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h1. Introduction

Brain Explorer{reg-tm}2 is a desktop software application for viewing brain anatomy and gene expression data in 3D. It is integrated with three Allen Brain Atlas online resources: the [Allen Human Brain Atlas|http://human.brain-map.org], the [Allen Mouse Brain Atlas|http://mouse.brain-map.org] and the [Allen Developing Mouse Brain Atlas|http://developingmouse.brain-map.org].

Using Brain Explorer 2, you can:
* View a fully interactive version of the Allen Human Brain Atlas in 3D for multiple donors.
* View cortical gene expression data on partially-inflated white matter surfaces.
* View expression data from different donors side-by-side.
* Explore anatomically-labeled MRI images and cortical surfaces for all donors.
* Investigate probes or samples of interest in more detail with direct links back to the Allen Human Brain Atlas.

For the Allen Mouse Brain Atlas and Allen Developing Mouse Brain Atlas, you can:
* View spatially registered gene expression data in 3D.
* View a fully interactive version of the associated reference atlas.
* View ISH expression data from different mouse developmental ages side-by-side.
* View ISH expression data from multiple genes superimposed on each other in 3D.
* Navigate the high-resolution 2D ISH images.
* Link to associated gene metadata on the associated web application.

h1. Contents

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h1. Before You Begin


h2. System Requirements


h3. Windows Minimum Configuration

Operating System: Microsoft Windows XP
CPU: Intel Core Duo or AMD 1.8GHz
System Memory: 1GB
Graphics Card: Hardware 3D OpenGL accelerated AGP or PCI Express with 64MB RAM
Screen: 1024x768, 32-bit true color
Hard Disk: 200MB free space

Note: Brain Explorer is known to work with the following video chipsets: nVidia GeForce 9400/9600, nVidia Quadro FX 1800/3800/5600, AMD Radeon 9600, AMD Radeon HD 3200/4550, Intel Q35/Q45 Express
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Please install the latest drivers for your video card for best compatibility and performance.
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h3. Mac Minimum Configuration

Operating System: OS X 10.5
CPU: Intel 1.8GHz
System Memory: 1GB
Graphics Card: 3D-capable with 64MB RAM
Screen: 1024x768, 32-bit millions of colors
Hard Disk: 200MB free space
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Please install the latest system updates from Apple to ensure you have the latest video card drivers.
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h2. Installation


h3. Windows

For the best performance, please check with your video card vendor for the latest available drivers before using Brain Explorer. The Windows version of Brain Explorer is available [here|http://www.brain-map.org/BrainExplorer2/BrainExplorer2.msi]. Double-click the downloaded BrainExplorer2.msi file and follow the prompts.

h3. Mac

The Mac version of Brain Explorer is available [here|http://www.brain-map.org/BrainExplorer2/BrainExplorer2Mac.zip]. Double-click the downloaded zip file to unpack Brain Explorer.

h3. Installing Atlases

A one-time download containing anatomy files is needed following installation of the Brain Explorer application. The first time you open Brain Explorer, you will be asked to choose to download files for the Mouse Brain, Developing Mouse Brain and Human Brain atlases. Click on the atlases you would like to use and then click the Install button.

To download missing atlases on the PC, go to the Help menu and select Download Atlases. On the Mac, the command is in the Brain Explorer 2 menu.

h3. Getting Updates

Brain Explorer will inform you when updates to the Brain Explorer application itself or its atlases are available. New data may not be available for viewing until you install the required updates.

h1. Quick Start: Viewing Gene Expression


h2. Allen Human Brain Atlas

To load gene expression data into Brain Explorer: go to the Allen Human Brain Atlas and perform a [gene search|http://human.brain-map.org/search/basic]. You can click on a gene category in the tag cloud or type in a gene in the search box. Your search brings back a heat map showing gene expression profiles over different structures in the brain. Click on a cell in the heat map - this selects a sample in your probe of interest. Then click on the Brain Explorer link to be taken to Brain Explorer to see the gene expression for the probe in 3D with the sample automatically highlighted.
!AHBA_BrainExplorerButton.png|align=center!
See also on the [Brain Explorer section|http://help.brain-map.org/display/humanbrain/Brain+Explorer] on the Allen Human Brain Atlas help page.

h2. Allen Developing Mouse Brain Atlas

To load gene expression data into Brain Explorer: go the Allen Developing Mouse Brain Atlas and perform a [gene search|http://developingmouse.brain-map.org/]. You can type in a gene in the search box or select a gene category. Your search brings back a list of genes. Click on the + button to expand all image series associated with a gene. Select a 3D File link to launch Brain Explorer to see the gene expression for that image series in 3D. 3D File links can also be found on each gene and image series details page.
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h1. 3D Controls and Viewing Brain Anatomy

