Author: Donald Doherty

Yesterdays post “Whole Brain Catalog: the Google Earth for the Brain” introduced the Whole Brain Catalog. Within the overall framework of a mouse brain hangs a lot of data. Today we’ll look at some of the data you may explore in the Whole Brain Catalog.

Note: Please read yesterday’s post if you haven’t installed the Whole Brain Catalog on your computer.

Let’s start by looking at brain cells (neurons). Data associated with cells of all types are listed under “Cells” in the Data Type area.

Go to the Data Type area to the left-bottom of the brain viewing area and click on the arrow to the left of “Cells.” This will open the list of cell types and groups of cells available to you. Find the “Mainen-Sejnowski Pyramidal” cell and check the box to the left of the label. Give Whole Brain Catalog a bit of time to download the data.

Tip: Keep an eye on the status bar at the bottom of the Whole Brain Catalog window. It’s busy if it says “Creating Objects.”

Once the data are loaded, double-click “Mainen-Sejnowski Pyramidal” in the Data Type area and Whole Brain Catalog will zoom through the brain and show you the pyramidal cell. The yellow wire box surrounds the neuron. To move around the cell click the “Rotate Camera” button. You’re now at a relatively small scale so when you zoom in and out be sure to press your mouse button down just once and hold (rather than twice and hold).

Would you like to place the brain back into the context of the whole mouse? Adding the skull helps me to do this. In the Data Type area expand “Mesh Models” and look for “Mouse Skull.” Check the box to the left and, after the data load, double click “Mouse Skull” to zoom out and view the skull.

Tip: You may also bring up a context menu. In Windows use your right mouse button and on Macintosh computers use the command button with your mouse click.

Now that we’re back at a high-level view of the mouse and its brain we’ll dive down to the very small molecular level and look at a protein molecule. The Whole Brain Catalog displays three dimensional molecular structure data from the Protein Data Bank.

Go to the Data Type area and click on the arrow to the right of “Mesh Models.” Use the scroll bar to the right of the Data Type area to scroll down until you see “Potassium channel.” Check the box to the left of “Potassium channel” and give Whole Brain Catalog a bit of time to download the data.

Double-click “Potassium channel” in the Data Type area and Whole Brain Catalog will zoom through the brain and show you the potassium channel. The yellow wire box surrounding the potassium channel is very small in this standard view. Select the “Zoom In” button and press your mouse button down and hold to get closer. We’re at such a small scale that this slower zoom seems fast. You may find yourself zooming past the molecule. Quick clicks using both “Zoom In” and “Zoom Out” should get you there. Be sure to admire the structure of this molecule by using the “Rotate Camera” button.

Other related blog posts:

Whole Brain Catalog: the Google Earth for the Brain

The Whole Brain Catalog is the Google Earth for the brain. Unlike the earth, however, there isn’t just one brain. There are any number of variations found across the brains of individuals and, of course, there are major differences between brains across species. For that reason alone, the “typical” mouse brain that the Whole Brain Catalog offers is just a start. It’s an impressive beginning.

There is a lot to explore in the Whole Brain Catalog so I’ll only attempt to introduce you to it here. Over the days to follow I’ll be highlighting different aspects of this important tool.

Running the Whole Brain Catalog requires Java, a good Internet connection, and a relatively powerful computer. Most recently purchased laptop and desktop computers should run it just fine. Check out the requirement specifics and download the application from the Whole Brain Catalog Download Page.

Note: Whole Brain Catalog is currently in what I’d call the alpha stage. Be prepared for some bumps.

When the three dimensional mouse brain appears I recommend clicking on the “Rotate Camera” button above the brain and towards left and then grabbing onto the brain and rotating it around. Do this by pointing to the brain, holding down your mouse button, and moving the mouse. This should help orient you.

Note: Do not click on the maximize window button and beware of resizing the window by dragging its corner. On my Macintosh running the latest version of OSX and Java this causes the computer to be completely inaccessible to me (including the Whole Brain Catalog). [Sometimes this happens and sometimes not. I haven’t been able to isolate the problem yet. Please post and let me know if you figure it out.]

While rotating the brain I found it helpful to zoom it out some (make it smaller). Click on the “Zoom Out” button above the brain and about in the middle. Then point to the brain, double click your mouse button and hold the button down on the second click. The brain will zoom out relatively fast as long as you hold the button. (Press once on your mouse button and hold to zoom slower. Use this when you’re working at a smaller scale like looking at single neurons.) Use the “Zoom In” button to the left of the “Zoom Out” button in the same way except that the brain will get larger.

Once you’re oriented to the brain, check out how fun it is to fly around and explore brain anatomy. By default only a subset of “Brain Regions” and “Mesh Model” data are loaded. You can see the available data and data that has been selected to view in the area titled “Data Type” to the left of the brain viewer and at bottom.

The default selections don’t come close to all of the data available even within these two high level categories. Keep in mind that the more data selected the longer it takes to download from the Internet. Also, with more data to handle, your computer may slow down significantly. Also take into account that the amount of data visible all at once on your screen may become overwhelming.

Leave the settings on default for now and move your pointer over the brain. Notice the label changing at the lower left in the brain viewing area? This label displays the name of the brain structure that your mouse pointer is flying over.

Click on the “Zoom In” button and double click and hold over the tangle of red (lateral geniculate body, optic tract) inside the brain. You can get close up and personal with brain structures.

Tomorrow I’ll write about some of the data associated with these structures that you can work with and view. Meanwhile have fun exploring the Whole Brain Catalog, which may become the hub for accessing the broad range of brain relevant data distributed in repositories across the Internet.