Celebrating 50 years of Computer Microscopy (1963 – 2013) Part II: The Impact of the Computer Microscope on Neuroanatomical Analysis


Overall view of the  computer microscope developed by Drs. van der Loos and Glaser (circa 1965).

Prior to the computer microscope era, quantitative neuro-anatomical studies were performed using the camera lucida method, an optical method allowing the scientist to see the neurons as if reflected on the piece of paper on which she will trace. These studies were painstaking and extremely time-consuming. Van der Loos and Glaser’s computer microscope was truly groundbreaking  in that it reduced analysis times dramatically, from twenty-four hours with the camera lucida and hand calculation techniques, to only thirty minutes with the computer microscope. Accuracy was also greatly improved thanks to accurate distance measurements in all three coordinate axes. Continue reading “Celebrating 50 years of Computer Microscopy (1963 – 2013) Part II: The Impact of the Computer Microscope on Neuroanatomical Analysis” »

Celebrating 50 Years of the Computer Microscope (1963-2013) – Part I: The First Semi-Automatic System for Neuroanatomical Analysis

neuron k3

Original figures published with permission from Dr. Ed Glaser

In 1963, Dr. Ed Glaser (co-founder of MBF Bioscience) and Dr. Hendrik van der Loos were at the John Hopkins Medical School putting the final touches on the first computer microscope, an analog computer connected to a light microscope. It was described as a system for attaching X-Y-Z transducers to a microscope stage, tracing the branches of a Golgi-stained neuron and outputting the result to a plotter (learn more about the origins of Neurolucida). The microscope stage was equipped with high-linearity linear motion transducers yielding output voltages proportional to the position of the microscope stage in all three dimensions. The computation of distances was performed by using a chord approximation to the curvilinear dendrites whose lengths were to be determined. Continue reading “Celebrating 50 Years of the Computer Microscope (1963-2013) — Part I: The First Semi-Automatic System for Neuroanatomical Analysis” »

We’re Kicking off a Year of Celebrations in Honor of the Computer Microscope’s 50th Anniversary

In the early 1960s, our company co-founder Dr. Edmund Glaser and his long time collaborator and friend Dr. Hendrik Van der Loos made some sketches on a paper tablecloth in the faculty dining room at John Hopkins Hospital, in Baltimore Maryland. That early diagram of a microscope included novel elements like transducers and a mechanical stage, and gave shape to their ideas about a faster way to conduct neuroanatomical research. It also laid the foundation for what was to become the first Semi-Automatic Computer-Microscope.

Next year marks fifty years since the invention of that revolutionary tool – a technologically advanced microscope, which sped up quantitative analysis, gave researchers the ability to create three-dimensional morphologies of neurons, and led to the development of some of MBF Bioscience’s most in-demand products, Neurolucida, Stereo Investigator, and Microlucida.

In honor of the occasion, we’re kicking off a year of celebrations starting next week at Neuroscience 2012. We’ll also be publishing photographs, slides, and stories about the microscope’s history throughout the year on our blog. We hope you’ll follow along, and join us in celebrating the 50th anniversary of the Semi-Automatic Computer-Microscope.

{The image shows one of the early neuron tracings done on the Semi-Automatic Computer-Microscope alongside a recent reconstruction of a neuron done with Neurolucida. Click on the image for a larger view.}

Woods Hole NeuroStereology Workshop

Interested in developing your design-based stereology skills? Dr. Mark West’s “NeuroStereology Workshop: An Introduction to Stereology for Neuroscientists” offers an excellent opportunity for scientists to refine their techniques.

The six-day workshop, held at the Marine Biological Laboratory in Woods Hole, Massachusetts, takes place April 17 – 22, 2010. A small group of graduate students, postdocs, and senior scientists will have the opportunity to design, supervise, and critically evaluate stereological studies of the nervous system, under the expert tutelage of Dr. West, neurobiology professor in the Anatomical Institute of Aarhus University in Denmark.

