Set for release this spring, the new and improved Stereo Investigator will include a new imaging engine, display engine, automatic camera alignment, automatic lens calibration, the double disector, and live video zooming.  

“I’m excited to say that Stereo Investigator keeps getting better in so many ways. What is common among all these new features is increased functionality, more efficiency and better performance,” says MBF Bioscience Product Manager Nathan Liese.  

The new imaging engine will especially help working with large images, whether they are from the SRS image acquisition, confocal or light sheet microscopes. “Users will be amazed by how much faster they can work with their images”, says Nathan. 

The software’s new automatic alignment and calibration features will be game-changers for researchers with large turn over, especially for those working in core facilities and large labs with many users.  

These new features eliminate the time-consuming process of manually aligning the camera and calibrating lenses. The new automatic camera alignment and calibration functionality promises to convert a formerly complex process that previously could take five to 20-minutes, to a simple one that takes a few minutes. 

Two other new features: Double Disector and Live Video Zooming were specific requests from our users, and help make Stereo Investigator an even more comprehensive tool for stereology studies. Double Disector facilitates the counting process in cases where populations of multiple types need to be quantified within the same study, and Live Video Zooming offers the added convenience of digital zooming to examine hard to see objects.  

Overall Stereo Investigator’s new imaging engine and new tracing engine make the software more powerful than ever, with the ability to handle larger images, load data files much faster, open and save files faster, and more effectively use your computer’s resources. 

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A baby makes eye contact with a passing stranger and his social development begins. Unable to resist the infant’s smile, the stranger smiles back and the baby starts to learn about human emotion through facial expression. But some babies, especially those on the autism spectrum, don’t make eye contact. What compels these tiny humans to avoid the eyes of people around them? Scientists specializing in developmental disabilities say the flocculus, a brain region in the cerebellum integral to eye movement control, may play a role in atypical gaze.

In their study of the postmortem brains of 12 autistic subjects and 10 control subjects, the research team, led by Dr. Jerzy Wegiel of the New York State Institute for Basic Research in Developmental Disabilities, in Staten Island, saw abnormally large flocculi in eight autistic subjects. According to the study, published last month in Brain Research, seven of these subjects exhibited “poor, very poor, or no eye contact” during the course of their lives.

Using an MBF Bioscience system consisting of Stereo Investigator controlling a Zeiss Axiophot microscope and an automatic stage, the researchers performed a stereology study to assess regional and cell volume changes in the flocculi of both groups, using Cavalieri’s method of point counting and the Nucleator probe.

In different subregions of the cerebellum, namely the molecular and granule layers, they saw profound changes in volume and organization in autistic patients as compared to control subjects. For example, instead of forming a neat layer, granule cells formed loosely arranged islands. They also saw fewer Purkinje cells, defective axons, and weak dendritic arborizations in the autistic brains.

The abnormalities, they say, are the result of altered mechanisms controlling the healthy development of these regions, particularly “cortical folding, neuronal migration, spatial arrangement, and connectivity.” According to the paper, these abnormalities cause the oculomotor system to develop in unusual ways, resulting in eye movement control defects in autistic subjects, including poor eye contact.

Together these findings expand the understanding of developmental defects that may underlie oculomotor dysfunction in autistic subjects.

{Wegiel, J., Kuchna, I., Nowicki, K., Imaki, H., Wegiel, J., Yong Ma, S., … & Wisniewski, T. (2013). Contribution of olivo-floccular circuitry developmental defects to atypical gaze in autism. Brain research.}

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Learning a new dance routine or how to ride a bike is possible because of Cerebellar Granule Cells (GCs) according to Galliano and colleagues in The Netherlands. To find out more about the role of these abundant brain cells, and why we have so many of them, the scientists silenced most of the GCs in a group of mutant mice. They found the rodents could balance and run as well as they ever did, but when it came to learning new activities involving motor function, the mice had a harder time.

