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Transgenic Characterization

From this tab you can browse and select from reporter lines and driver lines used in the creation of the Allen Mouse Brain Connectivity Atlas.


Search the Transgenic Mouse dataset by entering a gene name, symbol, or mouse line name into the search box. You will be prompted with suggestions once you have started typing. Click "Search" or hit the Enter key.

You can also browse through the data using the browse links on the search page; there are drop-down menus to view all of the #Driver Lines and #Reporter Lines used in this resource.

Driver Lines

Each driver line is represented by its name, a representative image (which is magnified when clicked) and a description of expression. Clicking on the line name will return results from all characterization experiments for that particular line.

Reporter Lines

This drop-down menu lists all the characterized reporter lines with a description of their expression patterns.

Search Results

Clicking on Search will return a list of experiments based on your search criteria with information on the Experiment ID, Line Name, Driver, Reporter, Probes, Age, Sex, Treatments and Image Count. Click on the Experiment ID to be taken to the #Experiment Detail Page

To compare multiple experiments, mark the checkboxes to the left of each row, then click the "Compare Selected Experiments" button. 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 Detail Page

Clicking on the experiment summary link returns a summary of the experimental details (see screenshot).

The various sections of the experimental detail page are outlined 1-6 as follows:

  1. Experimental Metadata: Experiment ID, Transgenic Mouse, Driver, Reporter, Related Gene (click for Adult Mouse data), Probes, Plane of Section, Treatments, Induction; Specimen Data: Specimen ID, Organism, Strain, Age, Sex. Related Institute Data
  2. #Image Viewer: Zoom and Pan Viewer
  3. 3-D Thumbnail Viewer: Rotate using the slider bar under the image
  4. Histogram: Relative gene expression in large structures of the brain (for stages older than P28). Hovering your mouse over the histogram will sync the image in the single image viewer with the section corresponding to that structure and expression.
  5. Transgenic Line Metadata: Transgenic lines involved in this experiment including the Type, Name, Stock #, Source (link to Jackson Laboratories), and the Originating Lab.
  6. Probe Information: Probe ID, Type, NCBI Accession, GI, Orientation, Forward Primer, Reverse Primer and Sequence.

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 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:



Select ISH, Nissl or Expression image type

Image adjust controls

Display all thumbnail images in a single 'contact sheet'

Open the selected image in the #High Resolution Image Viewer

Keyboard Commands

Use the keyboard to navigate through the image series and synchronize the viewers on the page. 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.

Expression Energy

The expression mask image display highlights those cells that have the highest probability of gene expression using a heat map color scale (from low/blue to high/red).

The Expression Energy was calculated as follows: Within a given area A (voxel or structure), expression energy = (sum of intensity of expressing pixels in A) / (sum of all pixels in A)

High Resolution Image Viewer

The image viewer enables you to view a high resolution image in its own re-sizable window. All other properties of this viewer are identical to the ZAP Viewer.

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