Tag Archives: 3D

A Preview of MorphoSource 2 Beta

January 20, 2021 Jocelyn Triplett

It’s an exciting time for the MorphoSource team, as we work to launch the MorphoSource 2 Beta application next Wednesday!

The new application improves and expands upon the original MorphoSource, a repository for 3D research data, and is being built using Hyrax, an open-source digital repository application widely implemented by libraries to manage digital repositories and collections. The team has been working on the site for the last two and a half years, and is looking forward to our efforts being made available to the MorphoSource community. At launch, users will be able to access records for over 140,000 media files, contributed by 1,500 researchers from all over the world.

While the current site is still available for browsing at www.morphosource.org, we are migrating the repository data over to the new site in preparation for the launch, and have paused the ingest of new data sets. When the migration is complete, users will be able to access the new application at the current url. Users with an account on the old site will be able to log in to the new site using their MorphoSource 1 credentials.

In my last post in June, I described some of the features that were in development at that time. In this post, I’ll highlight a few recent additions with screenshots from the beta site: Browse, Search, and User Dashboards.

Browse

Browse pages have been added as a quick entry point for users to discover data in several different ways. Users can use these pages to immediately access media, biological specimens, cultural heritage objects, organizations, teams, or projects.

Media Types and Modalities: Users can view all media records of a specific file type, such as image, CT image series, or mesh or point cloud. There are also links to records created by different methods, such as X-Ray, Magnetic Resource Imaging, or Photogrammetry.

Physical Object Types: Links to view either all the Biological Specimens or Cultural Heritage Objects in MorphoSource

Biological Taxonomy: Users can find specimen records through the taxonomy browse by drilling down through the taxonomic ranks. The MorphoSource taxonomy records have been imported from the GBIF Backbone Taxonomy or have been created by MorphoSource users.

Taxonomy browse page — Taxonomy Browse Page

Projects: Projects are user-created groupings of media and specimens. From the browse page, projects can be searched by title and sorted by title, description, team, creator, or number of associated media or objects.

MorphoSource 2 Project Browse — Project Browse Page

Teams: Teams are groups of MorphoSource users that share management of media and team projects. A Team may be associated with an organization. The Team browse page lets users search and sort teams in a similar way to the Projects browse page.

Organizations: Lastly, users can view all of the organizations that have biological specimens or cultural heritage objects in MorphoSource. An organization may be an institution, department, collection, facility, lab, or other group. From the Organizations browse page, users can search by name and sort by parent institution name or institution code.

Faceted Searching

In addition to the browse pages, records for Media, Biological Specimens, Cultural Heritage Objects, Organizations, Teams, and Projects can also be found through the MorphoSource search interface. Searching has been customized for the different record types to include relevant facets. The different search categories can be chosen from the dropdown next to the search box ‘Go’ button.

MorphoSource 2 Beta Media Search Results — Media Search Results

Search results for media records can be faceted by file type, modality, object type (biological specimen or cultural heritage object), organization, tag, or membership in a team or project, while search results for objects can be limited by object type, creator, organization, taxonomy, associated media types, associated media tags, and membership of associated media in a team or project. Organization and Team/Project searches similarly have their own sets of facets.

MorphoSource 2 Object Search — Biological Specimen and Cultural Heritage Object Search Results

User Dashboards

Users who register an account on the site will have access to a dashboard that enables them to manage their data downloads. The dashboard is accessed by clicking on the profile icon at the top right of the site, and will open to the user’s media cart. The media cart contains two sections – the top holds all media items that the user currently has permission to download, while the bottom has media items with a restricted status where download has not been requested or approved:

MorphoSource 2 Beta Media Cart — Default User Dashboard

Users who have been granted contributor access to the site will have a dashboard that opens to the media and objects that they have contributed:

MorphoSource 2 Beta Contributor Dashboard — Contributor Dashboard

From the menu at the left, all users can access their previous downloads, or projects, teams, or other repository content to which they have been granted access, and manage their user profile. In addition, contributors can also create and manage projects and teams.

We hope that the browse, search, and dashboard enhancements, along with the other features we have been working on over the last couple of years, will enable users to easily discover and manage data sets in MorphoSource. And although we are looking forward to the launch, we are also excited to continue working on the site, and will be adding even more features in the near future.

MorphoSource

MorphoSource: Features in Development

June 8, 2020 Jocelyn Triplett

For the last two years, developers in Software Services and Duke’s department of Evolutionary Anthropology have been working to rebuild MorphoSource, a repository for 3D research data representing physical objects, primarily biological specimens. MorphoSource 2.0 is being built using Hyrax, an open-source digital repository application widely implemented by libraries to manage digital repositories and collections. While Hyrax already provided much of the core functionality needed for management, access, and preservation of our data, the MorphoSource team has been customizing the application and adding additional features to tailor it to the needs of our users.