“Our findings indicate that a minority of functionally intact GCs is sufficient for the maintenance of basic motor performance, whereas acquisition and stabilization of sophisticated memories require higher numbers of normal GCs controlling PC firing,” the authors say in their paper published last month in Cell Reports.

Comprising more than half of all neurons in the central nervous systems of vertebrates, GCs are a particularly populous type of neuron, but why? To get some answers, the research team bred a type of mouse for which the output of most, but not all, GCs was inhibited, then they tested the experimental mice alongside control mice in a variety of motor performance tasks.

In open field, balance beam, and rotating rod tests, both groups demonstrated equal skill. But when the animals were tested on their ability to learn to walk on a rotating rod that spun faster and faster, the control mice performed significantly better than experimental mice. The mutant group also showed impaired learning after training, leading the scientists to speculate that the cerebellar system, which coordinates muscular activity, needs “a wider dynamic range of simple spike modulations of Purkinje cells to entrain its target neurons downstream” – a direct consequence of abundant populations of normally functioning GCs.

“These findings provide important experimental clues as to why vertebrates need an extreme abundance of functional GCs in daily life and to what extent this abundance is redundant,” they say.

During the course of the study, the researchers examined cell morphology, synaptic activity, and plasticity with methods that included whole-cell patch clamp recording, immunohistochemistry, and electron microscopy. They used Neurolucida to assess the morphology of neurons, and measured the dendritic length of GCs stained with Golgi-Cox staining with Stereo Investigator. They also used Sholl analysis to measure the dendritic arborization of Purkinje cells.

Find out more about the study in Cell Reports.

Galliano, E., Gao, Z., Schonewille, M., Todorov, B., Simons, E., Pop, A. S., D’Angelo, E., van den Maagdenberg, A., Hoebeek, F., & De Zeeuw, C. I. (2013). Silencing the Majority of Cerebellar Granule Cells Uncovers Their Essential Role in Motor Learning and Consolidation. Cell Reports. doi: 10.1016/j.celrep.2013.03.023

Image: Public domain figure of neurons in the cerebellar cortex from Cunningham’s Textbook of Anatomy (1913) via Wikimedia Commons.

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Founding Director of the Center for Stem Cell and Regenerative Medicine at Rosalind Franklin University of Medicine and Science, Dr. Daniel Peterson’s biannual “Practical Workshop in Confocal Microscopy and Stereology” takes place March 18-23 at Club Quarters Hotel in Chicago. The intensive, week-long workshop offers a comprehensive background in the theory and practice of modern histological preparation and microscopic analysis. The workshop covers the entire process of microscopic analysis from specimen preparation to the readying of images for publication. For more information read our Q&A with Dr. Peterson to find out more about his course.

Over on the East Coast, Dr. Mark West’s “NeuroStereology Workshop” takes place March 24-29 at the Marine Biological Laboratory at Woods Hole, on Cape Cod. Professor of Medical Neurobiology at The University of Aarhus in Denmark, Dr. West’s course focuses on how stereological methodology can apply to nervous system research. This year’s workshop will include lectures on the Cavalieri Principle, the Optical Fractionator, and Isotropic Probes. You can find more information about the course at the Neurostereology website.

March 18 – 23, 2012
Practical Workshop in Confocal Microscopy and Stereology
Instructor: Dr. Daniel Peterson
Club Quarters Hotel, Chicago

March 24 – 29, 2012
NeuroStereology Workshop
Instructor: Dr. Mark West
Marine Biological Laboratory, Woods Hole, Massachusetts

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Dr. William Seeley

MBF Bioscience congratulates our customer Dr. William Seeley on his 2011 MacArthur Foundation Fellows award.

Dr. Seeley is an Associate Professor of Neurology at the University of California San Francisco Memory and Aging Center. His research area is regional vulnerability in dementia—why certain dementias attack specific neurons.  Dr. Seeley leads the Selective Vulnerability Research Lab at USSF.

Read about the John D. and Catherine T. MacArthur Foundation, its work, and the 2011 Fellows at www.macfound.org.

