A Science Driven Life

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Archive for the ‘Andor Technology’ Category

Dendrite Pruning and Optical Methods in Neuroscience

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Screen Shot 2014-04-03 at 11.07.57 AMAs always this is meant to be a brief overview of a paper (and the methods used in neuroscience) I happened to have found interesting- for more details please refer to the manuscript itself.

I enjoyed reading a relatively recent paper published in Science from group in Japan (Kazuo Emoto, The University of Tokyo)  that suggests a role for Ca2+ signaling in dendritic pruning, a house-cleaning function in neurons that has been shown to be very important in learning and memory, as well as experience and some forms of cognitive deficits (such as autism and neurodegeneration).

Dendrites are highly branched areas of the cell that act as antennae receive information from neighboring cell.  Pruning refers to a highly complex, regulated, activity dependent process in which connections that are non-essential to the formation of the developing brain are cleaved.

In pruning, our neurons clean house.  Unnecessary connections formed during development are trashed as a way to reduce clutter and improve accuracy and efficiency of signaling.  Many of the basic mechanisms behind how pruning works have been identified.  Specific cascades of enzymes (caspases) as well as a key self-destruction pathway (proteosome-ubiquitin) work together to rid individual neurons of unnecessary connections.  While a lot is known about the processes that regulate the pruning, very little is known about the signaling that tells which dendritic arbors (branches of dendrites) are to be pruned and which of those is to be kept as a part of the neural network.

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Written by Michael Mohammadi

April 15, 2014 at 15:37

Targeting Light: Two recent papers that use active illumination!

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Screen Shot 2014-03-20 at 5.02.10 PMIn my day job I get to travel quite a bit and visit labs around the world who use methods in microscopy in imaging.  These labs range from neuroscience to developmental biology and everything in between, and many of these labs have very specific needs when it comes to light delivery.  The applications I most often work with can involve from high power lasers for ablation and thrombosis, or FRAP or photoconversion.  I’m very focused on optogenetics and uncaging, as well as any type of imaging, especially the use of genetically encoded indicators (for voltage, ions, temperature, pH, etc).  

While many people tend to use a simple configuration for single spot/point illumination, or full field illumination (and we provide these tools as well) where we are unique is in systems that allow for “targeted” or “active illumination.”  There are many methods for targeting light (possibly a good topic for an upcoming review) but the two of the main methods used are either using a galvo-mirror system (very fast mirrors that move a single spot of light in X-Y to create regions with the ability to target to a diffraction limited spot) or a digital micromirror device, or DMD.  

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Written by Michael Mohammadi

March 20, 2014 at 16:04

Astronomy: a not-too-technical look at CCDs, imaging applications, and why you need to spend summer nights outdoors!

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by Michael Mohammadi

I am a neuroscientist by training but in another lifetime I would have been an astronomer or theoretical physicist (as I suspect I would still not be talented enough for FIFA or the NHL).  Awe-inspring images, advanced mathematics, talking about quantum mechanics and actually understanding it (though as Feynman said “anyone who says they understand quantum mechanics, doesn’t understand quantum mechanics”), astronauts, and a life dedicated to the study of the cosmos and our cosmic origins would be an exciting way to spend a lifetime.

In my research and work in the life sciences I am fortunate to use advanced imaging techniques which translate to many areas of astronomy.  Rather than examining photons of light originating far away in the universe, we life scientists use the same high sensitivity/speed cameras to watch cells divide and die, monitor intracellular events and even track the movement of single particles.  These applications require photodetectors (cameras) that are very quantum efficient (QE) and can register very few photons (light) all the while differentiating the signal from the noise (measured as signal to noise ratio, or SNR).  Noise comes from thermal fluctuations in the camera, read out, and the environment and having a high SNR is essential for almost all imaging techniques.

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The most popular photodectors are based on charged-couple devices, or CCDs, though there is increasingly a shift (pun intended) to use of CMOS which I’ll discuss in an upcoming article).  CCD technology has been around since it was developed by  Willard Boyle and George E. Smith at the Bell Labs in 1969 (for which they won a Nobel Prize in 2009).


The sensor in  CCDs cameras consist of a number of light-sensitive pixels in an array of rows and columns (X and Y).  As photons hit a particular pixel they are converted to electrons via a phenomenon called the photoelectric effect(the basis of CCD imaging).  The build up of these electrons in the pixel (or the “well”, which can be thought of as a cup that is filling with water) becomes a stored charge (think capacitor) whic is what will be read out as a signal.  Just as a cup of water, the pixel has a specific volume of charge it can hold (“well depth”).  Once it becomes saturated, that pixel does not provide us with much real information (think of over-exposing with your DSLR) and can overfill into neighboring pixels (“blooming”) so knowing the right amount of time to expose a pixel to light is key.  The duration at which the pixel will build up electrons before it reads out a signal depends on the exposure time which the user can set (shutter time).  Once the exposure is completed, the charges are read out row by row (transferred pixel to pixel) and the signal is converted into numbers which can be then interpreted by a computer.  A more detailed analysis of how a CCD works can be found here.

