in or out, and (2) if we model a scale bar in the 3D digital model, it will affect the volume of the model, and can be rotated in front of or behind the model. We are open to suggestions from people that have experience with a good method for modeling in scale bars. However, the 3D models on the website are not without data on scale. The 3D digital files are accurate to size, and can be used in any 3D editing software by scientists for direct measurement. Also, the photographs provided of the scanned bones include scale bars, and allow website visitors to get view the size of the element.
Bones often have numerous small foramina that pierce the outer surface, and through which nerves and blood vessels enter and exit the internal bone cavity. Also, many bones in the bird skeleton are ‘pneumatic,’ because extensions of the pulmonary apparatus have invaded the interior surface of the bones, replacing bone and marrow with air-filled diverticula. One of the many benefits of replacing bone and marrow with air is a reduction in overall density, and flying birds tend to have a greater degree of ‘pneumatization’ of the skeleton than non-flying birds. Pneumatization of the skeleton leaves large, characteristic openings in the bony surface. In our 3D scans, all small and large foramina have been filled-in digitally. The main reason for this is that for many computational analyses and modeling studies, a completely closed, or ‘watertight’ model is required. Also, since the interior surface of a 3D model is most often invisible or see-through in 3D viewing programs, filling in the foramina helps avoid visual anomalies, where a model appears incomplete when viewed through a large foramen. Photographs of the bones associated with each scan provide an opportunity to distinguish foramina from depressions in the digital model, in case of ambiguity.
Our interactive 3D models of bones and skeletons are Java applets created with the program Wirefusion. Demicron has recently put out a new Beta version of Wirefusion creates applets that will run on the iPad or iPhone, but most of our 3D models were created in the previous version of Wirefusion. We will work on slowly replacing all our interactive 3D models when a new full version of Wirefusion becomes available.
Growth of the digital holdings of the Aves 3D database is fueled by a diversity of research projects, including avian ecomorphology, systematics, and geometric morphometrics. Undergraduate student research features prominently in scan generation, database expansion, and scientific analysis. We are always interested in research collaborations that use existing Aves 3D data, as well as projects that require the generation of newly scanned skeletal material for the Aves 3D database or present analytical methodological advances. We encourage you to contact the with concrete ideas or proposals.
Growth of the Aves 3D database is fueled by a variety of research projects. Undergraduate student research features prominently in scan generation,
database expansion, and scientific analysis.
Examples of Current Aves 3D Projects are:
Three-dimensional digital scans are made using non-contact laser surface scanning of skeletal material. We currently employ a Roland LPX 1200 and a Konica Minolta Range 7 red light laser scanner, and we are testing the DAVID laserscanner system for potential use in skeletal scan generation. The creation of a single scan shell of a skeletal object can take hours (LPX 1200) to seconds (Range 7), depending on the level of resolution used. The most time-consuming steps in scan generation are the merging of different scan shells into a single model, and the removal of scanner “noise” from the model. Most models available in the database represent at least 8 hours of work, and, depending on the size and complexity of the object, may have taken much more effort. We use the software package Rapidform™ for scan editing and Wirefusion™ for creating Java applets for the website. Detailed scanning protocols will be made available on this website in the future.