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The main Brain Explorer window is shown to the right. It is divided into 3 main areas. The 3D view shows brain anatomy and gene expression in 3D. The structural ontology panel is the dominant feature on the right hand side of the window and shows the color-coded hierarchy. The ontology can be switched between hierarchical and alphabetical mode by clicking on the corresponding buttons below the list. The Bookmark button displays saved default and custom views. At the bottom right hand side of the window is the list of genes shown in the 3D view (empty in this screenshot).
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h2. Viewing 3D Structures

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Each 3D view is based upon one underlying 3D volume; depending on the data resource, the volume maybe a magnetic resonance (MR) image or a 3D reconstruction of down-sampled serial sections, such as Nissl stained histology.

When multiple 3D views are present you can zoom into one 3D view by clicking on the magnifying glass icon near the view label. To close a 3D view click on the adjacent close icon. To restore all views, choose Show All Views from the View menu.

To view brain structures in a 3D view:
- Go to the Atlas menu and select Show Outer Structures.

Look at the checkboxes in the ontology list. You will see there are checks in the "A" column (short for Atlas) for the structures that are now visible. Structures can be turned on and off as desired using these checkboxes. The Transparent option from the Atlas menu is useful when viewing expression data.

You can rotate and pan the view to see structures which are hidden behind other structures in the view. Click and drag the ball in the upper right corner of the window to rotate the brain. If you get lost, go to the View menu and select Reset to return to a default view of the brain.

If the cursor is moving when you release the mouse button, the view will continue rotating until you click again. The rotation speed is based on the speed of the cursor. You can turn this automatic animation feature off from the Options item in the View menu.
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To center the rotation around a particular structure:

!BE_Rotation_Pan_SelectionTool.png|align=right!
- Choose the Panning tool in the toolbar
- Click near the bottom of the 3D view and drag towards the top of the window until the structure is centered.
- Move the zoom slider (located at the bottom of the window) to the right to enlarge the 3D objects in view. If you have a scroll wheel on your mouse, rotating the wheel will also zoom the view.
- Keep zooming and panning until the structure approximately centered.
- Move the cursor to the ball in the upper right corner, and click and drag the mouse to rotate about the structure.

Selecting a structure in the ontology will highlight the corresponding 3D structure in bright green. Selecting the structure in the 3D view will also highlight the corresponding structure in the ontology.
- Choose the Selection tool in the toolbar.
- Click on various structures in the 3D view and note how the ontology list selection changes.
- Click on blank space to deselect the selected structure.

h3. Shortcuts

!BE_MouseButtonMapping.png|align=right!

At this point, you have learned how to rotate, pan, and select. Since moving between these actions quickly is very common, the tools have been mapped to the buttons on a multi-button mouse. When the Rotation tool is selected, the view tools correspond to the mouse buttons as shown to the right. The left mouse button will rotate the view, the middle button (or clickable scroll wheel) will pan the view, and the right mouse button will select objects in the view. When the Selection tool is clicked, the function of the left and right mouse buttons is swapped.

Sometimes, you may want fine control over rotation and panning. The view can be nudged a small amount by using the following shortcut keys.
- The arrow keys rotate the view
- Ctrl + arrow keys pan the view in Windows
- Command + arrow keys pan the view in Mac OS X

h2. Viewing 2D Sections

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In addition to the 3D polygonal structures, you can also turn on planar views of the underlying 3D volume and associated annotations.
- From the View menu, choose Reset.
- Click on the Sagittal Sections icon in the toolbar. Sometimes the volume can be quite large, so your computer may pause while it is loading. When loading is complete, click the coronal and horizontal section toolbar icons.

In the screen shot you are looking at three planar views of the volume with annotations superimposed on top of it.
You can locate the planar views in any section of the brain you choose:
- Rotate the view so that the axes are diagonal.
- Click on one of the planar views.
- With the left mouse button held down, drag the cursor to move that planar view along its axis. Note that the images changes to reflect the section at the current location.
- Click and release the mouse on any annotated part of a section to identify the structure underneath the cursor. Note that you must not drag the mouse while the mouse button is down or you will end up dragging the section instead of selecting a structure.
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h3. Shortcuts

The following keyboard controls can be used for fine control over section selection.
| F1 | Show/hide sagittal section |
| F2 | Show/hide coronal section |
| F3 | Show/hide horizontal section |

h2. Clipping Planes

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Although you have fine control over the visibility of structures using the controls in the ontology list, sometimes you may want finer control over parts of structures we have not subdivided. Or perhaps you would like to look inside one or more structures. Using the clipping planes tool, you can specify a volume of interest to view.
- From the View menu, select Reset. Also, hide the planar views if desired.
- From the Atlas menu, select Show Outer Structures.
- From the toolbar, select the Clipping Planes icon.