Learn more, and register for the workshop at Neurostereology.info.

See the full list of this year’s Stereology courses presented by MBF Bioscience

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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 neurorenew.com to enroll.

{Image courtesy of Neuro Renew Inc.}

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We Listen to Our Customers

MBF Bioscience Customer Service

At MBF Bioscience, we are committed to delivering innovative products and unrivaled support to our customers and collaborators. Our development team and staff scientists actively engage with leading scientific researchers to develop new technology as they work to further advance the field.

Recently, several of our customers worked closely with us to advance virtual slide technology to create high resolution brain atlases and morphometric analyses using very large files. A number of these features are included in version 9. One user, Dr. Harvey J. Karten, Professor of Neurosciences and Psychiatry at UCSD School of Medicine, says, “MBF Bioscience was highly responsive and innovative in helping me achieve my research goals. I wanted to analyze extremely large virtual histology images in Neurolucida that were originally created using the Aperio and Hamamatsu Nanozoomer image file formats. MBF initiated the dialog with each company and was able to add the support. They further modified Neurolucida to meet the needs of the unique problems and benefits associated with virtual images. Great company to work with.”

Our customers are our greatest ally on our constant quest to improve our products and services. Customer comments and feedback guides the ongoing development of each product. Frequently, we add specific analyses or features to our software based on individual customers’ research needs. MBF Bioscience stays in touch with our customers with follow-up emails and surveys, soliciting customer input and suggestions. If you would like us to add something for you, please contact us. We are only satisfied when our products and services exceed your expectations.

First published in The Scope, fall 2009.

Stem Cell Transplants Aid in Spinal Recovery


by Dan Peruzzi, PhD.

Thousands of people in the United States have spinal cord injuries (SCIs), with associated loss of movement and sensation below the site of the injury. Neural and glial cell transplants into research animals after SCI have correlated with recovery of function. The improvement may be caused by the transplanted cells; it’s thought that remyelination by the transplanted glial cells is the main reason for the improvement. Also, if adult neural stem cells are transplanted, there is evidence they form new neurons. In “Analysis of Host-Mediated Repair Mechanisms after Human CNS-Stem Cell Transplantation for Spinal Cord Injury: Correlation of Engraftment with Recovery” (2009, Hooshmand MJ, Sontag CJ, Uchida N, Tamaki S, Anderson AJ, Cummings BJ, PLoS One) the authors use Stereo Investigator’s powerful quantitative tools to determine whether changes in the host environment may also be correlated with improved function.

Using Stereo Investigator, specific aspects of the host milieu were compared between spinal cord injured animals (Non-Obese-
Diabetic-severe combined immunodeficient mice) that received transplants of human central nervous system-stem cell neurospheres (hCNS-SCns) and those that did not. The sampling parameters such as section interval, grid size, and counting frame size, were determined by checking the coefficient of error to make sure it was low. In some cases, additional post-hoc power analysis of data from previous publications was used to demonstrate that the parameters were appropriate for the required precision. Serotonergic fiber length was estimated using the Isotropic Virtual Planes probe with a 60X objective. Blood vessel length was estimated using the Space Balls probe with a 40X objective. The areas and volumes of lesions, spared tissue, and astrogliosis, were estimated using the Cavalieri probe with a 20X objective. Stereological results were complimented by biochemical protein analysis. In addition, the Optical Fractionator probe was used to estimate a non-host parameter, the number of neurons that live and proliferate from the hCNS-SCns transplant.

