Versions Compared


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

Projection Dataset


This dataset allows you to browse an image database of axonal projections labeled by viral (rAAV) tracers and visualized using serial two-photon tomography. To search this dataset, browse and select from a list of primary injections sites. Selecting an injection site will return a list of experiments.

This list outlines the experiment ID, Structure Name, Mouse Strain, Sex, and Age. Clicking on an experiment ID will launch a contact sheet viewer. Clicking on the checkbox next to the experiment will allow you to select one or more experiments to view in more detail by clicking "View Selections". Experiments will continue to be selected until you click the "Clear Selections" button.

Experiment Image Viewer

The Experiment Images view displays images for each selected experiment in a Zoom and Pan viewer. This view makes it easy to compare experiments with each other and with the Reference Atlas.

Multiple image series can be opened on the same page to enable side-by-side comparisons. Arrange the experiments by dragging a viewer by the title bar and dropping in a new location. Add a reference atlas by selecting one in the "Atlases" drop-down menu in the upper-right hand corner of the window.

If you are viewing more than one experiment, open the configuration options to change the number of columns displayed in the window. The configuration options are accessible by clicking on the button with a "gear" icon to the right of the "Atlases" menu.

The gene symbol is displayed in the title bar along with the Allen Institute image series ID. Additional details are displayed across the top of the viewing area, including the image index, tissue index, and tissue location.

Thumbnails for the entire image series are displayed across the bottom of the viewer in section order. Click a thumbnail to select it for viewing, or use the keyboard to navigate through the set. The current selection is outlined in black.

Contact Sheet Viewer

The contact sheet viewer shows serial sections of the selected experiment. Background fluorescence in the red channel illustrates basic anatomy and structures of the brain, and the injection site and projections are shown in the green channel.

Double-clicking on individual images on the contact sheet will launch a High Resolution Image Viewer.

High Resolution Image Viewer

Thumbnail images at the bottom of the high resolution image viewer can be selected to display individual sections in the main viewer. The viral tracer is visualized in the green channel, while background auto-fluorescence, seen in the red channel, is useful to provide anatomical context. No information was collected in the blue channel.

Within the Image Viewer, the contrast and brightness can be adjusted and the individual color channels can be turned on and off by moving both range sliders in a channel to zero.

Keyboard Commands

In the High Resolution Image Viewer, use the keyboard commands to navigate through the image series to keep desired pan and zoom selections activated. 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.

<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="e6ac6cf051b3050e-503723df-4afc4324-8e789afc-41a523ca920bfec351541395"><ac:plain-text-body><![CDATA[


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.