Projection Dataset

Searching

The Adult Mouse Connectivity Atlas comprises a searchable image database of axonal projections labeled by viral (rAAV) tracers and visualized using serial two-photon tomography.

Search this dataset using 1) #Source Search, 2) #Target Search or 3) #Spatial Search.

There are example searches in the "Browse the Data" subject box on the landing page to demonstrate the various ways in which you can find data relevant to your research. You can also browse experiments from the 3-D interactive mouse brain. Hovering your mouse over the dots (colored according to the Reference Atlas) will indicate the primary injection structure of that particular experiment. As of the June 2013 release there are over 1000 experiments online.

Source Search

To filter your search by injection site, select a structure(s) from the structure ontology that opens when you click in the "Filter Source Structure(s)" text box.

From the Source Search you also have the option to filter by mouse line. Clicking in the "Filter Mouse Line" text box and either select from Wild Type or cre line, or start typing in the text box to search tags from the various cre-dependent cell lines.

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 injection structures" and include them in the results list as they may also contain interesting scientific information. To view these experiments as well, uncheck the "Primary Structure Only" box.

As you select filtering criteria, notice that the number of experiments in the 3-D rendered mouse brain decreases to fit your criteria. For example the following search for any injection (primary or secondary) in the somatosensory cortex limited to cre lines returns 69 experiments.

The search results display the experiment ID, Primary Injection Structure, Secondary Injection Structure(s), Mouse Strain, Transgenic Line and Sex. Clicking on an experiment ID will launch the experimental detail page. If your search returns include an experiment(s) performed on one of the transgenic lines, clicking the "Transgenic Line" link will take you to the characterization experiments for that line. 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". You can also display data from our Reference Data. 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.

Clicking on any row will load that experiment into the box on the right hand side of the screen. You can then do a 'Correlative Search' on this projection experiment, view a thumbnail view of the 3-D projection pattern or launch the experiment in the Brain Explorer 3-D viewer. Where applicable, a description of the expression pattern of the transgenic line is also displayed.

Target Search

Spatial Search

Using the Multiplanar Viewer to Search

Correlative Search

Experimental Details Page

The experimental detail page illustrates the projection experiment in an informatically quantified fashion. This page contains the Manual Injection Summary, the Quantified Injection Summary, a 3-D thumbnail viewer, a Zoom and Pan (ZAP) Image Viewer, and a histogram quantifying the signal in each region, displayed either by Projection Volume or Projection Density.

1. Manual Injection Summary: This section lists the manually annotated primary injection structure, secondary injection structure(s), the stereotaxic coordinates from Bregma in the anterior/posterior, dorsal/ventral, medial/lateral orientations and the angle of injection (AP, DV, ML, <) and the mouse strain. If the experiment shown is from a transgenic line, you will also have a description of the infected cells and a link to the Transgenic Characterization of that line.
2. Quantified Injection Summary: This section shows the calculated injection sites (as a percentage of the whole). When the mouse is hovered over each bar, the percentage of total signal, and the structure is displayed. Note: the manually determined and informatically calculated injection site(s) may differ.
3. 3-D Thumbnail Viewer: This viewer offers a rotating preview of the projection signal in 3 dimensions. You can click on the "View in 3D" link to view the experiment the Brain Explorer software.
4. ZAP Image Viewer The ZAP Image viewer allows you to browse the experiment in 2-D. You can scroll through thumbnails of each section, zooming in or out and panning through areas of interest.
5. Histogram: This sections illustrates the quantified signal in each structure either by projection volume (mm3) or by projection density (fraction of area occupied by signal compared to the whole structure). Toggle the two representations of the data using the drop down menu at the top of the histogram. The selected structure ontology can be expanded or collapsed and the number of structures shown can be changed using the threshold slider bar at the top of the histogram. When you click on a structure in the histogram, you will be taken to that area of the brain in the 3-D and 2-D image viewers. A red cross-hair pinpoints the center of that structure in each of the image viewers.

Data from this page can be downloaded as XML.

Experiment Image Viewer

The experiment image 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, and with the Reference Data.

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 injection site, section number and experiment ID are displayed in the title bar. Experiments using transgenic mice will also report the name of the transgenic line. 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, on-screen navigation buttons 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.

A dropdown menu allows you to view either the raw images or the projection segmentation view. Clicking on the icon will bring up the #Image Controls, and clicking on the toggle button will remove the multi-planar viewer panel. The button allows download of the single image.

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

When the image controls icon is selected, you will be presented with a menu that allows you to adjust the dynamic range of each channel with a slider bar. What each color represents is outlined above each slider bar and you can exclude any of the channels by unchecking the box next to the slider bar. Once you have adjusted the properties of any channel, you can reset to the default settings by pressing the 'Reset' button.

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.