Modern imaging devices can produce data sets sized in the TBs. For example, our cutting edge ClearScope light sheet theta microscope allows researchers to image large intact tissue specimens in 3D with subcellular resolution, and generates gigabytes or even terabytes of data per experiment.

We’ve been working diligently to engineer solutions for the amazingly increased image sizes in image data collection. We have developed and recently released new high-performance technology that addresses the three main pillars of working with big data: managing, viewing, and analyzing big data.

Specifically, we’ve greatly improved the efficiency of our image handling and processing algorithms. Over the last two years, we’ve massively upgraded our core imaging technologies. Our new imaging engine makes viewing and processing the massive files generated by current imaging tools orders of magnitude more efficient.

A quote that highlights the amazing progress we’ve made in the big data realm comes from Peter Lang of our Technical Sales team. He says, “Huge data sets that used to take 45-minutes or more to load, now take about five-seconds to open. File size doesn’t really matter anymore”. These improvements also mean that image processing tasks like automated cell detection now take minutes instead of hours. This new imaging technology is included in all of our latest software offerings.

Our recent image handling and processing improvements fit perfectly with Biolucida, our cloud-based platform for storing, viewing, and accessing big image data. Biolucida lets researchers view and access large data sets from a web browser or any MBF Bioscience analysis software from anywhere with internet access. Big data doesn’t need to be copied around; it can be kept and accessed at one secure location.

Imaging technologies continue to advance, and data sets will get larger and larger. MBF Bioscience is ready. “Microscopic image data image will soon include Z-stacks comprised of tens-of-thousands of planes for characterizing whole organs at high resolution. Our software engineering team has created a format and architecture that’s ready for efficiently storing, viewing and analyzing these truly huge images.” said MBF Bioscience Product Manager Nate O’Connor. “We’re so excited to be ahead of the curve on not just big data acquisition, but also on being able to manage, view, and analyze it.”

The post MBF Bioscience Solves Your Big Data Challenges appeared first on MBF Bioscience.

Williston, VT — October 6, 2020 — Big science produces big data. At laboratories around the world, researchers from every scientific discipline face a similar problem — how to manage the massive image files generated by large-scale experimental imaging workflows.

MBF Bioscience has solved this problem by leveraging our scientific imaging expertise to produce MicroFile+, a freely available software tool for the scientific community. MicroFile+ converts 2D and 3D images into compact files that are easy to store and share, so that your image data can be viewed and organized in an efficient, standardized manner.

MicroFile+ uses state-of-the-art compression technology to convert images from slide scanners, confocal microscopes, light sheet microscopes, and other microscope sources into a jpeg2000 file format — a web-friendly format that efficiently stores big image data for fast retrieval, viewing, and analysis. Images can also be converted to the OME tiff format, which is widely used in research microscopy.

MicroFile+ has the ability to:

• Convert nearly any type of image to the jpeg2000 standard or to the OME tiff format.
• Compile individual images, such as serial sections or cleared tissue, into 3D volumes.
• Handle complex data formats generated by light sheet and fast scanning imaging platforms.
• Produce standard data visualizations from big image data sets including deep focus, and maximum and minimum intensity projections.
• Accommodate multi-terabyte 3D images from light sheet microscopes.
• Ensure that metadata and imaging parameters are maintained as datasets are organized, analyzed, and shared.
• Process images in batches, for workflow efficiency by cueing many datasets for unattended conversion.

If you have any questions about how MicroFile+ can help with your big data needs, don’t hesitate to contact us: https://www.mbfbioscience.com/microfileplus

About MBF Bioscience: MBF Bioscience creates quantitative imaging and visualization software for stereology, neuron reconstruction, vascular analysis, c. elegans behavior analysis and medical education, integrated with the world’s leading microscope systems, to empower research.

Our development team and staff scientists are actively engaged with leading bioscience researchers, constantly working to refine our products based on state-of-the-art scientific advances in the field.

