Select an image series by clicking the checkbox in the first column, then click the "View Selected Experiments" button to view all of your selections' images. Click "Clear Selection" to deselect all of your selections, or click "View Cart" to manage them.
Zoom and Pan (ZAP) Image Viewer
The ZAP Image Viewer allows you to navigate through an image series' thumbnails to select an image to view at higher resolution. Once selected, you can manipulate it with your mouse and use the keyboard or toolbar to take additional actions.
Choose a different viewer size by selecting it from the dropdown menu above the viewer(s). If you are viewing more than one image series, choose a different table layout by selecting a different number of columns. Drag viewers to other cells in the table to rearrange them.
Multiple image series can be opened on the same Web page to enable side-by-side comparisons. You can swap viewers' locations on the page by clicking on the first viewer's title bar and dragging it to the second viewer's location.
The gene symbol or treatment type is displayed in the title bar along with the Allen Institute image series ID. Additional details are displayed across the top of the viewing area, including the image index, tissue index, and tissue location.
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.
Side by Side Nissl Viewing
Once you click on the full screen viewer button, you will be taken to a screen with side by side viewers. The left hand viewer shows the ISH image series and the right hand viewer displays the Nissl image series from the same specimen block. To show the nearest Nissl section to the ISH image you are interested in, click the "Sync" checkbox. Clicking on another ISH image will automatically display its nearest Nissl section. Clicking on an image thumbnail in the Nissl image series will automatically take you to the nearest ISH image. While the "Sync" box is checked the Pan and Zoom functions will affect both ISH and Nissl images.
Shows the current viewing resolution of the image, in microns. This value dynamically changes as you zoom in/out of the image. You can position the scale bar anywhere on the main image by dragging the scale bar by its ruler.
You can toggle the orientation of the scale bar from horizontal to vertical by clicking on the scale bar text.
Expression Mask Colors
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).
Specimen Detail Information
Specimen Block Layout
Specimens are received as variable sized blocks of frozen tissue. Before they are sectioned for ISH experiments they are divided into a number of sub-specimens. Throughout this site, when we refer to a specimen we are actually referring to one of these sub-specimens.
The specimen block layout diagram is intended to put the current sub-specimen in context of its original tissue block, and to help navigate to nearby sub-specimens.
In the block diagram, the green block represents the current sub-specimen. Sibling sub-specimens are shown as grey blocks. Clicking on one of the siblings updates the current page to show the sibling's information.
pH - tissue sample pH
The sectioning diagram attempts to depict the relationship between the sections taken from a specimen, the position of each section, and the genes for which experiments have been run on those sections.
Each section consists of 100% of the specimen in the plane of sectioning. The section number, or "section index" is an indicator of relative depth into the specimen.
To the left of the section diagram is a preview image. As you move your mouse pointer over the section diagram squares, the preview will be updated to show the corresponding image. You can get a larger view of the preview image by clicking your mouse on the section squares to launch an image viewer on a separate page.
Each of the colored squares at the top of the diagram represents one section. By default, the sections are ordered by section index. The different colors are mapped to the different genes tested against each section. The color-to-gene mappings can be found in the rectangular gene symbol map appearing below the set of sections.
Each rectangle in the gene symbol map has the same color as one or more of the section squares, and represents either the genes targeted for ISH, or the particular stain applied to the corresponding section blocks.
Hovering the mouse pointer over the rectangles will highlight the associated section squares for easy identification. Each rectangle is labeled with either a gene symbol or a stain treatment abbreviation.
You can click your mouse on the rectangles to go to an Image Summary page, where you can get more information about the section images generated from a particular treatment, and get summary information about gene probes.
On the right of the titlebar of the Sectioning Diagram, you will find two diagram display tools, which are described below.
Drag this slider to the left or right to adjust the contrast of the preview image. Dragging the slider to the left makes the image lighter, dragging the slider to the right makes the image darker.
Click this button to sort the section diagram by gene rather than section index. Click it again to return to the default ordering.
Gene Detail Information
This page summarizes the data regarding the selected gene. The main section details its full name, entrez gene id, alternate gene symbols, chromosome, organism, links to related data in other projects, and gene categories that have been applied to it. A link below this section allows you to bring up a summary of all of the experiments (image series) for this gene.
Image Series Information
The image series details include the gene and probe associated with the experiment, as well as information regarding the specimen.