Zeineb Yousif | Movers & Shakers 2021–Digital Developers | Library Journal

“Yousif was hired as the inaugural digital initiatives librarian at the Chester Fritz Library at the University of North Dakota (UND) in 2016, tasked with getting their institutional repository (IR) off the ground and promoting open access to scholarly resources. Under her leadership, UND’s IR has compiled nearly 30,000 digital objects, including theses and dissertations, research data sets, and a complete inventory of the university’s art collection. Work has begun on 3-D scanning more than 40,000 fossils for the geology department. Yousif also develops policies and guides for the IR, manages digitization projects, and works on digital exhibitions….”

Accelerating Standards for 3D Data to Improve Long-Term Usability – Association of Research Libraries

“3D data means different things to different people. Most are probably familiar with highly processed outputs, like the previous examples, which often lack documentation describing how the data has been created and processed. In fact, depending on the creation method, the creator may not even have access to the processing information due to the use of proprietary tools. However, even when 3D data is well documented through the best efforts of a creator, data steward, or repository, the data’s description is generally bespoke, and the terms used are ambiguous. This gives 3D data a steep slope to climb to achieve findability, accessibility, interoperability, and reusability (FAIR-ness).

The use of 3D technologies has grown exponentially in the last 10 years. As a result, research libraries have invested significant infrastructure, services, and people into supporting research, teaching principles, and modeling applications of 3D technologies and data. Research libraries have begun creating and capturing 3D data using a variety of methods and formats, establishing 3D immersion labs, opening 3D printing shops within their library spaces, and adding 3D data to their repositories. As use of these tools and services has become more widespread, appropriate stewardship of the digital data is critical for ongoing accessibility, but not yet widely established or agreed upon. Enter the Community Standards for 3D Data Preservation (CS3DP) initiative.

Organized by colleagues at Washington University in St. Louis, the University of Michigan, and Iowa State University, CS3DP aims to be an open, radically inclusive, and collaborative community invested in creating standards. Composed of working groups from national and international participants, the CS3DP community has increased awareness and accelerated the creation and adoption of best practices, metadata standards, and policies for the stewardship of 3D data….”

How 3-D Scanning Is Reinventing Paleoanthropology – Scientific American

“My principal job on site is to reconstruct fossils, and so I was tasked with putting together the DNH 155 skull. It took around a week to fully remove the skull fragments and all the sediment gluing the pieces together from their original resting place within the Drimolen Main Quarry. As each of the roughly 300 fragments were painstakingly removed, they were digitized with an Artec Space Spider, a professional handheld 3-D scanner. The scanner shoots patterns of light that distort based on the geography of the object it is hitting and bounce back to the scanner—like a bat using sonar, but in this case, light rather than sound is what’s bouncing back and forth. This technology was used to create high-resolution digital records of each piece of the cranium’s location within the sediment in case any pieces unexpectedly dislodged….

The first phase of reconstruction was completed by manually putting the pieces together. But, even after manual reconstruction, there were some elements of the cranium that couldn’t be placed because the contact point was too small, or a tiny part of the edges had been lost. In these cases, the Artec software was used to digitally situate the parts in relation to one another. Specifically, the face of DNH 155 cannot safely be attached to the rest of the cranium. This fusion was achieved digitally. Although it could have been glued, joining the pieces in this fashion would have been risky and would likely have caused permanent damage to the fossil. The published reconstruction of the DNH 155 cranium would not have been possible without 3-D technology, which would have been a huge blow to the ability of other researchers to assess the fossil in the future….

Reconstruction was only one part of the research program designed to reveal the secrets of this rare skull. Many of the researchers who work on fossils from South Africa are unable to travel to Johannesburg to work on the originals. This is especially true for researchers who are not based at wealthy institutions, and for cash-strapped students in general. It is for this reason that the Drimolen team have invested significant capital to digitize the DNH 155 cranium and most of the Drimolen fossil assemblage. As a Ph.D. student myself, I am particularly interested in the potential for high quality 3-D scanners such as the Space Spider to democratize research by allowing free and easy access to research-quality data. While permissions and access to such data are controlled by the University of the Witswatersrand (in the case of the Drimolen fossils) it is our ultimate intention to share our data with researchers, particularly early-career researchers, who are pursuing a topic related to the South African hominin fossils…..”

A versatile and customizable low-cost 3D-printed open standard for microscopic imaging | Nature Communications

Abstract:  Modern microscopes used for biological imaging often present themselves as black boxes whose precise operating principle remains unknown, and whose optical resolution and price seem to be in inverse proportion to each other. With UC2 (You. See. Too.) we present a low-cost, 3D-printed, open-source, modular microscopy toolbox and demonstrate its versatility by realizing a complete microscope development cycle from concept to experimental phase. The self-contained incubator-enclosed brightfield microscope monitors monocyte to macrophage cell differentiation for seven days at cellular resolution level (e.g. 2??m). Furthermore, by including very few additional components, the geometry is transferred into a 400 Euro light sheet fluorescence microscope for volumetric observations of a transgenic Zebrafish expressing green fluorescent protein (GFP). With this, we aim to establish an open standard in optics to facilitate interfacing with various complementary platforms. By making the content and comprehensive documentation publicly available, the systems presented here lend themselves to easy and straightforward replications, modifications, and extensions.

