Projection Dataset

Searching

This dataset comprises 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 from the structure list, or select a structure from the drop-down menu. Selecting an injection site will return a list of experiments that include your search criteria either as the primary or secondary injection site.where the viral tracer was injected into that structure or into one of it's smaller component structures.

Although every effort was made to limit the injection site of the viral tracer to a single brain structure, it was
often the case that cells in neighboring structures were also infected. We refer to these as "secondary structures"
and include them in the results list as they may also contain interesting scientific information.

The search results outline the experiment ID, Primary Injection Structure, Secondary Injection Structure, Mouse Strain, Transgenic Line, Sex, and Injection 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". Your choices are stored in a browser 'cookie' on your computer and will remain in effect until you click the "Clear Selections" button, or clear your Web browser cookie cache.

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 associated reference atlas.

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

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 experiment ID is displayed in the title bar along with the injection site and the section number. Icons in the toolbar allow for you to take actions on the current image.

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.

Using the 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 or the keyboard to zoom in or out.

Select other images in the experiment by clicking on a thumbnail image below the main viewer.

Scale Bar

Drag the scale bar with your mouse to the desired location. Click the scale bar text with your mouse to toggle between horizontal and vertical scale bars.

Using the ZAP Viewer Toolbar

Use the toolbar to take actions on the current image. Toolbar controls include:

Keyboard Commands

Use the keyboard to navigate through the image series and synchronize the viewers on the page. Keyboard commands include:

You can also use the arrow keys to pan the current image.

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

The High Resolution Image Viewer consists of the main image viewer, a scale bar, and a multi-planar viewer. The multi-planar viewer shows the three orthogonal views of the fluorescent projection; the coronal images and the sagittal and horizontal planes were reconstructed from the coronal sections with cross-hairs indicating the current location in the main viewer. Navigate the coronal images by clicking on the planar views or by using the keyboard commands.

Clicking on the icon will bring up the #Image Controls, and clicking on the toggle button will remove the multi-planar viewer panel.

Keyboard Commands

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

You can also use the arrow keys to pan the current image.

Image Controls

Each serial two-photon tomography image is stored as a three channel Red-Green-Blue (RGB) image with 16-bit per channel resolution. Since web browsers only support 8-bit viewing, we use intensity windowing to compress 16-bit data to 8-bit data. All pixel values below the specified minimum are displayed as black, pixel values above the specified maximum are displayed as green (or red/ blue depending on the channel). The pixel values in between are linearly stretched over the 8-bit range.

To make an image appear brighter, move the window sliders to the left, to make an image darker move the window sliders to the right. To increase contrast, move the sliders towards each other, to decrease contrast move the sliders away from each other.

The image below gives an example of how to brighten an image to enhance low intensity projections.

This next example shows how to darken and increase contrast of an image to look at details at the injection site. Note: turning on the blue channel may increase the resolution of individual cell-bodies at the site of infection.

Note: the first three-quarters of the slider-bar represents the lower (0,4095) pixel value range in linear scale. The last quarter of the slider-bar represents the remaining upper (4096, 65535) range in log2 scale. The dual scaling allows for a compact representation of the full range, while allowing for fine-scale control at the lower end.