MBIV 1.0 User Guide
1. Getting Started
When the MBIV browser is either launched as an web-based applet or installed and run on the users local machine, initial dialog windows will inform the users about the progress and necessary actions. The user is notified once the initial processes are done. A screen shot of MBIV browser at this stage is illustrated here:
The browser is the client part of the client-server system. Together with the sever part, it manages
the access to the images and atlases in our database. Before an image/atlas can be displayed and visualized,
it must be uploaded from our remote database sever to MBIV. This is done via the "File"
selection in the browser menu bar. The two selections under "File" are:
"Open": Upload remote database images.
"Import" : Import local image datasets. Currently, this option is not yet available.
When the user selects "Open->Remote Database Image",
a Graphical User Interface (GUI) opened up within the browsers desktop area as illustrated below:
2.1 Instructions About the "Atlas Database User Panel
As previously mentioned, the "Atlas Database" user
panel allows querying the datasets matching the
given selection criteria in our database. The two selection criteria are a) the genetic
strain and b) the data type. The genetic strain is self-explanatory and described on the main mouse brain
The data type as in our current release includes: raw MRI images of individual mouse brains,
associated individual mouse brain atlases, averaged (minimum deformed)
MRI brain image and corresponding atlas and a probabilistic atlas set. The list of MRI brain images and associated atlases
is given in two scroll windows as illustrated below:
The user can then select the images and/or atlases that he/she wants to upload using the
mouse. Multiple selections are allowed by using the SHIFT key in conjunction
with the mouse. Also, deselect ion can be accomplished using CTRL key with
mouse. As can be seen on the interface, there are three upload choices:
a. Image/Atlas: Upload selected MRI images together with their corresponding atlases (whether or not the atlases have been explicitly selected) or with any other selected atlases.
Note, in addition to a list of selected images and atlases, the dialog box also contains
an option for selecting a uncompressed version of the selected images
(compressed 8 bit, ~34MB vs. uncompressed 16bit, ~64MB). The user can Continue or
operation. If Continue is selected, a progress bar will keep track of the ongoing uploading status.
Depending on what was selected to be uploaded, there could be more than one
A single progress bar in the progress monitor is illustrated in here . The Name field is the internally generated name of the upload operation. The user can query the images and/or atlases that are being uploaded by moving the cursor over the name in the first column; a tool tip window will appear, describing what is being uploaded. The Progress field displays the current progress of the associated operations, Upload Time is the time that the operation has taken and Status shows the current status: "In progress" indicates the task is still running, "Completed" indicates the task has completed or "Aborted (exception") indicates the task was aborted due to some errors.
Once the images and/or atlases have been successfully uploaded, they can be displayed
via the Display Image/Atlas panel. At the top of the interface panel is a
pull down menu containing all of the images that have
been uploaded and a scrolling window with a list of available atlases. Appended
to each atlas name is a a status indicator: [P] Pending (still loading), [L]
for Loaded and [D] for displayed. Also, an atlas is marked with (*) to
indicate the correspondence with the currently displayed MRI image.
There are three display types as described below. The display type can be selected from the pull down list in the Display
Selection area of the panel. Then by clicking on the "Open Display" button,
the selected graphic window will show up.
a) Single View Display:
A single slice of image displayed in a single graphic window with one of the
Coronal, Transverse or Sagittal views.
b) Multiple View Display:
All three views (Coronal, Transverse, Sagittal) of the image are displayed
simultaneously in multiple windows.
c) Multiple Slice Display: A series of consecutive slices from a same image are displayed side-by-side in a single graphic window. This function is not yet available.
Here is a single view graphic window:
The left of the graphics window contains a scroll window listing the color coded brain structure names. The captions in the main display window can be turned off/on from the Option pull down menu, such as the structure legends, image and atlas information, brain structure name and the intensity at the current mouse pointed location.
The following features are also provided in both single and multiple display windows:
Traversing slices: Moving the slice slider bar will display slices in increasing or decreasing order.
Brightness and Contrast: The brightness and contrast of a displayed image can be changed using the menu option, "Tools->Brightness and Contrast: The brightness and contrast of a displayed image can be changed using the menu option, "Tools->Image Intensity", which opens up a intensity control dialog . A user can independently change the intensity of each image or simultaneously change all in a multiple view display.
2.3 Displaying Regular Atlas
Regular atlases(individual atlases and minimum deformation (average) atlases) are displayed as color coded regions (or closed polygons edges), corresponding to the identified structures in the mouse brain. The color coded structures from the atlas are typically overlaid on the original MRI image Figure.
