Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

• View a fully interactive version of the Allen Reference Atlas in 3-D.
• View gene expression data in 3-D at 200 µm 3 resolution.
• View expression data from multiple image series superimposed on each other in 3-D.
• Navigate the high-resolution 2-D ISH images using the 3-D model.
• Link to associated gene metadata on the Allen Mouse Brain Atlas web application.

...

Installation

Windows

Systems requirement: minimum configuration

...

The Brain Explorer application 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.

...

Viewing Gene Expression

To load gene expression data into the Brain Explorer viewer: go the Allen Mouse Brain Atlas and perform a gene search. You can type in a gene in the search box or click on a structure name to retrieve differential enriched genes. Your search brings back a list of experiments. Click on a row to select an experiment of interest. A 3D thumbnail of the expression pattern of that experiment will appear to the right. Click on the blue “3D” file link to launch the Brain Explorer application.

...

This section displays the gene probes you have selected and downloaded in this session. Right clicking on the gene probe name will bring up a menu where you can, 1) view the gene detail page (Get Info), 2) be taken to a zoomed-in image from this experiment (View Images), 3) copy meta information to the clipboard, such as symbol, name, Entrez ID, image-series ID (Copy Info), 4) activate a Correlation search, finding experiments with similar expression profiles (Find Similar) or 5) close the experiment and remove it from the list and the 3-D view (Close).

...

Gene Search

To search for genes within the Brain Explorer application: go to the Search box located above the ontology panel and type in the gene symbol or part of a gene name.

...

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.

...

Troubleshooting

Windows

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.

...