A microscope for everyone: Researchers develop open-source optical toolbox

“Modern microscopes used for biological imaging are expensive, are located in specialized laboratories and require highly qualified staff. To research novel, creative approaches to address urgent scientific issues—for example in the fight against infectious diseases such as COVID-19—is thus primarily reserved for scientists at well-equipped research institutions in rich countries. A young research team from the Leibniz Institute of Photonic Technology (Leibniz IPHT) in Jena, the Friedrich Schiller University and Jena University Hospital wants to change this: The researchers have developed an optical toolbox to build microscopes for a few hundred euros that deliver high-resolution images comparable to commercial microscopes that cost a hundred to a thousand times more. With open-source blueprints, components from the 3-D printer and smartphone camera, the UC2 (You. See. Too.) modular system can be combined specifically in the way the research question requires….”

New dimensions in data management: Understanding sharing and reuse practices for 3-D data | Wittenberg | College & Research Libraries News

“As 3-D digitization becomes more accessible and research institutions expand support for 3-D modeling, researchers are increasingly leveraging 3-D models and methods. For instance, a paleontologist might use a micro CT scanning process to capture images of the inside of a specimen that would otherwise be destroyed by such an analysis. An archaeologist might use photogrammetry to construct digital representations of artifacts that can then be examined in a way that would be difficult or impossible in a museum setting. The emergence of 3-D modeling as a research practice presents several challenges for libraries working to support and facilitate the dissemination and reuse of 3-D data packages. At present, there is significant work to be done in the community to create a culture and infrastructure that facilitates sharing 3-D research.

Understanding data sharing and reuse among researchers is critical to the success of collection, dissemination, and preservation efforts among memory institutions. Existing literature on data sharing, reuse, trust, quality, and review can inform approaches to evaluating how researchers might share or reuse 3-D data. However, 3-D data have characteristics that make them unique—rapidly changing technology, intersections with lucrative commercial sectors like virtual reality gaming, and the expectation that a model will render—or be accessible for user interaction—when shared. This project offers a unique and necessary contribution to the literature in analyzing creation, reuse, and publishing of 3-D through interviews with expert researchers. This provides substantial value to libraries, archives, and museums that work with 3-D by enabling memory institutions to design digital collection and repository systems that meet patron needs and foster innovation….”

Crafting a High-Def Human Tissue Atlas | Department of Biomedical Informatics

“HuBMAP (the Human BioMolecular Atlas Program) has released its inaugural data for use by the scientific community and the general public. Included in this release are detailed, 3D anatomical data and genetic sequences of healthy tissues from seven organ types, at the level of individual cells as well as many bulk tissue datasets. HuBMAP’s ultimate goal is to provide the framework required for scientists to create a 3D atlas of the human body.

HuBMAP’s tools and maps are openly available for research to accelerate understanding of the relationships between cell and tissue organization and function, as well as human health. Visitors can find the data at portal.hubmapconsortium.org.

HuBMAP is a consortium of 18 diverse collaborative research teams across the United States and Europe. HuBMAP values secure, open sharing and collaboration with other consortia and the wider research community. The consortium  is managed by a trans-National Institutes of Health (NIH) working group of staff from the NIH Common Fund; National Heart, Lung, and Blood Institute; National Institute of Biomedical Imaging and Bioengineering; and the National Institute of Diabetes and Digestive and Kidney Diseases….”

Destroyed Ancient Temple Now Open for Virtual Exploration

“Five years after its destruction, the ancient Temple of Bel in Palmyra, Syria has been digitally reconstructed by the UC San Diego Library’s Digital Media Lab (DML) using cutting-edge 3D methods and artificial intelligence (AI) applications. Inspired by a past collaboration between the Library and UC San Diego’s Levantine Archaeology Laboratory, this project has resulted in the digital preservation of more than a dozen lost reliefs, sculptures, frescos and paintings, all made publicly available on the Library’s Digital Collections website….”

Julich-Brain: A 3D probabilistic atlas of the human brain’s cytoarchitecture | Science

Abstract:  Cytoarchitecture is a basic principle of microstructural brain parcellation. Here we introduce Julich-Brain, a 3D atlas containing cytoarchitectonic maps of cortical areas and subcortical nuclei. The atlas is probabilistic to consider variations between individual brains. Building such an atlas was highly data- and labor-intensive and required to develop nested, interdependent workflows for detecting borders between brain areas, data processing, provenance tracking, and flexible execution of processing chains to handle large amounts of data at different spatial scales. Gap maps complement cortical maps to achieve full cortical coverage. The atlas concept is dynamic, i.e., continuously adapted with progress in mapping, openly available to support neuroimaging studies of healthy subjects and patients, as well as modeling and simulation, and interoperable, to link with other atlases and recourses.

 

Julich-Brain: A 3D probabilistic atlas of the human brain’s cytoarchitecture | Science

Abstract:  Cytoarchitecture is a basic principle of microstructural brain parcellation. Here we introduce Julich-Brain, a 3D atlas containing cytoarchitectonic maps of cortical areas and subcortical nuclei. The atlas is probabilistic to consider variations between individual brains. Building such an atlas was highly data- and labor-intensive and required to develop nested, interdependent workflows for detecting borders between brain areas, data processing, provenance tracking, and flexible execution of processing chains to handle large amounts of data at different spatial scales. Gap maps complement cortical maps to achieve full cortical coverage. The atlas concept is dynamic, i.e., continuously adapted with progress in mapping, openly available to support neuroimaging studies of healthy subjects and patients, as well as modeling and simulation, and interoperable, to link with other atlases and recourses.