As a preview, here are some of the features we’re developing for the MorphoSource community:

Guided Submission Process

MorphoSource is open to subject experts, collection curators, and the public to submit their data and make it accessible to others. The MorphoSource submission process will guide users in entering metadata that provides additional description and context for the files being uploaded. Users will be able to save information about the specimen that was scanned, the equipment that was used to capture the 3d data, the data capture process, and related media in MorphoSource. The form is multi-step and nested, with different fields available or data pre-filled in depending on what the user has already entered in earlier sections of the form. The user also has opportunities to search for related organizations, devices, specimens, and media to link to their submission. Once the submission process is complete, depositors are able to return to their data page to edit metadata and redefine relationships to other MorphoSource records.

Morphosource data submission screenshots — A user proceeds through the MorphoSource media submission process.

In the gif above, a MorphoSource user proceeds through the submission process. If the media being uploaded (such as an image stack or 3d mesh) is a derivative of another object that is already in MorphoSource, the user can search for that media and link it to their submission, whereupon related metadata will be auto-filled for them. If it is a totally new submission, the user will proceed from filling in information about the object that was scanned (ownership, taxonomy, and descriptive details) to devices and processing steps used before attaching their files. This ability to nest, search and associate metadata from the organization level all the way down to an individual object component in a single interface is unique to MorphoSource and is a substantial addition to Hyrax’s code.

Displaying and Updating Media Records

Screenshot of a Media Record in MorphoSource — A media record in MorphoSource.

Following submission, the depositor can view their completed media record, as shown above. Data owners (and other users who have been granted edit permissions by the data owner) have the ability to freely edit their submissions at any time. The edit view (below) allows the user to move between tabs to update metadata or change links to other records in MorphoSource. These tabs offer a fast summary of the types of associated data that are typically collected for complex objects and digitization strategies. This system is also designed to encourage best practices in project and object documentation by reminding the user of critical metadata categories.

3D Viewer

Through a collaboration with Mnemoscene, MorphoSource has created Aleph, a web viewer for 3D models and volumes that can be used by itself or as an extension to the popular library document viewer Universal Viewer. A live example of a specimen in the viewer is below. You can rotate the object by clicking and dragging inside the frame, or switch between slices and volume view by changing the mode under tools.

The Media Cart and Restricted Downloads

A media depositor can choose from several different publication statuses for their data, allowing the data owner to retain different levels of control of both their data sets and the metadata record describing their deposit. While some may choose to publish both their metadata and data sets with an open status, allowing other users to freely view and download them, it is also possible for depositors to restrict either their records or data to other users or organizations, or require that a user is granted permission before they are permitted to download data.

When data owners choose to publish using restricted download, other users are able to view metadata and preview the 3D data in the Aleph viewer, but can’t download the data set until they are granted permission by the data owner, and are required to fill out a request including the manner they intend to use the data. Data owners can easily review and manage these download requests from their user dashboard.

Above is a view of a user’s media cart, where they collect media they intend to download. The top section has media items the user is free to download, either because the media was published with an open publication status or because the user was approved to download by the media owner. Users can download any or all of these items at one time. The bottom section of the page contains items with a restricted download publication status, and allows the user to request these items individually or as a group. Users can also track the status of their request from this page.

In the next image, a data owner views requests to download their media. Requests are grouped by requesting user and then the intended use of the data. Data owners can approve, deny, or clear any or all of the requests. When approving a request, the data owner specifies the amount of time that the media will be available for the requester to download. This person can also clear a request if they want more information from the requester before they approve the download. Requests that have already been decided are available for review in the Previous Requests tab.

Organizational Teams

Organizational teams are the final substantial addition to the new MorphoSource. Any organization, such as a university, museum, or department, can create an organizational team that stores metadata about the team and assigns roles to individual members. Members of the organizational team can also curate team projects, grant other users access to the team’s media, edit the organization’s metadata, and view any media created from objects in their collections. Below is the public view of one of our first sample organizational teams, the Nasher Museum.

Screenshot of an Organizational Team in MorphoSource — An organization page in MorphoSource. Image via Boyer, Silverton, and Winchester, 2020. MorphoSource: Creating a 3D web repository capable of archiving complex workflows and providing novel viewing experiences

The MorphoSource team is looking forward to unveiling the beta version of MorphoSource 2.0 later this year. In the meantime, please visit the current repository at www.morphosource.org. For further reading, check out the recent EuropeanaTech article MorphoSource: Creating a 3D web repository capable of archiving complex workflows and providing novel viewing experiences.

