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Transgenic Characterization

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


Search the Transgenic Mouse project by entering all or part of a gene symbol into the search box, then 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 Database.

Search Results

Click anywhere on a result row to see details on the experiment.

To compare multiple experiments, mark the checkboxes to the left of each row, then click the "Compare Selected Experiments" button. Any selections you make will remain selected until you click the "Clear Selections" button.

Search results can be sorted by clicking on any of the column headers. Click the header again to sort in the opposite order.

Experiment Detail Page

The experiment page shows all of the images from one or more experiments, along with meta data, as described below.

Image Viewer

All of the images in a series are displayed as a scrollable set of thumbnails. Clicking on one of the thumbnails will load the image into the large viewer above.

The larger image can be panned by dragging it with your mouse, by clicking on it and then using your keyboard's arrow keys, or by clicking the toolbar buttons to the right of the image




Launch a High Resolution Image Viewer

Launch a contact sheet viewer

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Pan left

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Pan up

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Pan down

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Pan right

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View fluorescent image

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View ISH image

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View expression mask

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View the nearest Nissl

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Reset image defaults

The image can be zoomed by scrolling your mouse wheel, by using the +/- keys on your keyboard, or by clicking the Zoom-in & Zoom-out buttons on the toolbar to the right.

To launch a full-page high resolution viewer for the current image, click the Enlarge button on the toolbar to the right. See more about the high resolution viewer below.

To see all of the images from the experiment on a single contact sheet, click the Contact Sheet button on the toolbar. See more about the thumbnail contact sheet view below.
Image Type

There are up to two related images available for each of the primary images in the experiment--

The expression mask. This image is constructed from the signal detected by our image analysis algorithms. This is a false-color image where the "hotter" areas indicate stronger signal. The color map is shown here to the right.
The closest Nissl stained section.

NOTE that not all image series will have either one of the associated image types.

Clicking on the black button in the "associated image" toolbar group will swap out the current image and swap in the expression mask image. To return to the primary image, click on the CISH, Fluorescent, or IHC button. Likewise, clicking on the "nearest Nissl" button will swap out the current images and swap in the nearest nissl images.
Image Adjustment

Dark field images, such as XFP, DFISH & some IHC can be enhanced one color-channel at a time. To the right of each color slider control is the name of the probe expressed in that channel. The center position is neutral, that is the image is neither enhanced nor diminished in that channel. Move the slider to the right to enhance the color, and to the left to diminish the color.

Bright-field images, such as colorimetric ISH and Nissl stained images have a single contrast slider control. Center is neutral, right is brighter, left is darker.
Experiment Metadata

Much of the background for each experiment is contained in the metadata panel. Where applicable, there are hyperlinks to the Jackson Laboratories web site for further information on the mouse lines represented in the experiment. In most cases, there is also a link to the Allen Brain Atlas for the driver gene.

NOTE also that applicable probe details will be made visible by clicking on the "Show Probe Details" bar at the bottom of the metadata panel.