There are several options of the atlas display mode via the display mode panel located in the lower half of the
-Filled: In this mode, the brain structures in the atlas are represented
as filled color-coded regions. There is also a slider that can be
used in this mode to control the transparency of the color-filled regions
(transparency ranges from 0.0 (invisible) to 1.0 (opaque)).
-Outlined: The mouse brain structures in the atlas are represented as color-coded outlines.
The browser provides the following additional functionality for selectively displaying
regions and manipulating region colors. Also, the user can query the
statistics and measurements for the selected region:
Brain Structure Selection:
A list of the brain structures and their corresponding colors is provided in
the sub-window located on the left of the graphic
window. The user can enable/disable the display of any selected region. First, the user has to select a region using the mouse (left
button), highlight the item in the list, click the middle mouse
button and the corresponding colored region is rendered transparent in
the graphics window. To enable the region, click the middle mouse
button, which toggles the region on/off.
The original color assigned to a region can be changed by a user in an
interactive fashion. Selecting "Tools->Atlas Color" opens up a
In order to change the color of a region, it must be selected
(highlighted) in the "Structures" scroll window.
Brain Structure Statistics & Measurements:
Users can query brain structure statistics and measurements. This can be
done in two ways. First, by positioning the mouse over the structure of
interest and right clicking the mouse which will pop up a menu from which
a user can choose to query statistics or measurements. Selecting one will
open up a dialog with the requested information. Second (which is not yet
enabled), by right clicking on a highlighted region in the scroll window and following the same steps.
Displaying Multiple Atlases: By default, the atlas associated with the selected MRI image is displayed. It is possible to overlay more than one atlas on a MRI mouse brain image. When the user opens up a single image display via the local image user interface in the main browser, multiple atlases can be chosen by selecting other atlases from the list under the "Display" option in the menu bar. Given that our individual MRI mouse brain images/atlas are not aligned in a common space (in order to reduce interpolation error to the original data), it might not make any sense for this kind of visualization at this point. We keep this functionality for future display flexibility.
2.4 Displaying the Probabilistic Atlas
Probabilistic atlases are spatial probability maps of a group of mouse brains, in which each voxel value represents the probability p (0.0 ~1.0) of the brains having the same structure at this voxel. A probabilistic atlas is super-imposed on a chosen reference MRI image against which the whole group has been registered (Figure). Note that the user interface functionality for probabilistic atlas displays are different from those for regular atlases. Below is one unique function designed for the probabilistic atlas:
2.5 Displayable Captions
There are several captions that can be "turned on/off" and rendered in the graphics window. Enabling/disabling display of these captions is done via the "Options" selection in the display's menu bar. The available captions are:
a) Color coded legends: Displays region names and associated colors.
b) Probabilistic atlas color bar: Displays mapping of color to probability value.
c) Image caption: Displays information about the brain image (name, dimension, and resolution, etc.)
d) Atlas caption: Display information about the atlas (name, dimension,
etc.) Note: Display of image & atlas captions is done in a mutually exclusive manner (i.e., both cannot be visible at the same time)
e) Display caption: Displays mouse coordinate information, the brain structure name and the image intensity at where the mouse is currently positioned.
This section describes some problems that can arise when running the browser or the downloadable version with suggested solutions.
The only way to monitor the status of an applet is to open up a Java Console. All output (stdout, stderr) from the applet is redirected to the console, so that if there is a unrecoverable error (i.e. java.lang.OutOfMemoryError), the user will be aware of it. Also, the console serves as a tool by which errors can be diagnosed. So, when sending bug reports/errors, please include the contents of the console (cut and paste into email).
This occurs when the JVM (Java Virual Machine) runs out of memory. If this
occurs, the browser has to be restarted, either by refreshing the page or
closing the current page and reopening the browser. The images
that are uploaded are on the order of 35MB (compressed) to 64MB
(uncompressed), so the user may be limited by the memory capacity of his/her local machine. In this
case, care has to be taken when uploading multiple images.
Unfortunately, when images are no longer needed, there is no ready way to
"free" that memory immediately. In a future release, the user will be able
to free memory, but reclamation of freed memory will still be under the
control of the garbage collection mechanism in the JVM.
One other factor that could contribute to java.lang.OutOfMemoryErrors is the JVM used to run applets in a web browser that has not been configured to run with a larger heap (memory area). Please refer to the Setup section.
3.2 Connection Error
Since the browser talks to remote servers, an image server and a database server, there could be connection problems if network problems are occurring. Connection to the servers could be lost while using the browser or during initialization. Moderate checking for connection/network errors has been added to the browser, but some could be unrecoverable. If a connection cannot be established after many retries, it's possible the machine hosting the servers is down.