Behind the Scenes, MorphoSource, Technology

Describing 3D Data in MorphoSource 2.0

January 17, 2020 Jocelyn Triplett

Header Image: Collection of extinct and extant turtle skull microCT scans in MorphoSource: bit.ly/3DFossilTurtles

MorphoSource (www.morphosource.org) is a publicly accessible repository for 3D research data, especially data that represents biological specimens. Developers in Evolutionary Anthropology and the Library’s Software Services department have been working to rebuild the application, improving upon the current site’s technology and features. An important part of this rebuild is implementing a more robust data model that will let our users efficiently discover, curate, disseminate, and preserve their data.

A typical deposit in MorphoSource is a file or files that represent a scan of all or part of an organism – such as a bone, tooth, or entire animal. The files may be a mesh or series of images produced through a CT scan. In order to collect all the information necessary to understand the files, the specimen that the files represent, and the processes that created the data, the improved site will guide the researcher in providing additional context for their deposit at the same time that they upload their files. The following describes what kind of metadata the depositor can expect to provide as part of the submission process.

The first step is to determine whether the researcher’s current deposit is derived in some way from data that is already in MorphoSource, or if the depositor would like to also submit those files and metadata. For example, they may be depositing a mesh file that was created from original photographs that are already available through the site. By including links to the raw data in the repository, users can reprocess the files if needed, or run different processes in the future.

MorphoSource collects metadata to provide context for 3D data in the repository

Next, the researcher is asked to identify or describe the biological specimen that was imaged to create their data, either by entering the information themselves or importing it from another site like iDigBio. Metadata entered at this stage includes the information about the institution that owns the specimen, a taxonomy for the specimen, and additional identifying information such as the institution’s collection or catalog number. When the depositor fills in these fields, other users will be able to search for and compare data sets for the same specimen or species.

Moving on from the description of the organism, the depositor then provides information about the device that was used to image the specimen, either by selecting a device that is already in the repository’s database, or by creating a new record, including the manufacturer, model, and modality (MRI, photography, laser scan, etc.) of the device.

Once they have described the specimen and device used for imaging, the depositor then enters metadata about the imaging event itself, such as the technician who did the imaging, the date, and the software used.

With the imaging of the specimen described, the depositor then enters data about any processing that was done to create the files being deposited, including who was responsible, what software was used, and what the process was – for example, creating a mesh or point cloud from photographs. This metadata is important in case there is a need to reprocess the data in the future.

Finally, the researcher completes their deposit by uploading the files themselves. While some technical metadata is extracted automatically, MorphoSource will rely on data depositors to provide other information that is helpful for display, such as the orientation of the scan, or to identify the files, like an external id number. This technical metadata is important for long term preservation of the data sets.

morphosource media page — Screen capture of example media page in MorphoSource

While the submission process asks the researcher to enter quite a bit of metadata, when users view the data on MorphoSource they have an understanding of what the data represents, how it was created, and how it relates to other data in the repository. It becomes easy to discover other media files representing the same specimen, or the same species, or to explore other items from the institution or researcher’s collections.

Behind the Scenes, Digitization Expertise, Equipment, Technology

Can You (Virtually) Dig It?

May 9, 2014 Zeke Graves

A group from Duke Libraries recently visited Dr. Maurizio Forte’s Digital Archaeology Initiative (a.k.a. “Dig@Lab”) to learn more about digital imaging of three-dimensional objects and to explore opportunities for collaboration between the lab and the library.

2014-04-29 15.37.39 — These glasses and stylus allow you to disassemble the layers of a virtual site and rearrange and resize each part.

Dr. Forte (a Professor of Classical Studies, Art, and Visual Studies) and his colleagues were kind enough to demonstrate how they are using 3D imaging technology to “dig for information” in simulated archaeological sites and objects. Their lab is a fascinating blend of cutting-edge software and display interfaces, such as the Unity 3D software being used in the photo above, and consumer video gaming equipment (recognize that joystick?).

Zeke tries not to laugh as Noah dons the virtual reality goggles.

Using the goggles and joystick above, we took turns exploring the streets and buildings of the ancient city of Regium Lepedi in Northern Italy. The experience was extremely immersive and somewhat disorienting, from getting lost in narrow alleys to climbing winding staircases for an overhead view of the entire landscape. The feeling of vertigo from the roof was visceral. None of us took the challenge to jump off of the roof, which apparently you can do (and which is also very scary according to the lab researchers). After taking the goggles off, I felt a heaviness and solidity return to my body as I readjusted to the “real world” around me, similar to the sensation of gravity after stepping off a trampoline.

Alex--can you hear me? — Alex–can you hear me?

The Libraries and Digital Projects team look forward to working more with Dr. Forte and bringing 3D imaging into our digital collections.

More information about the lab’s work can be found at:

http://sites.duke.edu/digatlab/

Mike views a mathematically modeled 3D rendering of a tile mosaic.

(Photos by Molly Bragg and Beth Doyle)

Notes from the Duke University Libraries Digital Projects Team