h1. Brain Explorer

Brain Explorer® 3-D Viewer is an 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, the Allen Mouse Brain Atlas and the Allen Developing Mouse Brain Atlas.

Using Brain Explorer, you can:

View a fully interactive version of the Allen Mouse Brain Atlas in 3D.
View overlapping expression data from different genes.
Investigate probes or samples of interest in more detail with direct links back to the Allen Mouse Brain Atlas.
Navigate the high-resolution 2D ISH images.

h3. Installation

h4. 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.

h4. 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.

h4. 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  Developing Mouse 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.

h4. 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.

h3. Brain Explorer{reg-tm}{reg-tm} 2 3-D Viewer

The Brain Explorer 2 software is a desktop application for viewing human  neuroanatomy and the       Allen Human Brain Atlas microarray gene  expression data in 3-D in the framework of the Magnetic       Resonance Images  of the sampled brains.

Once you have chosen a gene of interest (by clicking on the heat  map), you can explore a three-dimensional representation of its  gene expression by clicking on the "Brain Explorer" link over       the  heat map. When the Brain Explorer 3-D Viewer opens, you will be taken to a screen that  displays the [#Image Viewer], the [#Structure Ontology Viewer], and the  [#Gene List].


h4. Image Viewer

The Image Viewer will automatically show the 3-D expression  representations of your gene of interest on every       sampled brain.  Cortical gene expression is overlaid on an inflated white       matter  surface for each donor brain, with spots under the white surface  representing gene       expression in the subcortical regions of the  brain. A striped expression pattern on the cortical       surface is a  result of having sampled from every other slab of cortical tissue. Under  each       representative brain is the heat map for the probe you  selected. Clicking on that heat map will       pinpoint the area in the  brain from which the sample was taken.

The gene expression colors correspond to the settings in the Atlas  with which you were viewing       the original heat map. To change the  gene expression representation, click on the "Gene" tab in       the top  left hand corner of your screen and choose either Z-score or raw colors (as per App).

A compass in the right hand corner of the image viewer depicted by a  stylized head can be used       to rotate the brains by clicking and  dragging your cursor. You can look at a single brain by       clicking  on the magnifying glass above that brain. Choosing a data point, either  by clicking on       the heat map below the brain or on a brain region  itself, will bring up the gene symbol, the       location of the sample  and the expression level and z-score in the left hand corner of the  Image       Viewer.

You can zoom using either the wheel on your mouse or using the Zoom  scrollbar in the lower       right hand corner of the Image Viewer.

h4. Structure Ontology Viewer

The Structure Ontology Viewer shows the entire collapsible ontology  for the       human brain including the color coding used by our expert  annotation team to visualize structural       boundaries. Two columns to  the right of the ontology determine the type of data displayed in the        Image Viewer. "A" represents annotation and when checked, will show  a visual representation of       that structure in the Image Viewer.  "G" represents gene expression and when checked, will show       gene  expression in that structural domain.

The default organization for the Structure Ontology is the  Hierarchical View, but if you are       unfamiliar with the ontology,  you can click on the Alphabetical View to see the structure list in        alphabetical order.

The Bookmarks tab is a space where you can create and save favorite  views of the brain. Several       default views are already saved that  will rotate the brain back into common viewing frames.

h4. Gene List

This section displays the gene probes you have selected and  downloaded in this session. When       more than one gene probe has been  downloaded, clicking on one probe will show its gene       expression  profile in the image viewer. Right clicking on the gene probe name will  bring up a       menu where you can view the gene detail page (Get  Info), be taken to the Planar View of       the probe (View Images)  or copy the gene information for use in another application.

h4. Toolbar

|!brain_explorer_rotation.jpg|border=1,align=center!| Selects cursor rotation tool mode |
|!brain_explorer_pan.jpg|align=center,border=1!| Selects cursor pan tool mode |
|!brain_explorer_selection.jpg|align=center,border=1!| Selects cursor selection tool mode |
|!brain_explorer_sagittal.jpg|align=center,border=1!| Toggle Sagittal Atlas section viewing |
|!brain_explorer_coronal.jpg|align=center,border=1!| Toggle Coronal Atlas section viewing |
|!brain_explorer_horizontal.jpg|align=center,border=1!| Toggle Horizontal Atlas section viewing |
|!brain_explorer_center_viewer.jpg|align=center,border=1!| Centers the Viewer on the current pinpointed expression data point |
|!brain_explorer_cutting_planes.jpg|align=center,border=1!| Turns on the cutting planes |
|!brain_explorer_ontology_genes.jpg|align=center,border=1!| Toggles the Structure Ontology and Gene List View |

h4. Advanced Features

*Atlas Tab:*

You can show opaque three dimensional structures of the brain by  "showing" or "hiding"       structures from this menu. The "Transparent"  function allows you to see transparent views of       the structures to  view the anatomical relationships between them.

Selecting the sagittal, coronal or horizontal sections (or clicking  on one of the        section image buttons in the toolbar) will  superimpose a single plane of the MRI images from each brain on your  image       space. These planes can be moved once the selection tool  mode button in the toolbar is selected. Selecting       "Show Annotation  on Section" from this menu will color the MRI images according to the  brain       structure ontology.

*Gene Tab:*

When you have a gene selected, the Gene Tab menu allows to you to  show all expression, hide       all expression (for instance to then  select a single structure) or toggle expression (for instance,        unselect your region of interest then toggle to see expression in only  that region).

You can also show or remove threshold controls and choose the visual  representation of your       data (raw data vs. z-score) from this menu.

To be taken to the gene detail page, select "Get Info". To see the  Planar View, choose       "View Images". These functions are also  available by right-clicking on the gene name in the       Gene List.

*Clipping Planes:*

When this function is selected, either by toggling the        cutting  tools button in the toolbar or selecting       "Clipping Planes" from  the View drop down menu, you can make coronal, sagittal or horizontal        cuts in your view of the brain and related data. To cut in a  particular plane, make sure the cursor       is in selection tool mode,  and then click and drag on the plane you are interested in clipping.

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].