American Association of Anatomists Launches Virtual Microscopy Database powered by Biolucida

Free resource for educators and researchers features thousands of downloadable histology slides

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, ( 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.


Nathan O’Connor, Ph.D.

Product Manager/Technical Sales


Dr. Julie Simpson to Give a Stereology Talk at the University of Iowa

On Friday, October 5, MBF Bioscience Staff Scientist Julie Simpson joins a group of scientific experts at the Iowa Microscopy Society‘s Fall Meeting, where she will give a presentation on the principles of design-based stereology and experimental design.

During the presentation, Dr. Simpson will offer an introduction to the concepts of design-based stereology and discuss the proper implementation of stereological protocols to generate unbiased estimates.   Her talk will also highlight why stereology is considered the gold standard for reporting cell estimations, volumes, and length.

You can get the full day’s program, and register for the event at the University of Iowa’s website.

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Meet the Team: Ben Haydock, Senior Software Engineer

Name: Ben Haydock

Position: Senior Software Engineer

How long have you been working at MBF Bioscience? 10 years

What do you do? I develop software. Most recently, I’ve been working on our imaging system and hardware integration. For imaging, I develop advanced features that help the user acquire the images they want. Another feature I worked on lets the user modify the display of those images for optimum image analysis.

On the hardware integration side, I work on code that communicates with motorized microscopes, light sources, filter wheels, and stages. The code I write allows our software to move all those pieces of hardware so the user doesn’t have to. Recently, I integrated our software with the current family of Zeiss laser confocal microscopes.

What do you love most about your job? I love graphics, I like to make hardware go, and I enjoy seeing my co-workers every day.

Tell us about the last vacation you took. My brother holds a cross country ski race every year on some land that we share with our sister here in Vermont. So I took some time off to help shovel snow out of the woods onto the cross country ski trails. After the race, my kids and I went skiing on those trails. That’s my  idea of vacation.

How do you spend your free time? I spend it playing with my kids, riding my bike, and skiing when I can find some snow.

SVI Partnership Means Clearer Images for Researchers Worldwide

The microscopic world just got a whole lot clearer for scientists around the world who use MBF Bioscience software. When images are magnified as intensely as they are in today’s world of highly advanced scientific research, they don’t always appear crystal clear. But by incorporating the clarifying process of deconvolution to microscopic images, previously hidden details emerge, allowing scientists to work with greater facility.

Deconvolution is a processing technique that improves the appearance of microscopic images by removing blurriness.

Thanks to our new partnership with the Dutch company SVI (Scientific Volume Imaging, BV), researchers who use Neurolucida and Stereo Investigator will see images with greater clarity than ever before.

“We’re always striving to find ways to help scientists become more productive and to open new pathways to discovery,” said MBF Bioscience founder and CEO Jack Glaser. “We’ve incorporated SVI’s Huygens technology into our own software, Neurolucida and Stereo Investigator, and we’re excited by this opportunity to make SVI’s Huygens deconvolution software available to scientists doing other kinds of research as well.”

{Image: Macrophage fluorescently stained for tubulin (yellow), actin (red) and the nucleus (DAPI, blue). Left: original image, recorded with a wide field microscope. Right: the same dataset, deconvolved using Huygens Professional. Data courtesy of Dr. James Evans, Whitehead Institute, MIT Boston MA, USA. Image courtesy of SVI}

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Science Events: The Brain Institute at the University of Utah March Symposium – Imaging Neurons

On Monday, March 1, the Brain Institute at the University of Utah hosts its March Symposium – Imaging Neurons. We are pleased to report that two of the neuroscientists speaking at the event are MBF Bioscience customers. Dr. Erik Jorgensen, a biology professor at the University of Utah will discuss fluorescence electron microscopy. Dr. Karl Deisseroth, a professor of bioengineering and psychiatry and behavioral sciences at Stanford University, will present developments in optogenetics, a new field that involves observing neurons through a combination of genetic engineering and light.

Who: Dr. Karl Deisseroth and Dr. Erik Jorgensen

What: The Brain Institute at the University of Utah March Symposium – Imaging Neurons

When: Monday, March 1, 2010, 2-6pm

Where: Utah Museum of Fine Arts, Marcia & John Price Building, 410 Campus Center Dr., Salt Lake City, Utah

{Image courtesy of The Brain Institute at the University of Utah}

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Confocal Microscopy and Stereology Courses

Dr. Daniel A. Peterson’s practical training courses offer excellent, hands-on instruction in the use of confocal microscopes and design-based stereology. Each year, Dr. Peterson, a Chicago-based neuroscientist and Executive Director of the Center for Stem Cell and Regenerative Medicine at Rosalind Franklin University holds two training sessions. This year’s events take place March 8-12 and August 16-20.

