Behind the Science: About the Data

starburst, bipolar cell, eyewire, neurons, Nature, citizen science, neuroscience, brain, commectome, MIT, Seung Lab, Alex Norton, neurons, synapse
Starbursts and bipolar cells. Image: Alex Norton

Have you ever wondered where the EyeWire data comes from?

EyeWire’s data set consists of the retinal neurons of a mouse, and it is called E2198. E2198 was created by scanning a section of the mouse’s retina with a Scanning Electron Microscope (SEM).

A Scanning Electron Microscope is a machine that produces images using electrons instead of photons. It shoots electrons at the sample, and these electrons bounce off the sample and hit a sensor. This sensor counts the number of electrons that hit it, and where the electrons came from. In the slices of your cubes, the darkest spots mean the most electrons had bounced off those locations.

In order to get any data from biological samples, they need to be stained with heavy metals, or else the electrons won’t bounce off them correctly.

You may be thinking that it would be better to just take normal pictures, using photons, rather than electrons, but it is impossible to get data at these scales using photons. Photons are bigger than electrons. In fact they are much larger than the things we are trying to image. Trying to image with photons would produce a lower resolution image because each pixel would occupy more space.

high res low resThink of it in photography terms. Using photons is analogous to using a low resolution camera, while using electrons would be analogous to using a high resolution camera.

Imagine you take a picture of two people off in the distance. With a 5 MP camera, the people appear as a blurry single object. But with a 50 MP camera, you can see that there are two distinct people in the image.

Think now of neurons. We aren’t satisfied with simply seeing that something is there. We need to differentiate objects so we can see things like synapses. Using electrons in stead of photons, we are able to generate higher resolution images, just as a photographer generates a crisper image with a 50 MP camera.

Serial Block Face Electron Microscopy (SBFSEM) was specifically developed for imaging neurons. After the sample is stained with a heavy metal, it is inserted into the the SEM. The surface of the sample is imaged and then it is shaved off, exposing a layer of the surface underneath the layer that was just imaged. While this is a very effective process, it is also destructive to the sample; if a mistake is made, there is no second chance.

Want to know more about E2198? Check out some of it’s history!

Looking for a more technical explanation of Serial Block Face Scanning Electron Microscopy? Check out the this wiki page!

Keep an eye on the blog for the next installment of Behind the Science.

Leave a Reply

Your email address will not be published.