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Spiral star Cluster from SuperWASP project.
Courtesy of Dr Don Pollaco, Queen’s University of Belfast, UK

On example of CCD cameras hard at work is the Andor iKon camera which is used every night in two giant robotic observatories which are searching for new planets (Super Wide Angle Search for Planets (SuperWASP).  Cameras such as the iKon are cooled to very low temperatures (-100C) to reduce the amount of noise during a long exposure.  Further, the sensor can be read-out very fast 5 MHz) to allow for fast focusing and fast processing.  At SuperWASP, the observatory consists of an array of 8 lenses (200 mm, f 1.8, Canon) each paired with an iKon CCD.  This detector is ideal because of its huge sensor (2,000 x 2,000 pixels, or around 4 megapixels, which may be less than your DSLR but here is why “megapixels” are overrated for most science) and slow scan speed and is perfect for monitoring the sky for new planets.  With hundreds of billions of stars in our galaxy and trillions of planets (with hundreds of billions of galaxies) there is great potential to identify new planets such as our Earth that may host some type of life forms.  To date the SuperWASP observatories have identified over 70 planets and with over 100 gigabytes of new data every night I think it’s safe to say they will continue to discover many more.

The study of nebula (nebula-onomy?) is definitely my favorite use of our CCDs.  Nebulae are cosmic dust clouds filled with ionized gases (mostly hydrogen).  At their center are massive stars that give off UV energy (light in the 10-400 nm wavelength) that interact with the dust and gases to form beautiful stellar bodies.  They are thought to be areas where new stars or galaxies are forming through a process that involves the collapsing of giant clouds of gas and cosmic dust.  A quick google image search of “Nebulae” will produce some of the most breath-taking, mesmerizing images in the history of photography, of which the scale, interpretation, implications and simplicity of it all can bring you to tears.

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The Little Dumbbell Nebula, also known as Messier 76, NGC 650/651, the Barbell Nebula, or the Cork Nebula, is a planetary nebula in the constellation Perseus. This image was acquired using an iKon-L 4 MP CCD on the 1 meter telescope at Observatoire du Midi in France.
Courtesy of Francois Colas, IMCCE

As with the search for planets at SuperWASP, we image Nebualae with CCD cameras such as the Andor iKon (or a specialized type of camera called EMCCD).  Adding one of these very sensitive CCD-based detectors to an optical telescope gives astronomers the ability to capture and analyze very distant light deep into the cosmos.  For those looking for an advanced discussion of camera technologies for astronomy I point you to a webinar by Andor Technology applications specialist Colin Duncun.

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Orion Nebula from the Hubble Space Telescope in 2006. This is a file from the Wikimedia Commons.

The closest nebula to our Earth (around 1,345 light years away) is “M42”, or the Orion Nebula (seen here).  You may have seen the Orion constellation on a clear night, easily identifiable by the three stars that make up “The Hunter’s” belt.  Imaging this massive (20 light years in diameter) nebula has been pivotal in improving our understanding of how our universe develops.  Interestingly, it has been proposed that at the center of this massive nebula is a black hole.  It is hard to sum up in words how awesome these images are, a sentiment felt by others I’ve seen try.

There really is something special about looking deep into the cosmos.  It is important to understand where we came from, but it is equally as important to know how astronomers and physicists use a variety of tools to learn more about our humble beginnings.  This is true with all science disciplines and all scientists.  We must take responsibility to educate the public as to what our methods are, how they work, why they work and what are their limitations.  With this transparency we will develop a better trust with the public and hopefully they will give back a willingness to learn, teach their children and support funding for science that in the end, benefits us all.

With the warm months of spring and summer approaching (for those of us in the northern hemisphere) I urge you to head out into the country, take binoculars, or a digital SLR camera (DSLR) and a tripod and find an area with few trees covering the shimmering sky.  Spend a few hours finding constellations, nebulae, and try some time-lapse photography (a hobby of mine).  Be a kid again, and if you can take your child, grandchild, niece, or nephew with you even better.  Don’t be afraid to sit with wonder and amazement at how simple and beautiful the universe is and consider how we go about learning about our cosmic origins.