As with the planar views, it's easiest to control the clipping planes if the view is rotated off axis. Place the cursor on each face of the cube outlined in green and drag the faces to cut away parts of the brain.
- You may also deselect View Clipping planes or press Ctrl+L to toggle off the clipping plane controls and display only the cut brain view.

Note: The performance of this feature is highly dependent on your video hardware. It may not work well on certain chipsets. If performance is slow, reset the view to disable all clipping. Then try to move as few planes as possible from their starting positions. Also, try to remove as many objects as possible from view. Show only essential structures and genes of interest.
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h1. Bookmarks

Certain aspects of the 3D view can be saved as bookmarks so that you can go back to the same view later.

h2. Basics

!BE_BookmarkPanel.png|align=right!
First, reset the view and switch to the bookmarks view.
- From the View menu, choose Reset. Close each item in your gene list. From the Atlas menu, make sure Transparent is off and choose Hide All Structures.
- Click the Bookmarks tab in the main window.

Some standard anatomic views are provided in the initial set of default bookmarks. Bookmarks can be organized in groups.
- From the Atlas menu, choose Show Outer Structures.
- Click on Coronal - Caudal to Rostral bookmark under Views. The view should rotate to the caudal to rostral orientation.
- While holding down the Control (Option on Mac) key, click on Coronal - Rostral to Caudal. The view switches right away instead of animating when the Control (Option on Mac) key is held down.
- The animation speed can be adjusted in the Options command in the View menu (Preferences in the Brain Explorer 2 menu on Mac). You can also highlight bookmarks using the keyboard and navigate to them by pressing the Enter key.
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{column:width=70%}Now let's define a new bookmark.
- Rotate the view to about 45 degrees off the sagittal left to right view and zoom in a bit.
- Deselect all bookmarks by clicking on an empty area in the bookmarks list. Make sure no items are highlighted in the bookmarks list.
- From the Bookmarks menu, choose New Group. Type in a name and press the Enter key.
- Choose New Bookmark from the Bookmarks menu.

The first 2 checkboxes correspond to the A and G columns in the Alphabetical and Hierarchical atlas ontology views. If you bookmark Atlas Structures, then the state of all checkboxes in the A column are saved. For instance, if you have the checkbox in the A column next to Cerebral cortex (CTX) checked and create a bookmark with Atlas Structure enabled, then returning to this bookmark will show the cortex and hide all other structures.
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The View Angle option corresponds to the rotation of the 3D view. The View Zoom corresponds to the position of the Zoom slider beneath the 3D view.
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Atlas Sections records the visibility and position of the coronal, horizontal, and sagittal sections. Clipping Planes records the position of the clipping planes.
- Type in a name and click Save. You can edit the bookmark name or delete the bookmark by right-clicking on it and selecting the appropriate menu item.
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h2. Snapback

When you go to a bookmark, your view is automatically saved as a temporary bookmark. You can go back to the previous view by choosing Go Back from the Bookmarks menu. You can set the temporary bookmark manually by choosing Mark for Snapback from the Bookmarks menu.
- Rotate the view and adjust the zoom.
- Click on the bookmark you created above.
- Choose Go Back from the Bookmarks menu.

Keep in mind the snapback bookmark can restore your previous view if you accidentally click on a bookmark.


h1. Gene Expression Viewing and Controls


h2. Allen Human Brain Atlas

Each sample from the Whole Brain Microarray Survey has been mapped to the 3D context of the donor's MR image. These mapped positions allow the gene expression to be represented in 3D space.

To obtain gene expression data for display in Brain Explorer 2: go to the [Allen Human Brain Atlas website|http://human.brain-map.org] and perform a gene search. Search returns are shown as a heat map where each row represents a probe and each column a sample or structure. The colors in the heat map represent relative gene expression over different samples/structures in the brain. Selecting a cell on the heat map identifies both a sample of interest and a probe of interest. Clicking on the Brain Explorer link, will launch Brain Explorer and open the probe of interest for visualization. The selected sample of interest will also be highlighted.
!BE_HBA_Example_1.png|align=center!
!BE_HBA_Example_2.jpg|align=center!
Samples from the cerebral cortex are overlaid on an inflated white matter surfaces for each donor's brain, while samples in the subcortical regions of the brain are represented as spheres below the inflated surfaces.
- Click on a patch on the inflated surface or a sphere. Samples can be deselected by clicking on blank space.