From graduate students, to post doctorates, to advanced laboratory technicians, anyone in the biomedical field who uses qualitative and quantitative microscopy in their research would benefit from the week-long courses. Attendees will gain a comprehensive overview of  modern histological preparation and microscopic analysis, and are encouraged to bring their own material for discussion and customized consultation.

Registration for the March course ends February 26. Go to to enroll.

{Image courtesy of Neuro Renew Inc.}

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MBF Unveils Neurolucida and Stereo Investigator 9

Neurolucida 9

Image courtesy of Juan Carlos Tapia, PhD, Harvard University

Now available, release 9 of our flagship Neurolucida and Stereo Investigator systems represent one of the largest changes in the history of these products. With many new features and an improved interface, we’re listening to you, our loyal customers, and delivering products with innovation, power, and speed.

Stereo Investigator and Neurolucida New Features

Image Handling: We’ve been busy when it comes to handling and visualizing your valuable image data. High bit depth, Nchannel (up to 16 bits per channel) image files are now accessible via an intuitive user interface. Acquire up to 6 independent channels of high bit depth data per image from any of our cameras. You can even load dozens of image stacks at once. Our new image handling lets you work with the latest image file formats from the major confocal microscope manufacturers. We’ve enhanced your ability to work with virtual slides to include 3D virtual slide stacks and allow you to save portions of these large montage images (and stacks) to separate files. All of this is controlled by a new image display control feature providing precise histogram adjustments.

Automatic Contouring: Automatically trace contours while you watch the software identify the tissue boundaries from images, image stacks, virtual slices, and even off the live camera feed. If you need to move the stage, the software does it automatically and continues tracing the outline of your region.

Automatic Object Detection: Now with just a few clicks you can let the software find cells, synapses, grains, or similar objects of interest in your images. Mark and count the objects or ask our software to automatically trace around the outside of an object. JPEG2000 Image File

Support: We now offer state-of-the-art image file storage with JPEG2000 support, which dramatically reduces disk space usage for all your image data. For instance, you’ll see image stacks that were 100 MB shrink to about 5 MB, depending on the image data and compression ratio you choose. Create very large virtual slices that exceed the computer’s physical memory by using JPEG2000 support, and store these files
using manageable file sizes. An example, we recently captured a large virtual slice (556,800 x 520,000) that compressed to only 40 GB; with earlier technology, it saved as an 800 GB image file.

Multiple User Setup: If you have a system that serves many users, you’re life just got easier. Use one login with all users or give each user a private login with their own customized settings. If you have a system with multiple hardware setups, this also makes it easy to keep the settings separate and switch between them.

Support for Aperio and Hamamatsu Nanozoomer Files: Now you can load Aperio SVS and Nanozoomer virtual slide files into Neurolucida or Stereo Investigator for analysis.

Improved 3D Visualization: A fully redesigned 3D visualization window makes it easier to view, manipulate, and understand image stacks and tracings. We’ve included cut planes in the X, Y, and Z axis from any view angle. Manipulate the image transparency to get the look you want from your image and tracing data. Look for the new automatic rotation tool that lets you adjust the angle of rotation
and speed.

Hardware: We’ve added support for monochrome and color cameras under 64-bit Vista and Windows 7. Our streamlined camera interface gives you the image you desire easily and quickly. Now, swap between multiple cameras without exiting the application to easily utilize the multiple camera ports on your microscope. Zeiss AxioCam, QImaging, and Baumer cameras are part of our line as well, along with tight integration for the Zeiss ApoTome and support for the Qioptic Optigrid structured illumination offerings.

Simplified Menus and Hot Keys: Streamlined workflows with more intuitive menus and dialog, along with new navigation keys help you maneuver around with less effort.

Drag and Drop: Drag and drop your images, image stacks, and data files for easier loading and display.

Tracing with Transparency: Ever want to look at or trace something where the tracing was in the way? Now simply adjust the transparency of the tracing to see the underlying image while tracing.

Serial Sections: Do you trace your sections separately and combine them later? We’ve made it much easier and intuitive to combine files together into a complete data file with fewer steps. Use the improved Serial Section Manager to define many sections in one step and view multiple sections.

These are just some of the new enhancements found in version 9.

More Neurolucida 9 Additions

Neurolucida has added new analysis tools for tracing and classifying dendritic spines, and improved editing features to correct your AutoNeuron tracings.

And More In Stereo Investigator 9

Stereo Investigator has a number of other new features including the Connectivity Assay (Pulmonary Edition). New enhancements for the Optical Fractionator include faster counting of multiple cell populations, new displays for the results, and improved Excel export for easier and more comprehensive reports. The Area Fraction Fractionator is also faster and more streamlined. An important
new tool, the Oversample and Resample allows you to methodologically pick the most efficient sampling parameters for your material.

First published in The Scope, fall 2009.

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