Category Archives: oa.3d

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

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“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

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“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

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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

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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

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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

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“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

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“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.”

 

Sketchfab Launches Public Domain Dedication for 3D Cultural Heritage

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“We are pleased to announce that cultural organisations using Sketchfab can now dedicate their 3D scans and models to the Public Domain using the Creative Commons Public Domain Dedication (CC0). This newly supported dedication allows museums and similar organisations to share their 3D data more openly, adding amazing 3D models to the Public Domain, many for the first time. This update also makes it even easier for 3D creators to download and reuse, re-imagine, and remix incredible ancient and modern artifacts, objects, and scenes.

We are equally proud to make this announcement in collaboration with 27 cultural organisations from 13 different countries. We are especially happy to welcome the Smithsonian Institution to Sketchfab as part of this initiative. The Smithsonian has uploaded their first official 3D models to Sketchfab as part of their newly launched open access program….”

Open science takes on the coronavirus pandemic

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“Nextstrain is just one example of how an open ethos has driven the scientific response to the COVID-19 pandemic. Academics, online data repositories and home hobbyists with 3D printers are adopting new practices of rapid data sharing and collaboration that are appropriate to the urgency of the crisis. Many hope it will change the way science is done even after the pandemic subsides….”

Open science takes on the coronavirus pandemic

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“Nextstrain is just one example of how an open ethos has driven the scientific response to the COVID-19 pandemic. Academics, online data repositories and home hobbyists with 3D printers are adopting new practices of rapid data sharing and collaboration that are appropriate to the urgency of the crisis. Many hope it will change the way science is done even after the pandemic subsides….”

Glia

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“Glia uses an open-access research, development and distribution model to create high-quality low-cost medical devices that are then clinically validated

We want to change the way people interact with their devices. Providing communities with open-access low-cost medical devices fosters a culture of self-reliance and sustainability. If low-resource communities can access the equipment they need via an open-access model, they are empowered to troubleshoot problems, customize designs to meet their needs and share their findings with others. The ability to share successes in an open-access environment allows medical and technical communities to work together and avoid duplication of work and long feedback cycles. This model allows off-patent devices to exist as high-quality low-cost generic models, which also exerts downward pressure on prices for high-quality premium brands….”

Robotic microscopy for everyone: the OpenFlexure Microscope – preLights

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“Microscopes are an essential tool for clinical applications including diagnosis of infectious pathogens in endemic areas, and for scientific analysis in basic biology and physics labs. However, in much of the world, access to microscopy is limited by the cost of acquisition and maintenance of the imaging equipment. Moreover, in resource-limited settings, the chain of supply of parts that might need repair or replacement might not be as easily available, leading to high-end microscopes being out of service for long times until maintenance can take place. Open-source hardware has the potential to revolutionise the distribution of scientific instrumentation, impacting research in multiple ways, as well as local manufacturing, and education. To this end, in multiple contexts including research and clinics, 3D printers have become increasingly available. As a direct result of this, 3D printing has become a useful platform for prototyping and manufacturing laboratory devices. In their preprint, Collins et al (1) present the OpenFlexure Microscope design, a 3D printed automated microscope capable of motorised sample positioning and focus control (Figure 1)….”

Leveraging Open Hardware to Alleviate the Burden of COVID-19 on Global Health Systems[v1] | Preprints

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Abstract:  With the current rapid spread of COVID-19, global health systems are increasingly overburdened by the sheer number of people that need diagnosis, isolation and treatment. Shortcomings are evident across the board, from staffing, facilities for rapid and reliable testing to availability of hospital beds and key medical-grade equipment. The scale and breadth of the problem calls for an equally substantive response not only from frontline workers such as medical staff and scientists, but from skilled members of the public who have the time, facilities and knowledge to meaningfully contribute to a consolidated global response. Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) currently being developed and deployed to bolster access to personal protective equipment (PPE), patient treatment and diagnostics.

 

‘A worldwide hackathon’: Hospitals turn to crowdsourcing and 3D printing amid equipment shortages

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“Earlier this month, the CEO of an Italian 3D-printing startup learned that a hospital near the center of the coronavirus outbreak in Italy was running short on a small but crucial component: the valves that connect respirators to oxygen masks.

The company that makes the valves couldn’t keep up with the demand, and doctors were in search of a solution.

 

“When we heard about the shortage, we got in touch with the hospital immediately. We printed some prototypes. The hospital tested them and told us they worked,” the CEO, Cristian Fracassi, told Reuters. “So we printed 100 valves, and I delivered them personally.”

Similar efforts have popped up around the world. In Liverpool, New York, Isaac Budmen and Stephanie Keefe were printing more than 300 face shields for workers at a coronavirus test site in Syracuse this week, according to The Post-Standard of Syracuse. Budmen and Keefe, who run a business, Budmen Industries, selling custom 3D printers out of their home, turned to a fleet of 16 3D printers in their basement….”

Ultimate Medical Hackathon: How Fast Can We Design And Deploy An Open Source Ventilator? | Hackaday

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“What we need is a Nasal cannula-based NIV. This system humidifies air, mixes it with oxygen and then pushes a constant stream of it into people’s lungs.  If we can design a simple and working system we can give those plans to factories around the globe and get these things made. If the factories fail us, let’s also have a version people can make at home….”