The Digital Fish Library

Software Requirements

Internet Browser: For best viewing experience of the DFL website, we recommend Firefox, Google Chrome, and Safari. Occasionally, Internet Explorer does not display our web pages in an expected way. Also, Javascript must be enabled.

Video & Cladogram Viewer: To view videos and use our Cladogram Viewer or view other Flash animation content, you need to have Adobe Flash Player installed. Click here to download.

Digital Fish Viewer: To use our Digital Fish Viewer, you must have Java Runtime Environment ready on your computer. If you do not have this, you will need to download and install Java on your system. Click here to download.

Exploring the DFL Database

The DFL database can be explored in different ways. Selecting the ‘Explore Library’ tab at the top of the page or clicking the large flash animation on the homepage provides access to browsing the database with our Cladogram Viewer or with various arrays of tiled images organized alphabetically by species scientific name which are accessed using the additional tabs on the Explore Library page. You can also use the Search the DFL text field or Quick Find pull-down menus on the homepage and all Explore Library pages to go directly to any Class, Order, Family or Species page of interest.

Cladogram Viewer: This interactive flash animation displays thumbnails of all DFL imaged species organized by evolutionary classification, beginning with the five exclusive Classes of fish (click here to learn more). Note that this only shows Orders and Families that have at least one scanned species and does not list those currently without any imaged representatives. Selecting a Class of fish will highlight it in yellow and the associated imaged Orders within that Class will appear in the column to the right. Use the mouse to roll over the white triangular arrowheads at the top and bottom of each column to scroll through the available specimens. Selecting an Order will then also highlight it in yellow and the associated imaged Families within that Order will appear on the right. Similarly, selecting a Family will result in the available imaged specimens appearing to its right along with an MRI image thumbnail. The chosen species will highlight in yellow and the View Species Account button will appear. Selecting this will open its Species Page.

Species Pages: Here, specimen MRI data can be explored using the DigifishViewer or movies and images of this data viewed by clicking the image thumbnails provided. This page also provides information on species classification and nomenclature as well as a pull-down menu with links to additional online resources for the species. The Specimen & Scan Info tab provides data on how the specimen was imaged, where it was sourced, its institutional ID, standard length, and information on its collection and curation found using the SIO Link which opens its specimen collection entry (or its species entries if the specimen is uncatalogued) in the online SIO Marine Vertebrates Collection database. The Species Info tab on the far right of the Species Page provides compiled information on its general biology.

Digital Fish Viewer

Each of our species pages provides access to launch the Digital Fish Viewer. This is a 3D Java program that we have created for viewing MRI slice data and volume renders, as well as segmented volumetric structures where available. Click the DigiFishViewer thumbnail near the top right of the species page to launch the Viewer. This will open a dialog box in the browser asking to Open with ‘Java™ Web Start Launcher ’. Click OK. A small plain text file is then automatically downloaded and the DigiFishViewer will be launched. This can be deleted when you close the DigiFishViewer.

Slice 2D Viewer: This displays the Horizontal (Dorsal-Ventral), Sagittal (Left-Right), and Axial (Rostral-Caudal) series of MRI slices in individual windows. The slider bars on the right side of the viewer window allow you to scroll through the slices. With a standard PC mouse, use any of the buttons to click anywhere in a 2D slice and that location will be updated in the other slice orientations. To zoom in or out, hold the right mouse button down and drag. The center mouse button or scroll wheel can be clicked, held down and dragged to move the image around the window. The distance in millimeters between any two points within a slice can be measured by clicking with the left mouse button at the desired locations. This is displayed in the text area in the lower right along with the point coordinates. The Dataset Summary provides the number of slices in the 3D MRI slice matrix (Dimensions) and the image voxel resolution (Grid Spacings) in millimeters.

Slice 3D Viewer: This displays the Horizontal, Sagittal, and Axial series of MRI slices in the same volume, of which you can elect to display any combination of these at one time. The slider bars on the right allow you to scroll through individual slices in a select orientation. Use any of the mouse buttons to click on a pixel within a 2D slice and the other slice orientations will update to that location. Click in the window with the left mouse button to rotate the image. Image zoom and move are also available (sees Slice 2D Viewer). Snap to View can be used to instantly change the perspective to a selected orthogonal view.

Volume Viewer: This feature creates a volume rendering of the MRI data. The image contrast, or brightness, of the rendered image can be adjusted with the Contrast Adjustment Level and Window sliders. Note that this also adjusts the contrast in both the Slice 2D and Slice 3D Viewers. The Reset button sets the contrast to its original default values. This window also has the rotate, zoom and move functions described above.

Structure Viewer: This feature displays 3D rendered soft tissue segmentations where available. This window also has the rotate, zoom and move functions described above. Each segmented organ or organ system has a unique color and their identities are labeled in the listed on the right. The left mouse button is used to click and highlight a selected organ or organ label and its corresponding label or segmented volume will be highlighted. Shift-click will allow selection of multiple structures. Clicking the organ or highlighted label a second time will de-select it. Clicking on the species name at the top of the list of labels will deselect all highlighted structures.