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Developing Mouse Reference Atlas

Reference Datasets

To provide a neuroanatomical framework for gene expression data, the Allen Developing Mouse Brain Reference Atlas was created with the expertise of Professor Luis Puelles, M.D., Ph.D. (University of Murcia, Spain). Sagittal full-color, high resolution web-based digital reference atlases have been created for seven stages of mouse brain development accompanied by a systematic developmental taxonomy of mouse brain structures.

The Allen Developing Mouse Brain Reference Atlases were designed to:

  1. Allow users to directly compare gene expression patterns to an annotated developmental atlas;
  2. Provide templates for the creation of 3-D computer models of the developing mouse brain;
  3. Serve as a neuroanatomical foundation for informatics-based analysis tools.

In 2013, the reference atlas was updated to provide a deeper level of annotation. For more information on the reference atlas update and a description of the ontological levels, please refer to the Reference Atlas whitepaper located under the Documentation tab. Access to the previous reference datasets are available via links on the Reference Atlas landing page.

To access the reference atlas, you can click on one of the links from the landing page or you can select the key icon from the High Resolution Image Viewer to view the atlas in context with a gene expression experiment.

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.

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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

Given there are two structure ontologies for the mouse brain in the Allen Brain Atlas resources, we have created a way to overlay the Structure Ontology from Adult Mouse Atlas and the Developing Mouse Brain Atlas.

While in the "Developing Mouse Atlas, P56", select "P56 Adult Mouse" atlas from the second drop-down menu and select "Outlines" from the Tools icon drop-down. This will show both Structure Ontologies overlayed together.

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Structure Ontology

The Structure Ontology for the Developing Mouse is listed hierarchically in the left-hand panel of the Interactive Atlas Viewer. By default the atlas is opened to level 3. Please see the Reference Atlas whitepaper available from the Documentation tab for more information on the Structure Ontology levels.

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.

Reference Atlas Viewing with Gene Expression Data

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.



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:



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:




Advance to the next image in the series


Go back to the previous image in the series


Advance to the last image in the series


Go back to the first image in the series


Zoom in


Zoom out

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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

Clicking on the ontology icon ( ) will open up the Developing Mouse Ontology defaulting at level 3.

The ontology levels in the Developing Mouse Atlas range from Level 00 (Neural Plate) up through higher differentiation levels to Level 13. Please see the Reference Atlas whitepaper available from the Documentation tab for a deeper explanation of the ontology levels. By clicking on the Ontology Levels (numbered squares above the ontology list) you will open the ontology to the level of detail indicated by the highlighted level.

Searching using the text box in the Ontology pane will allow you to browse through the ontology looking for specific regions. Using the "Sync" icon ( ), you can sync either image to its partner to view the gene expression in context with the reference atlas.

Given the difficulty of sectioning and programatically aligning these small specimen, you have the option of viewing a reference dataset with each gene expression specimen that will also outline a small structure of interest. To do this, choose the reference atlas from the Atlas dropdown menu (either Feulgen-HP or Nissl, depending upon the age) and select on the reference data set to outline your desired structure.

In the below image, gene expression is located in a region of the prethalamus.