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From the Reference Atlas landing page, you can also add reference data into your cart to enhance your exploration of gene expression data by clicking the checkboxes next to the desired reference dataset. Clicking "View Experiments" will allow you to view all selected datasets (including experimental data already present in the cart).
Viewing the Interactive Reference Atlas Viewer
Access to the Interactive Atlas Viewer is from the "Reference Atlas" button from the Data Portal, from the "Reference Atlas" tabs in the Adult Mouse, Developing Mouse, or the Developing Human Atlases or from the High Resolution Image Viewers. From the Reference Atlas tab in the Developing Mouse Brain Atlas, clicking on one of the links in the "Reference Atlas" box will launch the Interactive Atlas Viewer.
The Interactive Atlas Viewer is divided into the thumbnail strip along the bottom, the main image viewer and the Structure Ontology list.
Main Image Viewer
The image in the thumbnail strip outlined in blue is the image shown in the main image viewer. From the first drop-down menu in this viewer, you can access all seven of the Developing Mouse references atlases, the Adult Mouse coronal and sagittal atlases, as well as the Human Brain Atlas Guides. Reference datasets (Nissl or Feulgen-HP) are accessible from the second drop-down menu in the top right-hand corner. A settings menu is also available from the "Tools" icon.
Navigation of the images requires using the on-screen navigation tools or the Keyboard Commands. Hovering the mouse over the image will outline the current structure as well as load that structure name in the top left-hand corner of the main viewer. Clicking on a structure will color that structure purple and highlight it in the Structure Ontology.
Translation Between the Adult and Developing Mouse Ontologies
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Each of the Developing Mouse atlases was drawn to a specific level and only those levels that were drawn will be available to navigate by clicking on the name. Those that are not available will be greyed out. Clicking on a structure name will take you to that drawn structure in the main image viewer.
Using the High Resolution Image Viewer
The image viewer enables you to view a high resolution image in its own re-sizable window. It is possible to open multiple images by opening multiple windows.
Interacting with the High Resolution Image Viewer is similar to using the ZAP Viewer with some enhanced features accessible from icons in the top right hand of the main image viewer.
Icon | Description |
|---|---|
| View ISH, Expression Energy, or Reference Stain (Nissl or Feulgen-HP Yellow) |
| View experiment side by side with the Interactive Reference Atlas |
| Allows you to access setting options, including downloading the current image |
Zoom and Pan (ZAP) Image Viewer
The Zoom and Pan (ZAP) Image Viewer is a powerful tool to navigate and view the images in an experiment. The main part of the viewer is an interactive window where an image can be repositioned by dragging with a mouse. Use the scroll wheel, the onscreen navigation buttons or the keyboard to pan or zoom in or out.
Scale Bar
Drag the scale bar with your mouse to the desired location. Click the text with your mouse to toggle between horizontal and vertical.
Using the ZAP Viewer Toolbar
Use the toolbar to take actions on the image that currently has focus. Toolbar controls include:
Control | Function |
|---|---|
| Move the slider bar to the left to intensify the contrast or color |
| Select ISH, Nissl or Expression image type |
| Display all thumbnail images in a single 'contact sheet' |
| Open the selected image in the image viewer tool |
| Synchronize all other Zap viewers on the page that support synchronization to the currently selected image |
| Open a new browser window to review metadata for the image series |
| Close the Zap viewer |
Keyboard Commands
Use the keyboard to navigate through the image series. Keyboard commands include:
Key | Function |
|---|---|
F | Advance to the next image in the series |
D | Go back to the previous image in the series |
R | Advance to the last image in the series |
E | Go back to the first image in the series |
A | Zoom in |
Z | Zoom out |
+ | Zoom in. Please note that some keyboards may require the [Shift] key be held down while pressing the [+] key |
- | Zoom out |
You can also use the arrow keys to pan the current image.
Side-by-Side Reference Atlas Viewing
By clicking the key icon whilst in the High Resolution Image Viewer, you can view your experiment side-by-side with the Reference Atlases.
Ontology Levels
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