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A longtime MBF customer, Dr. Hof uses Stereo Investigator and Neurolucida in his laboratory. In fact, some of their features are due to Dr. Hof’s suggestions to our development team.

Read more about Dr. Hof and his vision for The Journal of Comparative Neurology on the Journal’s website.

The post Congratulations to Dr Patrick Hof appeared first on MBF Bioscience.

He spoke to us about the atmosphere in the classroom, what kinds of students take his course, and what aspects of the workshops participants get most excited about.

What do you enjoy most about teaching?
The week or so before the course, I start wondering again why I was crazy enough to do this. After all, I am running my own lab and there is the constant worry about grants and getting our papers out, etc. However, when I am in the midst of the course, I find it very rewarding when the participants acquire new tools for their research and discover new ways to assess their experimental outcomes. As we discuss their research objectives, I find I am always learning new things and this helps make it all worthwhile for me.

Is there anything new you’ll be introducing in next week’s workshop?
I will introduce a session on estimating length of structures within tissue. This will be, in the end, an explanation of the principles behind the Spaceballs probe in Stereo Investigator^®. More and more participants have wanted to use this probe, and I believe this represents an expansion of the use of stereology within research laboratories.

What’s the atmosphere like in the classroom?
An interesting transition takes place over the week. In the beginning, you have a group of 15-20 strangers who probably think they have little in common. Very quickly, participants start to realize they share similar objectives and face similar problems. Individual personalities emerge and friendships start to form. By the end of the week, when we have our farewell dinner, there is usually genuine sadness about parting ways. In many cases, long-term personal and professional friendships form between the participants.

Do most students arrive equipped with their own projects and research materials, or do they use materials offered in the course?
The participants can vary widely in their starting points. Those who are brand new graduate students often arrive without their own material. However, most of the participants, including technicians, come with their own material and spend a considerable amount of time working through their personal objectives over the week. We have material for general instruction, but there is really no replacement for evaluating your own material as you learn new skills.

What aspects of the workshop do students seem to get most excited about?
Working with the equipment. Instead of getting demonstrations or watching someone else drive, course participants get to do the driving themselves. Though ending the night with the group out at the bar is probably a close second!

What kinds of backgrounds do the students have?
Some are completely new to the field and are starting from scratch. Others are senior professors who need to add another form of analysis to their program and are pragmatic enough to know they can benefit from an intensive introduction. However, for the most part, participants have some experience and some even are quite expert already.

Are there any prerequisite skills students should have before taking the course?
I try to teach the course at the graduate level and I recommend that it is suitable for advanced technicians and those at a post-graduate skill level in biological sciences. Nevertheless, we have had Bachelor’s level students who have performed quite well. It is really less a matter of credentials and more about some having a sense of curiosity about how microscopy and stereology work.

What are some examples of research fields the students come from?
Neuroscience represents about half of the participant population. A similar proportion comes from academic research labs. We have also had participants from government labs, regulatory bodies, and industry labs. Some of the fields represented include pathology, immunology, vascular physiology, kidney disease, cancer research, heart disease, and a variety of stem cell research applications. We have routinely had participants bring material from humans, non-human primates, and of course, mice and rats. We have also had more exotic samples, including zebrafish and even whale brains.

Do you teach the workshops alone?
In this course, I give all the lectures myself. This is a circumstance where a single voice is more effective while building the story from specimen preparation to imaging to quantitation. I do have help with the tutorials as one person can only stretch so far.

How far do participants come to take your course?
One of the enjoyable parts of the course is the understanding of the global nature of science. We have had participants from Sweden, Germany, Spain, Poland, Italy, Switzerland, France, the United Kingdom, Israel, South Africa, India, Japan, Australia, New Zealand, Chile, Argentina, Brazil, Colombia, Peru, Mexico, and Canada—the list goes on. In some cases, more than half of the participants come from institutions outside the USA. In one course, we had a large group of Spanish-speakers from Spain, Puerto Rico, Mexico, and Argentina and I think about half of that session was conducted in Spanish.

