What if? Microsoft Kinect and Confocal Microscopy

It is a well-known phenomenon that you come up with some of your best ideas when you are thinking late at night.  Such an occurrence happened to me, and I wanted to share with you some of my thoughts.  But first, I have to cover a little background.

Confocal Microscopy

Immunofluorescent Microscopy: adding visual effects to science!

Much of my undergraduate work involved immunofluorescence: a type of staining in which fluorescently-tagged antibodies are applied to a specimen, target your epitope of interest, and fluoresce when exposed to certain wavelengths of light.  In other words: they glow under the right conditions, showing you exactly the structures of the cell you want to see.  In effect, this means that when you look through the eyepieces of a fluorescent microscope, the cellular world explodes in a vivid landscape of vibrant hues before your eyes.

If you don’t believe me, check out the gif below.  With the help of some excellent people at the University of Iowa’s microscopy core, we were able to visualize the lizard neuromuscular junction using a confocal microscope so sensitive it can distinguish between fluorophores of extremely similar wavelengths: it could tell the difference between two hues of red, for example.  The result, in my opinion, both intellectually and aesthetically pleasing.


Now, the microscope I was using for these experiments moved the slide around much the way a traditional microscope does: the right hand controls movement on the x and y planes while the left hand focuses on the z plane.  This begins to feel quite intuitive after repeated use.

The microscope I used this afternoon though, has no such controls.  You can’t even see the slide.  You simply put the slide on a plate, put the plate in the machine, and close the lid.  The rest of the work – light exposure, positioning, everything – is done by software provided by the microscope’s manufacturer.  This means the centuries old stereotype of a scientist hunched over at his microscope is becoming obsolete.  Instead, in our technological age, a scientist is simply a person at a computer, flicking through tissues and cellular components with casual keystrokes and mouse clicks.


An important paradigm shift as a result of this change is that the people who will now be controlling how we view the microscopic world are computer scientists and software engineers.  This means that our microscopic world is beginning to be manipulated with the infinite possibility of the digital realm.  Already we have seen incredibly detailed computer simulations of the cell and proteins visualized in 3D on your smartphone.  What will the ever-improving world of computer science give to biology next?

I don’t know what industry leaders are planning, but if it were me, I’d want to make the microscopic world fun and accessible.  The mouse clicks and keystrokes I was using to control my collaborator’s microscope this afternoon represent an interface between me, the software, and consequentially the microscope.  This interface could be switched with more accessible, intuitive interfaces.  The next step would undoubtedly be a touch surface, probably first through a touch desktop machine and possibly simplifying to a tablet.  And normally I would say that would be cool enough – God knows I would start drooling at the idea of making in-depth images from actual slides through something so simple as a tablet.

But I walked past the Microsoft store the other day, and one of the workers was playing with a Kinect.  The gestures were so simple and intuitive, and I suddenly imagined viewing the microscopic world in such a way.  The Kinect, after all, is simply another interface.  It is within the realm of possibility – given current technology – that I could image cells at resolutions smaller than than a micrometer using only hand gestures.  Switch objectives with a wave, change emitted wavelengths by voice command, and take an image with the snap of the fingers: to me, this is far cooler than mouse clicks and key strokes.

On the Eloquence of Intelligence

This morning I had the privilege of listening to Dr. Darius Ebrahimi-Fakhari discuss some of his latest work regarding mitophagy in neurons.  He had oodles of cool videos depicting mitochondria trucking back and forth down the axon – similar to the gif below (pulled from Dr. Kittler’s lab at UCL).


The work itself was elegant, with an organized methodical approach utilizing the most novel techniques available.  However, what truly captured my attention was the fluency with which he spoke of his work.  Becoming a scientist is not hard: you just have to look at questions in a certain way.  Working within a specific field IS hard.  You have to become intimately familiar with the relevant signalling pathways, how they operate under different conditions, and of course, the nonsensical and often multiple names for different proteins within the pathway.

Not only that, but SO much emphasis is placed on knowing who published what in where and when.  It is not enough to say, “p62 knockdown causes mitochondria to accumulate within the soma of the neuron.”  Rather, as Darius did, you should say, “oh, Alessia in her 2009 paper showed that p62…” etc. etc.

Now, some of this comes with sheer time.  Once you’ve been working in the same environment talking about the same thing, concepts become ingrained.  But I’ve been a research technician in this lab for over two years and I’m only JUST beginning to be able to name some of the ancillary proteins of the mTOR pathway offhand.

Also, when you and I talk, we use a lot of “filler” sounds; “um,” “uh,” and “like,” to name a few.  These verbal spaces are reflective of our mental states: we’re still searching for the right words.  However, if you want to sound intelligent (and scientists especially do), you have to entirely remove those filler words.  Not only will this provide a more cogent speech pattern, but also give you confidence.  This in turn will make the listener more confident that you actually know what the heck you are talking about, which is the crux of scientific discourse.

This is not to say you should sound like a research paper when you’re talking, but rather that you can find the appropriate names for all of those wacky proteins at the tip of your tongue, and you know EXACTLY what they do and WHO discovered they do that.  Oh, and in what model and in what context would also be helpful.

I know, I know, this all sounds like a headache and a half.  However, if you can master this lexicon of the esoteric, you will sound like the smartest guy alive.