Founded as MicroBrightField, Inc. in 1988, we changed our name to MBF Bioscience in 2005 to reflect the expansion of our products and services to new microscopy techniques in all fields of biological research and education. While we continue to specialize in neuroscience research, our products are also used extensively in the research fields of stem cells, lung, kidney, cardiac, cancer, and toxicology.

MBF Bioscience has grown into a global business, with offices in North America, Europe, Japan, and South Korea, and a dealer network active on five continents. Our commitment to innovative products and unrivaled customer support has gained high praise from distinguished scientists who use our products all over the world. Our flagship products Stereo Investigator and Neurolucida are the most widely-used analysis systems for stereology and neuron reconstruction.

For more information visit www.mbfbioscience.com or follow MBF Bioscience on Facebook, Twitter, and LinkedIn, and track our Neuroart.com contest on Instagram.

Media Contact:
Pasang Sherpa
Marketing Manager
1-802-288-9290/ pasang@mbfbioscience.com

The post MicroFile+ Free Software for Converting Big Scientific Images into Manageable, Shareable, Standardized Files appeared first on MBF Bioscience.

Williston, VT (September 25, 2020)—To support the scientific community’s movement toward a more open and collaborative climate, MBF Bioscience is making their digital reconstruction file format, the Neuromorpholocial File Specification open and available to all researchers.

MBF Bioscience has a long history of supporting openness and collaboration in neuroscience research. MBF Bioscience’s file format has evolved for over 30 years, influenced by leading neuroscientists, new microscopic imaging technologies, and computational advances. During this progression, MBF Bioscience has continually augmented morphological modeling elements for performance, modeling accuracy, and analytical potential. Encoded in the well-recognized and readable XML format, modeling parameters specify microscopic neuroanatomies in a calibrated 3D coordinate system with appropriate units. The XML files can easily be viewed and parsed in a variety of software platforms (e.g., MATLAB, Python, R, etc.).

President and co-founder of MBF Bioscience, Jack Glaser says, “We hope this publication encourages the reuse of these rich data files for alternative analysis or reproduction of derived conclusions. This open specification encourages and enables the reuse of unique and important experimental data collected by users of our software.”

MBF Bioscience has also implemented development and design methodologies to ensure that our Neuromorpholocial File Specification complies with Findable, Accessible, Interoperable, and Reusable (FAIR) data standards. Abiding by FAIR data standards ensures the accessibility of original experimental data and its provenance, and facilitates inspecting, reproducing, and extending research.

Publishing this open and FAIR Neuromorpholocial File Specification data file specification benefits research in neuroscience, and in fields beyond, by increasing accessibility and sustainability of anatomical and morphological data. MBF Bioscience has submitted a publication, A comprehensive, FAIR file format for neuroanatomical structure modeling, to Neuroinformatics Special Issue: Building the NeuroCommons. It describes key elements of the file format, and details their relevant structural advantages. If you are interested in learning more, this paper is now publicly available on Biorxiv.

MBF Bioscience also recognizes the importance of community contributions, and a plan is in place to create an open community strategy through emails and existing discussion forums.

You can find the neuromorphological file format specification at www.mbfbioscience.com/filespecification. MBF Bioscience will continue to update and document the file specification to accommodate added or modified data elements.

In this webinar, MBF Bioscience demonstrates how to use MicroFile+ to convert microscopy image data from various proprietary file formats into the standardized OME-TIFF and JPEG2000 formats.

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About MBF Bioscience: MBF Bioscience integrates the world’s leading microscope systems with our revolutionary quantitative imaging and visualization software to accelerate research in the fields of: stereology, neuron and microvasculature reconstruction, vascular analysis, worm tracking, brain mapping and big image data management in medical research and education.

