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.

 

BEaTS-? an Open Access 3D Printed Device for in Vitro Electromechanical Stimulation of Human Induced Pluripotent Stem Cells – PubMed

Abstract:  3D printing was used to develop an open access device capable of simultaneous electrical and mechanical stimulation of human induced pluripotent stem cells in 6-well plates. The device was designed using Computer-Aided Design (CAD) and 3D printed with autoclavable, FDA-approved materials. The compact design of the device and materials selection allows for its use inside cell incubators working at high humidity without the risk of overheating or corrosion. Mechanical stimulation of cells was carried out through the cyclic deflection of flexible, translucent silicone membranes by means of a vacuum-controlled, open-access device. A rhythmic stimulation cycle was programmed to create a more physiologically relevant in vitro model. This mechanical stimulation was coupled and synchronized with in situ electrical stimuli. We assessed the capabilities of our device to support cardiac myocytes derived from human induced pluripotent stem cells, confirming that cells cultured under electromechanical stimulation presented a defined/mature cardiomyocyte phenotype. This 3D printed device provides a unique high-throughput in vitro system that combines both mechanical and electrical stimulation, and as such, we foresee it finding applications in the study of any electrically responsive tissue such as muscles and nerves.

 

European web conference on the value and use of 3D digital cultural heritage for resilience, recovery and sustainability | Shaping Europe’s digital future

“The crisis caused by the global coronavirus pandemic has had a major impact on our mobility, and it is changing our habits. In the context of such limitations, digital 3D technologies can be an effective solution for keeping our cultural heritage virtually accessible to citizens. Furthermore, 3D digital cultural heritage can provide important opportunities for cultural heritage institutions and for other sectors that re-use such content, including in particular in the tourism sector, for immediate resilience and recovery but also for long-term sustainability….”

Welcome to GLAM 3D | GLAM 3D Engelberg Center

“If you are thinking about starting a 3D Open Access program you have come to the right place!

This site will walk you through the entire process of planning, creating, and launching an Open Access 3D scanning program. It is designed to have something for everyone, from 3D beginners to 3D experts.

Glam3D.org is an open resource that welcomes contributions and suggestions from the community.”