A bit of what I’ve been up to at MIT

I recently moved to Cambridge, MA to take the best job of all time helping Sebastian Seung’s Computational Neuroscience Lab at MIT build a game to map the human brain. Yea. It’s called EyeWire and you should check it out.

Best job in the world for several reasons. For someone obsessed with thinking about thinking, this life is positively dreamy. ¬†I think I live one solid series of awesome moments. I love the people in my lab. I got to move to Cambridge and live one mile from Harvard and one mile from MIT. I love walking to work. I love work! It doesn’t feel like a job. I love going to hackathons. I love hanging out with geniuses. I love MIT Media Lab. I love working with neuroscientists. I love learning new things. I love being around curious people ready to share their passion for creating game-changing technologies. I love going to intellectual events at MIT and Harvard. I love connecting with so many TEDxers on the east coast! I love snow (though we haven’t had much yet). I love great food and even greater company. I love talking about molecules and python and infographics and chilling with scientists every day. Bascially, I love life. I love life very much.

I’m aslo helping a group at the Media Lab (which I’m not really supposed to talk about), developing a new app for TEDx music (also not supposed to talk about..but no one reads this blog ūüėČ and building an anonymized open-source database of health and lifestyle data with WIkiLife. Other things too..but it’s late and I want to read Nietzsche.

Below is a post I just wrote for the EyeWire blog. I blog at MIT now. Rad. Life is amazing. I hope you, dear reader, are following you passion and pursuing diligently the ideas that strike you most curious.  Reality will exceed your wildest expectations if you let it.

Cheers, much love.

Amy

It may come as a surprise that although we know much about how the eye works, neuroscience researchers do not fully understand how visual signals translate into perception.

We‚Äôve landed on Mars, can¬†grow organs, and even skydive from space, yet when it comes to a thorough understanding of the territory so close to home that it is home, much is missing. Neuroscientists don‚Äôt even know precisely how many different types of cells are in the brain. Here at¬†Sebastian Seung‚Äės Computational Neuroscience Lab at MIT, we‚Äôre taking a different approach: crowd-sourcing. In order to solve the mind‚Äôs great mysteries, we need you.

Why don’t we know how the mind works? One reason is that your mind is massive. Researchers estimate that there are 100 billion neurons in your brain with about one million miles of connectivity. A million miles is equivalent to driving around Earth 40 times. You can infer that in order for such great length of neurons to fit into your three micron scale image by FSUpound brain these structures must be very tiny. A large neuron is about 100 microns in diameter while the contact area of a synapse is about 400 nm in length.

In order to see neurons and the tiny structures called dendrites through which they function, researchers utilize a new imaging technique. ‚ÄúFix whole brain tissue, slice off layers just a few microns thick, image each slice with an electron microscope, and trace the path of each neuron,‚ÄĚ explains¬†David Zhou, Masters Student at Carnegie Mellon, on Quora. These gamechanging techniques generate terabytes of data for even a cubic milimeter of brain tissue. Now that we can see the brain at the synaptic scale, we have to¬†analyze¬†the images. How?

neuron cell reconstruction Seung Lab

The image above shows the process of layering image slices to render 3D reconstructions. Like most neuroscience labs, the Seung Lab uses a combination of AI algorithms and tracing (3D reconstruction) performed by humans. Why not just use algorithms? Images can be challenging to identify, particularly for a computer. Pure algorithms make many mistakes, such as slicing a single cell into thousands of pieces and merging multiple cells into one monstrously massive neuron. See below image for an example of AI missing a chunk of a neuron.

correcting a computer's mistake, Seung Lab

We hope to one day train computers to map neurons on their own; however, that day will be far in the future and we need to accelerate neuroscience discovery now.¬†To achieve this, we need something more intelligent than even the most powerful supercomputer‚ÄĒ you.

It takes an MIT-trained neuroscientist anywhere from 15 to 80 hours to reconstruct a single neuron. At that rate, it would take about 570,000,000 years to map the connectivity of an enture human brain, known as aconnectome. This is why we need your help.

Rather than mapping and entire brain, we’re starting with a retina. Our goal is to map the connections of a specific type of cell: J-Cells. These neurons are responsible for perception of upward motion. We plan to publish the outcome in a scientific journal and list EyeWire users as co-authors.

By playing the 3D game Eyewire, you become part of the Seung Lab at MIT by helping to map the connections of a neural network.

Scientific American¬†writes that ‚Äúno specialized knowledge of neuroscience is required [to play EyeWire]; citizen scientists need only be curious, intelligent and observant. Your input will help scientists understand how the retina functions. It will also be used by engineers to improve the underlying computational technology, eventually making it powerful enough to detect ‚Äúmiswirings‚ÄĚ of the brain that are hypothesized to underlie disorders like autism and schizophrenia.‚ÄĚ

We hope that you will help us trace the wires of perception through EyeWire. Play EyeWire and let us know what you think on Facebook.

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See the World Differently with Beautiful Photomicrography

Before you read this, pause and look at your hand.  Imagine that you could see ten, one hundred, a thousand times higher resolution.  What would your hand look like?  What world the world look like?

Photomicrography, the science of imaging through microscopes, is a window into an exotic world.

To illustrate the beautiful new perspectives made possible by advanced imaging technology, I’ve compiled some exquisite images from Nikon Small World. ¬†Can you identify them? You’re doing well if you get even one correct. Answers are at the bottom of this post.

1.

cricket tongue

2.

tapeworm head

3.

compound shrimp eye

4.

red ink mixed with acid, heated

5.

feather of a dove

6.

"fruit fly eye"

7.

"marine diatom"

8.