Since 1988, MBF Bioscience has forged a rich history of creating innovative products to empower biological researchers with the quantitative analysis tools they need to obtain accurate, unbiased results. With offices in North America, Europe, Japan, and South Korea, MBF Bioscience has helped researchers across the globe publish over 15,000 peer-reviewed papers in peer-reviewed journals. MBF Bioscience partners with the NIH and distinguished scientists across the world to continue their commitment to neuroscience research with their software technology, and also in the fields of stem cells, pulmonology, oncology, and toxicology. For more information visit www.mbfbioscience.com or follow MBF Bioscience on Facebook, Twitter, and LinkedIn.

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Media Contact:
Pasang Sherpa
Marketing Manager
1-802-288-9290/ pasang@mbfbioscience.com

The post MBF Bioscience Releases our File Format to Embrace FAIR Data Standards appeared first on MBF Bioscience.

As universities around the world move to online classes during the COVID-19 pandemic, educators suddenly need to find ways to create authentic learning experiences for their students. Biolucida for Medical Education creates that experience by giving students studying at home the same experience they would have in a lecture hall or sitting at a microscope.

At the Ludwig-Maximilians University of Munich, one of Europe’s most esteemed medical schools, Professor Christoph Schmitz teaches students neuroanatomy of the brain. Normally, Prof. Schmitz uses an on-site virtual microscope system to showcase histological slides that contain relevant brain regions. But when the Bavaria senate closed universities due to COVID-19, his department had to figure out a plan for the upcoming semester.

With the help of MBF Bioscience, Prof. Schmitz was able to move his collection of 3D brain sections off campus and to the cloud, giving him the ability to teach his classes online using Zoom for audio, and using Biolucida to share his slides with the 460 students enrolled in his class — nearly half of whom connect remotely from places as far away as Chile, Taiwan, and the United States.

“Moving our slides to a cloud-based Biolucida system allowed me to teach without any limitations or restrictions,” explained Prof. Schmitz. “There was no need for the students to be onsite, so nobody missed the class. Despite all the COVID restrictions, and despite the fact that our university buildings were closed, they were all able to take this class.”

First year medical student Laura Gajdi agreed that the class went very well. “A lot of students think it’s even better on the cloud. It was more flexible,” she said. “We had no problems with any connections, and it was very practical to always have access to the software for learning and for studying the slides. Another advantage is that you could choose how much time you want to spend with one slide — that’s not possible in the classroom.”

Normally, students only have access to the slides via the onsite system installed at the university.  But by taking the collection into the cloud, Prof. Schmitz gave his students the opportunity to access them at any time — something that Gajdi and the other students took advantage of, especially as they prepared for the final exam.

“Our students have previously asked us to move the entire thing into the cloud because they were bound to the times they could use the system on-site — a few hours a week, when we could open the room,” explained Prof. Schmitz. “If the room was closed, they couldn’t access it. That doesn’t work with the students’ schedules. They want to be able to access it on a Saturday evening. With the cloud solution they can do it 24/7, which is a huge advantage for them.”

After the successful experience with moving his course fully online with Biolucida, Prof. Schmitz is planning for his next semester, and is inviting other departments, including the immunology department, in his university to utilize this new resource.

“Basically, this is a great opportunity for every type of instruction or research that requires microscopic inspection of tissue sections,” says Prof. Schmitz. “It could be forensics, or even in clinical meetings where you need to look at sections. As long as you can share your screen and you have the resolution you need, it’s great.”

Learn more about Biolucida for Medical Education on our website: https://www.mbfbioscience.com/biolucida-medical-education

The post Medical Schools Take Learning Online with Biolucida During COVID-19 appeared first on MBF Bioscience.

Educators and researchers around the world now have free access to a database of whole slide images (also known as virtual slides) for histology and pathology. Featuring thousands of virtual slides contributed by 15 universities, The Virtual Microscopy Database, VMD, (http://www.virtualmicroscopydatabase.org/) is an online resource that allows educators to view and download virtual images and share their own.

