VisiGene Image Browser

VisiGene is a virtual microscope for viewing in situ images. These images show where a gene is used in an organism, sometimes down to cellular resolution. With VisiGene users can retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection.

Good search terms include gene symbols, authors, years, body parts, organisms, GenBank and UniProt accessions, Known Gene descriptive terms, Theiler stages for mice, and Nieuwkoop/Faber stages for frogs. The wildcard characters * and ? work with gene symbols; otherwise the full word must match.

Sample queries

   VisiGene Response:
nkx2-2 Displays images associated with the gene nkx2-2
hoxa* Displays images of all genes in the Hox-A cluster (Note: * works only at the end of the word)
NM_007492 Displays images associated with accession NM_007492
theiler 22 Displays all images that show Theiler stage 22
vgPrb_16 Displays images associated with VisiGene probe ID 16
allen institute Displays all images from the Allen Brain Atlas
mouse Displays all mouse images
xenopus Displays all images associated with frogs of genus Xenopus
mouse midbrain Displays mouse images that show expression in the midbrain
smith jc 1994 Displays images contributed by scientist J.C. Smith in 1994

Images Available

The following image collections are currently available for browsing:

Image Navigation

Following a successful search, VisiGene displays a list of thumbnails of images matching the search criteria in the lefthand pane of the browser. By default, the image corresponding to the first thumbnail in the list is displayed in the main image pane. If more than 25 images meet the search criteria, links at the bottom of the thumbnail pane allow the user to toggle among pages of search results. To display a different image in the main browser pane, click the thumbnail of the image you wish to view.

By default, an image is displayed at a resolution that provides optimal viewing of the overall image. This size varies among images. The image may be zoomed in or out, sized to match the resolution of the original image or best fit the image display window, and moved or scrolled in any direction to focus on areas of interest.

Zooming in: To enlarge the image by 2X, click the Zoom in button above the image or click on the image using the left mouse button. Alternatively, the + key may be used to zoom in when the main image pane is the active window.

Zooming out: To reduce the image by 2X, click the Zoom out button above the image or click on the image using the right mouse button. Alternatively, the - key may be used to zoom out when the main image pane is the active window.

Sizing to full resolution: Click the Zoom full button above the image to resize the image such that each pixel on the screen corresponds to a pixel in the digitized image.

Sizing to best fit: Click the Zoom fit button above the image to zoom the image to the size that best fits the main image pane.

Moving the image: To move the image viewing area in any direction, click and drag the image using the mouse. Alternatively, the following keyboard shortcuts may be used after clicking on the image:

  • Scroll left in the image: Left-arrow key or Home key
  • Scroll right in the image: Right-arrow key or End key
  • Scroll up in the image: Up-arrow key or PgUp key
  • Scroll down in the image: Down-arrow key or PgDn key

Downloading the original full-sized image: Most images may be viewed in their original full-sized format by clicking the "download" link at the bottom of the image caption. NOTE: due to the large size of some images, this action may take a long time and could potentially exceed the capabilities of some Internet browsers.


VisiGene was written by Jim Kent and Galt Barber. Contact Jim if you have an image set you would like to contribute for display.