What kind of response do you get from the students after they complete the workshop?
I am happy to say that participants have nearly always expressed satisfaction for what they have been able to achieve during the week. I credit this mostly to the fact that the instruction covers the theoretical basis, but mostly it emphasizes pragmatic and practical approaches. In addition, the students actually get to do something, rather than watch, which is always more satisfying.

What’s your favorite part of the workshop?
The farewell dinner—my job is done and I can finally relax.

Get more information on Dr. Daniel Peterson’s confocal microscopy and design-based stereology courses at www.neurorenew.com.

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Jack Glasser, president of MBF Bioscience said, “Ted was an outstanding neuroanatomist.  Among many of his accomplishments, his work on brainmaps.org was a great contribution to neuroscience. Ted was a longtime customer of MBF, and over the years we became friendly.  I always enjoyed our conversations, especially discussing his ideas about adding new features to our software. I will certainly miss him.”

Dr. Jones was the director of the Center for Neuroscience at UC Davis. A legendary expert in neuroscience, Dr. Jones was president of the Society for Neuroscience in 1998. He was elected to membership in the National Academy of Sciences in 2004. Dr. Jones performed groundbreaking research into questions about brain function in schizophrenia and bipolar disorder.

Dr. Jones earned a medical degree from the University of Otago (New Zealand) and a doctorate in neuroanatomy from Oxford University (England). He held academic and research positions in New Zealand, in Oxford, at Washington University in St. Louis, and at both UC Irvine and UC Davis.

He is survived by his wife Sue, son Christopher, daughter Philippa Barrett, and three grandchildren. Dr. Jones is also survived by his brother Peter and sister Pauline Martin in New Zealand.

A memorial service is scheduled for 11am, Friday 17 June 2011 at the Buehler Visitor and Alumni Center at UC Davis.

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Dr. Bradley Cooke of the Neuroscience Institute at Georgia State University studies sex-specific neural circuitry in the amygdala. His past investigations showed increases in regional volume and soma size of the medial amygdala (MeA), a control center in the brain for behaviors that emerge during puberty like aggression and an interest in mating. In his latest study, “Synaptic Reorganisation of the Medial Amygdala During Puberty,” published in the Journal of Neuroendocrinology, Dr. Cooke set out to discover how puberty affects the medial amygdala on a synaptic level.

Dr. Cooke compared the brains of two groups of 45-day-old male Siberian hamsters. One group had completed puberty, while the others were raised in an environment that delayed puberty’s onset. Stereological examination of the hamsters’ brains confirmed increased volume and size of the pubertal MeA as outlined in previous studies, but this time, Dr. Cooke saw changes in synaptic behavior. “The results suggest that numerous excitatory synapses are added to the MeA during puberty. More broadly, they show that the pubertal emergence of sexual behavior is accompanied by synaptic reorganisation of a key network involved in the expression of sexual behavior.” Dr. Cooke explained in his paper.

To quantify indicators of synaptic activity, including puncta immunoreactive for vGlut2 [vesicular glutamate transporter-2] and PSD-95 [post-synaptic density] in nissl-stained and immunofluorescent brain sections, Dr. Cooke used Stereo Investigator. “The software/hardware rig from MBF Bioscience was essential for the success of the project,” he said.

“The support staff at MBF is one of their greatest assets, almost equal to the software itself. Everyone I have dealt with has been friendly, helpful, patient, and interested in seeing us succeed. I am so happy that I selected this company for my quantitative neuroanatomy needs.”

Read the full article “Synaptic Reorganisation of the Medial Amygdala During Puberty” in the Journal of Neuroendocrinology.

Cooke, B. M. (2011), Synaptic Reorganisation of the Medial Amygdala During Puberty. Journal of Neuroendocrinology, 23: 65–73. doi: 10.1111/j.1365-2826.2010.02075.x

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Who: Harvey Karten, M.D., Professor of Neurosciences

Where he works: The University of California, San Diego

Research focus: The evolution of the organization of avian brains.

