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BDA vs. rAAV COMPARISON

This dataset compares the viral tracer recombinant adeno-associated virus (rAAV) to the conventional biotinylated dextran amines (BDA) tracer in specific brain regions. The red channel contains the BDA projections, the green channel contains the rAAV projections and the blue channel shows DAPI labeling.

Searching the Dataset

To view the dataset, browse and select from a list of injection sites, or select a structure from the drop-down menu. Your search will return a list of experiments that outlines the experiment ID, Primary Injection Structures, Secondary Injection Structures, Mouse Strain, Sex, and Injection Age.

Clicking on the experiment ID will launch a contact sheet viewer, showing an image series with each section from that experiment. Double-click on an individual image in the contact sheet to launch a High Resolution Image Viewer. Clicking on the checkbox next to the experiment on the Search Results page 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.

The results from your search are available to download by clicking the "This data is also available as XML" link.

Using the High Resolution Image Viewer

Thumbnail views of each section are displayed at the bottom of the viewer. Selecting from the thumbnail images will display the section in the main image viewer. To adjust the brightness of each individual channel, click the icon in the top right-hand corner (see below).

In the title bar are icons that allow you to interact with the main viewer.

Icon

Description

A dropdown menu to view BDA/AAV or SMI-32 images

Clicking on this icon will bring up a side by side synced view of the Interactive Atlas Viewer

Clicking this will bring up a menu to; download an image, adjust the image controls, remove the title bar or remove the multiplanar viewer

You can also view the closest SMI-32 images from the same brain by selecting "SMI-32" from the dropdown menu in the top-right corner of the viewer to provide anatomical context showing cell bodies, dendrites and thick axons (see below image).

High Resolution Image Viewer Keyboard Commands

In the High Resolution Image Viewer, use the keyboard commands to navigate through the image series to compare BDA and rAAV injection sites and projections. 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.

Experiment Image Viewer

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

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 it 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.

The experiment ID is displayed in the title bar along with the injection site and the section number. Icons in the toolbar enable 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, the on-screen navigation buttons or the keyboard commands 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.

Using the ZAP Viewer Toolbar

Use the toolbar to take actions on the image that currently has focus. Toolbar controls include:

Control

Function

View BDA or SMI-32 data

Adjust image controls

View all images in this experiment in a Contact Sheet Viewer

Display image in a High Resolution Image Viewer

Synchronize other viewers on page to same location

Close the Zap viewer

Keyboard Commands

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

Key

Function

A

Zoom in

Z

Zoom out

F

Step forward through the thumbnail images keeping the same location and scale

D

Step backward through the thumbnail images keeping the same location and scale

S

Sync all viewers on the page to the zoom level and location of the active viewer

+

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.

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