There were no differences found in the host characteristics between hCNS-SCns transplant animals and control animals. For example, there was no difference in the length of blood vessels. Platelet/ endothelial cell adhesion molecule immunohistochemistry was used to identify blood vessels. Some treatments following CNS trauma may promote behavioral recovery associated with vascular remodeling. Blood vessel length was estimated at the injury center, one mm rostral, and one mm caudal to the injury. There was no statistical difference between controls and hCNS-SCns transplanted animals (see figure, controls are vehicle and human fibroblasts (hFb)). Regarding the non-host characteristic of how many transplanted cells lived, multiplied, and migrated, the Optical Fractionator estimate showed that the transplanted cell number increased 194 percent after transplantation and migrated from the injection site. Ablation of some transplanted cells with Diptheria toxin correlated with a loss of locomotor recovery. This study shows that the direct consequences of the transplanted cells such as proliferation -
correlate with improved function – while the transplant does not have an effect on host characteristics such as lesion volume,
spared tissue, fiber sprouting, and angiogenesis, ruling out any correlation of an indirect effect of the transplanted stem cells with recovery.

Dan Peruzzi is a staff scientist at MBF Bioscience.

First published in The Scope, fall 2009.

Faster and More Powerful–AutoNeuron 4 Delivers

MBF Bioscience AutoNeuron

With the release of Neurolucida 9 comes version 4 of AutoNeuron. At MBF Bioscience our customers’ suggestions often become our newest features. What’s new and improved?

Windows 7/64-Bit: We’ve tested—and passed—Neurolucida and AutoNeuron on both 32-bit and 64-bit versions of Windows 7. The 64-bit version allows more memory and bigger data sets.

Interactive Mode: We’ve put a lot of work into making this easier to use. AutoNeuron now offers dynamic point-to-end-point display of the proposed tracing path while the user moves the mouse. Easily specify intermediate tracing points, too. Adding a new branch is as simple as a single click.

Regions of Interest: Identify one or more regions of interest for automatic tracing using contours, and specify the upper and lower Z limits for tracing. This makes it much easier and faster to limit tracing to just a portion of your 2D image or 3D image stack.

Editing Tools: Automated tracing can produce errors quite different from those seen with manual tracing. Our improved editing tools, which now include quick-splice and quick-detach tools for correcting tracing errors, make correcting errors easy.

Seed Placement: Apply distinct colors to differentiate between automatically- and manually-placed seeds used in automatic tracing. When you clear all seeds, choose to keep your manually placed seeds after the

Blended Channels: In previous versions, AutoNeuron could trace independent confocal channels. With our new release, you can trace selectively combined channels as well.

“AutoNeuron is the future of quantitative neuromorphology. I am particularly excited about AutoNeuron’s interactive function because it will allow for much more efficient tracing of Golgi stained neurons, which are notoriously difficult to quantify. Cajal would be proud!” – Bob Jacobs, PhD, Thomas M. McKee Professor in the Natural Sciences, Department of Psychology; Co-Director of Neuroscience, The Colorado College

Download Neurolucida 9 with AutoNeuron 4 at www.mbfbioscience.com.

First published in The Scope, fall 2009.

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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New, Easy Setup of Multiple-User Accounts

by Julie Keefe, M.S.

With version 9.0 of our software, you can now easily configure a Neurolucida or Stereo Investigator system to support multiple users, each with their own personalized settings.

There is no need to worry if the program is pointing to the right directory or accessing the correct configuration files for each user.

The new multiple-user setup only takes about 30 seconds for each user. It includes a Group option for different laboratories using the same system, and it also allows individual Profile log-ins within each group.

You can create different groups for your lab, or you can organize by experiment type, with shared parameters, to assure consistency among users.

To create a new profile, all you need to do is import the configuration file from an existing profile. In seconds, the settings and calibrations are completed, and you can begin working with the software. This feature is ideal for core facilities, since it has the added benefit of reducing the administrative overhead for the manager.

You can simply adjust your settings and be assured that those settings will be remembered whenever you return to work at that computer.

If you are an existing customer, this new setup uses the same configuration files you are already using. There is no need to perform another setup, and it automatically applies any needed updates.

Julie Keefe is the technical support manager at MBF Bioscience.

First published in The Scope, fall 2008.