Powered by MBF Bioscience‘s Biolucida^® for Medical Education solution, VMD gives educators an overview of individual slides and allows examination of various parts of the image at magnifications up to 40x. The users can take a screenshot or download the file at any time.

Funded by an Innovations Program Grant awarded by the American Association of Anatomists (AAA), the resource was developed by researchers from the University of Colorado, Drexel University College of Medicine, and the University of Michigan with corporate support from MBF Bioscience. With thousands of freely accessible virtual microscopy images, the VMD helps meet a growing need for better access to histology slides among educators and non-profit research organizations. The AAA foresees the images being used in a variety of educational ways such as for lectures, exams, and for creating supplementary course material as well as for non-profit research initiatives.

Collection of Virtual Slides in the Biolucida Viewer

“The greatest strength of the VMD is the availability of a large number of high quality virtual microscopy images to its users. The diversity and multiple examples of histological variations available in the VMD collections will enable histology and pathology educators to elevate the quality of their teaching by exposing their students to a broader variety of images and by experimenting with new pedagogical techniques in their classrooms.” (Lisa Lee, Ph.D., University of Colorado)

“We are proud to be part of the AAA’s efforts to improve the access of histology and pathology digital slides for medical educators and students by providing the underlying technology for this important resource. Any of the virtual slides in this new resource can be downloaded and used on an organization’s Biolucida on-premise or cloud-based server,” says Jack Glaser, president of MBF Bioscience.

Individuals affiliated with educational or research institutions may register to access the database. Once approved, users can browse files, or search for specific types of tissue. Currently, the VMD site includes over 2,600 virtual microscopy files, but as new users join the VMD file sharing community that number will grow as will the diversity of tissue and species type.

About AAA:

The American Association of Anatomists was founded by Joseph Leidy in Washington, D.C. in 1888 for the “advancement of anatomical science.” Today, via research, education, and professional development activities, AAA serves as the professional home for an international community of biomedical researchers and educators focusing on the structural foundation of health and disease.

About MBF Bioscience:

MBF Bioscience produces advanced microscopy imaging and analysis systems for biomedical research and education. The award-winning company was co-founded in 1988 by Edmund and Jack Glaser.

www.mbfbioscience.com

Contact:

Nathan O’Connor, Ph.D.

Product Manager/Technical Sales

nate.oconnor@mbfbioscience.com

1-802-288-9290

The post American Association of Anatomists Launches Virtual Microscopy Database powered by Biolucida appeared first on MBF Bioscience.

Analyzing cellular populations within specific anatomies in brain images requires expertise in both neuroanatomy and cellular identification. This typically involves a scientist comparing experimental images with a reference atlas and manually delineating anatomical regions and marking cell populations within. NeuroInfo^®, a revolutionary new technology from MBF Bioscience, enables researchers to automatically identify and delineate mouse brain regions based on the publicly available Allen Mouse Brain Reference Atlas.

“NeuroInfo has the potential to greatly improve our understanding of how mental disorders influence neuronal cell populations,” says Nathan O’Connor Ph.D., product manager at MBF Bioscience. “Because it makes identifying brain regions substantially faster and more accurate, researchers will be able to explore many more brain regions.”

“The Allen Mouse Brain Reference Atlas is a valuable tool to assist scientists in their research. We’re thrilled that MBF has chosen to integrate this resource into NeuroInfo,” stated Amy Bernard, Ph.D., Product Architect at the Allen Institute for Brain Science.

“Using this remarkable technology, neuroscientists will obtain more repeatable, objective analyses that have been possible to date. Thanks to the integration with the Allen Mouse Brain Reference Atlas, these analyses will be more standardized so that they can be compared across experiments and laboratories,” says Jack Glaser, President.

NeuroInfo can be used with MBF Bioscience’s slide scanning software and virtually all commercial whole slide scanners. The data from NeuroInfo seamlessly integrates with MBF Bioscience’s products including Neurolucida, Stereo Investigator, Biolucida, and BrainMaker.