MBF Bioscience software used: Neurolucida

Major scientific contributions: Neuroscientists use the bird brain model to better understand the organization and evolution of the human brain thanks to Dr. Karten’s research on nonmammalian vertebrates. In addition, Dr. Karten is a brain-mapping pioneer. He is a contributor to Brainmaps.org, an interactive brain atlas developed by Professor Edward Jones of UC Davis. Used by scientists around the world, BrainMaps.org features a database of extremely high-resolution images of the monkey, rat, bird, goldfish, and other vertebrate and invertebrate brains.

Elementary brain tracing: In the early days, Dr. Karten implemented a laborious process to reconstruct sections of the brain. The method used by scientists in the early 1960s involved macro projectors, hand tracing, and point to point matching aided by a microscope. “What you then tried to do in this somewhat enlarged drawing was to try to localize very small events. That’s very difficult to do. The difference in scale doesn’t allow for accurate localization,” he explained.

How Neurolucida helped: On a tip from Dr. Hendrick Vanderloos, who he heard speak about electronic applications of data collection in neuroanatomy, Dr. Karten started using transducers. “By using motorized stages with transducers on them, Neurolucida allows you to have a detecter on the stage that localizes axons and cells with a precision of better than one to two micrometers,” he said. “That’s an extremely powerful advance in tracing.”

Obtaining precise information at extremely high magnifications has always been the goal, explained Dr. Karten, who is often faced with the challenge of localizing objects that measure one micron in length in fields spanning upwards of 20,000 by 50,000 micrometers. “How do you accurately show that it’s in one specific position and not ten micrometers away from there? That is where the motorized stages and transducers came into such important play,” he explained. “Neurolucida allows very precise localization within the brain of the distribution of labeled cells and axons. That’s the critical thing. That was the strategy that was first developed by MBF Bioscience’s co-founder Ed Glaser back in 1961.”

Google Earth for the brain: A first hand witness and major player in the evolution of brain imaging, Dr. Karten says the most exciting period is the one we’re in right now. “Instead of trying to localize one axon at a time as you look at the actual slide, we can scan the whole slide with great accuracy, and generate a virtual Google Earth type of image of every single section of the brain,” he said.

Applications like Google Earth reveal new layers of images as you zoom in, Dr. Karten explained. The hidden layers feature higher levels of magnification, so the picture becomes more detailed the deeper you dig. “It’s like a giant pyramid,” he said. “The base of the pyramid has pictures that are so precise that you can see the chairs in your back yard. That is called pyramid viewing, and it’s the basis of much of the modern digital imaging that we now use in brain projects.”

Mapping the brain with Neurolucida: Dr. Karten uses Neurolucida to interpret these “Google Earth type images of the brain. He can now trace the entire outline of the brain in under a minute, a process that once took hours. “Neurolucida has the tools that allow us to trace the boundaries, to do all the things that involve mapping the information so that we can interpret it and make sense of it,” he said.

From his serial sections, he makes 3D models of the brain that he can “twist and rotate and turn back the layers the way you would turn back the quilt on a bed to see what’s underneath.”

“It’s multiple technologies all converging, and Neurolucida plays a big role in it—the technology to scan, to generate images, to look at the images, to extract the data,” he said.

One recent morning, Dr. Karten loaded BrainMaps.org on his computer. He clicked “Mus Musculus” and zoomed in on a section of the brain of the common house mouse. “This is astounding,” he exclaimed. “We might have been able to do this years ago, but collection of  one such picture would have taken days or weeks. We do that whole section in less than one minute, and at a resolution of better than 0.5 micrometers/pixel. You can take a picture with that much detail in less than one minute. This is the future of neuroanatomy.”

“In Focus” is a series that spotlights scientists who use MBF Bioscience products in their work. Thank you, Dr. Harvey Karten for participating.

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{image courtesy of UCSD Neurosciences Graduate Program}

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