The information at the upper left corner of the Brain Explorer window provides details about the sample including gene symbol, structure name, z-score, and log2 expression level for the currently selected probe.

Samples (either on the inflated surface or as spheres) are color coded by its expression value either as z-score or log2 intensity. The default color map and threshold range matches the user setting in the Allen Human Brain Atlas. To change the colormap, go to the Gene menu and select either the Raw Colors (log2 intensity) or Z-score Colors submenu. The threshold range can be manipulated by first making the threshold control visible (select Threshold Controls under the Gene menu).

Within a session, Brain Explorer keeps track of the probes you have downloaded in the gene list in the lower right hand corner of the window. If you have multiple probes loaded, you can switch between them by clicking on the probe name in the list.

Right clicking on the probe name will bring up a menu where you can view the probe detail page (Get Info), go to a multiplanar view of the probe (View Images), or copy the probe information for use in another application.

h2. Allen Developing Mouse Brain Atlas

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The 3D data shown in Brain Explorer 2 is generated from the same process employed in the search algorithms on the Allen Developing Mouse Brain Atlas website; see [Informatics Data Processing|http://developingmouse.brain-map.org/docs/InformaticsDataProcessing.pdf] whitepaper for more information.

There are two main ways to obtain gene expression data for display in Brain Explorer. At the [Developing Mouse Brain Atlas website|http://developingmouse.brain-map.org], perform a search and click on the "3D File" link in search results list.

The second way to search for genes is from Brain Explorer.
- Go to the Search box at the upper right hand corner of the Brain Explorer window.
- Type Rspo1 and click the Search button.

The list of results shows the age, gene name, gene symbol along with a 3D summary thumbnail of the expression for each experiment matching the search. The expression thumbnail represents a maximum expression projection rendering: the denser the expression in a region the more "solid" the appearance. Reference atlas colors are additionally layered on top. From the thumbnail shown here, we can see that at E13.5, the gene Rspo1 has dense expression in the Pallium (color coded red).

To load an experiment for viewing click on the "Download" button under the gene name.
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h3. View Controls

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By default, 7 reference time points will appear in the view. To focus on E13.5, click on the magnifying glass icon near the "E13.5" label.
The figure to the right shows the gene Rspo1 at E13.5. The spheres represent expression resampled to a 100μm grid resolution. Larger spheres correspond to a greater density of expression (in terms of pixels).
- Click on a sphere. Spheres can be deselected by clicking on blank space.

The original ISH image for the selected grid is displayed blended with the expression heat mask shown in the lower left hand portion of the screen. The blending can be adjusted by selecting Image Controls from the View menu and moving the Image Blending slider. The zoomed ISH image is shown with tick marks at 100μm intervals. Double-clicking on the zoomed ISH image will open the corresponding ISH image in a high resolution image viewer.

The information at the upper left corner of the main Brain Explorer window summarizes the expression detected in the selected grid location. These numbers include the average expression density and intensity (over pixels). The [Informatics White Paper|http://developingmouse.brain-map.org] describes how the measurements were obtained. In the Atlas menu, you can select Show Enclosing Structure to quickly see the anatomy surrounding the selection.

By default, each gene loaded is represented in a different color. This mode is useful for viewing multiple genes at the same time for comparison. Other modes can be accessed from the Colors submenu in the Gene menu. Atlas color mode correspond to search result thumbnail display. This mode is useful for quickly seeing the annotated regions where a gene is expressing. Expression Level mode display average expression intensity corresponding to the scale shown to the right. Expression level mode is good for identifying areas of very high expression or looking at a densely expressing gene that is not expressing at a uniform level everywhere in the brain.

_Note: Only one half of the brain is annotated. For sagittal data sets, most of the grid locations should have an annotation. For coronal data sets, half of the brain will not be annotated. There is a special "No Annotation" label at the bottom of the ontology list. You can toggle the "G" column checkbox for this label to show or hide grid locations that are not annotated._
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h3. Expression Thresholds

Another way to control expression visibility is by setting thresholds on expression values. This method can restrict visible spheres to different combinations such as low intensity and low density or high intensity and low density.