The tools in NeuroInfo allow researchers to automatically delineate anatomies in the experimental specimens, and detect cells within these anatomies. NeuroInfo yields data that can be invaluable to better understand the organization and composition of the nervous system, and to further knowledge in neurogenomics, transcriptomics, proteomics, and connectomics.

The National Institute of Mental Health provides funding to support the development of NeuroInfo.

The post MBF Bioscience unveils whole mouse brain automatic region delineation and cell mapping with the Allen Mouse Brain Reference Atlas appeared first on MBF Bioscience.

Dr. Robert Ogilvie has been teaching histology with virtual slides for over 15 years. He is a pioneer in the field of virtual microscopy; striving to make learning histology more active and accessible to the next generation of doctors and researchers.

Dr. Ogilvie has won numerous teaching awards throughout his 45 year teaching career, including the most recent one – the 2016 Henry Gray Distinguished Educator Award which is the American Association of Anatomists’ highest education award. He will accept the award on Tuesday, April 5 at the 129^th Annual Meeting of the American Association of Anatomists that is meeting at the same time as many other societies as a part of the Experimental Biology Meeting (EB2016) in San Diego, CA. After accepting the award he will present a lecture titled ‘On the Way to Virtual’ where he will discuss his experiences using virtual microscopy to teach histology. The talk will culminate with an example of a fully online histology course he teaches using Biolucida, Blackboard, and WebMic – a virtual microscopy program he helped develop. Enrollment doubled when the course was offered online, and it remains popular for students from a wide range of majors.

Watch a six minute video that illustrates and describes the essential components of the online histology course offered by the Department of Biological Sciences at the University of South Carolina

Watch this 3 minute video of Dr. Ogilvie teaching histology with virtual slides and Biolucida

The post Dr. Robert Ogilvie to Receive the Henry Gray Distinguished Educator Award appeared first on MBF Bioscience.

“Educators and students will now have easier and quicker access to virtual slides from the Iowa Virtual Slidebox,” said Dr. Nathan O’Connor, Biolucida product manager. “In addition, MBF can offer fully annotated versions of these slides that highlight specific structures or areas of interest within the specimens.”

The collection was curated by Fred Dee, MD, a pathologist at the University of Iowa who is a pioneer in using virtual slides for medical education. “We created this virtual slide collection with a grant from the National Library of Medicine to provide an efficient open source alternative for histology and histopathology course directors around the world, as traditional laboratory based glass slide microscopy was beginning to disappear from curricula,” said Dr. Dee. “The Iowa Virtual Slidebox has been hosted by MBF Bioscience since 2001. We are extremely pleased that MBF Bioscience will continue that tradition with their new Biolucida software.”

Biolucida is a learning platform that uses virtual slides  ̶  high-resolution digital images of tissue specimens  ̶  to simulate the experience of using a light microscope, complete with the ability to focus in z through specimens. It supports images that are hundreds of gigabytes in size, and it is web-based so educators and students can view the slides from any computer with an internet connection.

The post Popular open access virtual slide collection has a new home appeared first on MBF Bioscience.

Thanks to Biolucida Cloud 2.0, educators and students are no longer bound to the traditional classroom and lab, and the limitations of glass slides are a thing of the past.

According to Nate O’Connor, Product Manager, “educators can be sure that every student sees the same images, and they can give all students experience with rare cases without putting delicate glass slides at risk.”  Students can access tissue specimens from home or the library and “it’s much easier to collaborate with study groups using a computer monitor instead of taking turns looking through oculars,” adds O’Connor.

Biolucida Cloud’s architecture is specially designed to allow many users to simultaneously access big images (with file size reaching hundreds of gigabytes) and navigate through them quickly and smoothly. Moreover, it also allows educators to use any 2D or 3D virtual slide, whether it was acquired with a slide scanner or imaging software.

The post Bringing Virtual Slides to the Medical Education Classroom with Biolucida Cloud 2.0 appeared first on MBF Bioscience.