"moth wing"

9.

"crystallized mix of resorcinal, methylene blue and sulphur"

10.

"fossilized shells"

11.

"soap bubbles"

12.

"wrinkled photoresist"

13.

"actin bundles" image

14.

"cup fern longitudinal section" image

15.

"water crystal" image

16.

"bird of paradise seed"

17.

"Butterfly egg on pink powderpuff bud"

18.

microchip

19.

sand magnified 4x

20.

"mushroom gills"

Answers:

1. Cricket tongue by Christian Gautier

2. Head of a tapeworm by Vigar Zaman

3. Shrimp eye by John Douglass

4. Red ink mixed with acid, heated by Carlos Jimenez Perez

5. Feather of a dove by Leonard Cannone

6. Fruit fly eye by Guichuan Huo

7. Marine diatom by Wim Van Egmond

8. Moth wing by Charles Krebs

9. Crystallized mix of resorcinal, methylene blue and sulphur by John Hart

10. Fossilized shells by Wim van Egmond

11. Soap bubbles by Viktor Syorka

12. Wrinkled photoresist by Pedro Barrios-Perez (what is a photoresist?)

13. Actin bundles by Dennis Breitsprecher

14. Cup fern, longitudinal rhizome section by Stephen Lowry

15. Water crystal by Raul Gonzalez

16. Bird of paradise (plant) seed by Viktor Syorka

17. Butterfly egg on pink powderpuff bud by David Millard

18. Microchip by Alfred Paseika

19. Sand by Yanping Wang

20. Mushroom gills by Charles Krebs

A few more awesome images that may surprise you:

Pollen grains by Shirley Owens

Lysine by Nikolai Vsevolodov

Small intestine of mouse by Paul Appleton

All images sourced from Nikon’s Small World.

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Quantified Curiosity

I’m speaking today at Quantified Self Conference 2012 about Quantified Curiosity. ¬†Below are my slides as well as some videos referenced in my talk. [UPDATE: presentation video now included]

Amy Robinson – QS Conference 2012 – Quantified Curiosity from Steven Dean on Vimeo.

Beautiful, scientific technological videos:






XVIVO Making the Complex Simple.

Want to play with the data?  Email me amyleerobinson at gmail dot com.

Gephi Graph of Ideas PDF.

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TEDx Music Project on Soundcloud

Few things make me excited to be working after 10 pm on Saturday. ¬†The TEDx Music Project is one of them. ¬†I’m thrilled to share the next phase and give a quick update on our progress since TEDxSummit.

TEDx Global Music is on Soundcloud!

The first phase includes 17 tracks.  Follow us to be among the first with access to the latest music from TEDx.

Our team is hard at work building the next generation of TEDxMusicProject.com.  It will go live in a few short weeks and feature TED API integration.  The new site will showcase both video and audio versions of the best live TEDx performances.

Listen to the tracks, download them and share with friends. Which track(s) do you like most?

Finally, a massive¬†thank you to everyone who has helped make this happen and supported the TEDx Global Music Project along the way. ¬†Major props to Souncloud for¬†featuring us alongside audio sources such as The Economist and David Guetta. ¬†We managed to gather well over 1,000 followers..in our first 24 hours public (June 22). ¬†It’s only going to get bigger.

Follow the TEDx Music Project on Soundcloud.

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Be Inspired on Quora

How do you discover the web?

I’ve become a big fan of Quora, a Socratic social network. ¬†In the words of its founder, Adam D’Angelo:

When you want to know more about something, Quora delivers you answers and content from people who share your interests and people who have first-hand knowledge — like real doctors, economists, screenwriters, police officers, and military veterans. On Quora, it’s easy to create a personalized homepage of everything you want to know about by following topics, questions, people and boards.

UCSD’s Neuroscience Department¬†shared Quora with me on Twitter about a year ago. ¬†Yes, that’s right. ¬†Neuroscience labs are on Twitter. ¬†Follow some. ¬†But back to Quora.

If you already use it, do so more frequently.  And connect with me.

If you don’t use Quora yet, it’s pretty simple. ¬†Like Twitter, you follow people and they can follow you back. ¬†Link with Facebook and your “likes” automatically become Topics you follow. ¬†This means that when someone adds a question to a topic you follow, it shows up in your feed. ¬†You can also follow questions. ¬†Play around with Quora.

Ask questions.

Add and explore answers.

Shuffle and discover random and hilarious questions, like

Create boards.

Today I built “Be Inspired” featuring ongoing questions like

(The crowd loves Euler’s equation)

Quora rocks.

Share links to your favorite Quora questions in the comments.  Add the most delightful questions to Be Inspired.

Amy

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inverse dictionary

I have a lot of ideas. ¬†So many, in fact, that I need more words than I know, more time than I have, and more tools than I understand how to use in order to bring them to fruition. ¬†Until Matrix-esque plug-in knowledge (a la “I know kung fu“) rolls around, ¬†I would love a tool that helps me find a word I wonder about by inputting the definition. ¬†Does something like this exist? ¬†I think it would inspire me just by being cool.

I read a great quote yesterday: “you can’t do much about the length of your life, but you can do something about its width and depth,” ¬†True. ¬†I hope all of you are living well and exploring the unknown and doodling and sharing ideas and writing to people who inspire you. ¬†That last one is the trick to loving your inbox. ¬†When people I respect send thoughtful correspondence it makes me smile at least 1/4″ wider.

I’ve been looking for a word that means “interesting, stimulating, challenging, exciting” for about 6 years now. ¬†I will give it one more year until I pull a Shakespeare and make up my own. ¬†Creativity, procrastination or patience hmm.

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