The graph in the lower right hand corner shows a dot for each data point (sphere) in a gene expression file, and the color of the dot corresponds to the anatomic annotation in the same way the atlas colors display mode works. Each data point is plotted according to its density on the x axis and its intensity on the y axis.

The color scale on the left hand side of the graph corresponds to the expression level heat map used to color the spheres. The numbers along each axis show the values at the yellow triangles.

The thresholds can be changed by resizing the white box. Any edge or corner of the box can be clicked and dragged to resize it. You can also click and drag in the center of the box to move the box.

In the figure above, the thresholds were adjusted to show grid location with high intensity values.


h1. Advanced Controls


h2. Preferences

Customization options are available from the Options command in the View menu. These options are:
| Automatic update checks | If enabled, informs you when new versions of Brain Explorer and its associated atlases are released. |
| Automatic rotation | Enables or disables automatic rotation animation when releasing the mouse button while dragging. |
| Bookmark animation speed | Controls the length of time spent on animating to bookmarked views. Move the slider all the way to the right (Instant) to disable the animation. |
| Draw faster but at lower quality | Brain Explorer will use simpler 3D representations with this option on. This option can significantly increase the frame rate for some video cards. |
| Synchronize drawing with monitor vertical refresh | Turning this option off can increase the frame rate at the expense of some graphical "tearing". An example of tearing would be seeing parts of the screen drawn with the brain at different rotation angles. Turning this option on can minimize tearing at the expense of frame rate. |
| Multisampling | This option reduces polygon "jaggies" but at the expense of frame rate. Turn this option on only if you are comfortable with your present frame rate. |

h1. Shortcuts Summary

| F1 | Show/hide sagittal section |
| F2 | Show/hide coronal section |
| F3 | Show/hide horizontal section |
| Arrow keys | Rotate view |
| Ctrl (or command on Mac) + arrow keys | Pan view |
| Ctrl (or command on Mac) + select object | Center the view on the object |

h1. Troubleshooting


h2. Windows


h3. Graphics

If you are using a desktop computer, you should obtain drivers from the video card manufacturer. First, identify the video card. Go the Start menu and open the Control Panel. Open the Display control panel and go to the Settings tab. Click the Advanced button and go to the Adapter tab. Your video card vendor and model name will be displayed at the top of the window under Adapter Type. Please go to the manufacturer's web site, locate the driver download, and follow the instructions on the website or included with the downloaded file.

If you are using a laptop computer, you will need to go to your laptop manufacturer's web site to locate the latest video drivers.

You can also activate an alternate drawing mode in Brain Explorer. Go to the View menu and select Options. Check the Draw faster but at lower quality button and uncheck the Synchronize drawing with the monitor's vertical refresh button. Set the Multisample setting to Off.

If you are using multiple video cards from different vendors, the 3D display may not work correctly on all attached monitors.

h3. Uninstalling

Use the Add/Remove Programs control panel or the uninstall link in the Brain Explorer folder in the Start menu. Additional data that are not automatically uninstalled are located at the following locations:

Windows XP

Atlas data: C:\Documents and Settings\userid\Local Settings\Application Data\Allen Institute\Brain Explorer 2
User settings: C:\Documents and Settings\userid\Application Data\Allen Institute\Brain Explorer 2

Windows Vista and Windows 7

Atlas data: C:\Users\userid\AppData\Local\Allen Institute\Brain Explorer 2
User settings: C:\Users\userid\AppData\Roaming\Allen Institute\Brain Explorer 2

h3. Proxy Settings

If you use a proxy server, Brain Explorer will use the proxy settings from the Internet Options control panel in the Windows Start menu. Please refer to the Windows documentation for help on proxy settings.

h2. Mac


h3. Uninstalling

Drag the Brain Explorer 2 icon to the trash. Brain Explorer generates the following files, which can also be dragged to the trash.
* \~/Library/Application Support/Brain Explorer 2
* \~/Library/Preferences/org.alleninstitute.BrainExplorer2.plist

h3. Performance

If Brain Explorer is not running smoothly, first try to free up as much memory as possible by quitting all other open applications. You can also activate an alternate drawing mode. Go to the Brain Explorer 2 menu and select Preferences. Check the Draw faster but at lower quality button and uncheck the Synchronize drawing with the monitor's vertical refresh button. Set Multisampling to Off.

h1. Contact Us

If after working through this tutorial you still have questions or suggestions, please [Contact Us|http://www.alleninstitute.org/contact_us/index.html].