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  1. Introduction
    1. First run
  2. Menus and controls
    1. Main Atlas3D window
      1. File
      2. Edit
      3. Visual
      4. Tools
      5. Atlases
      6. Objects
      7. Help
    2. Atlas3D 3-D viewer window
  3. HOWTO
    1. Load an atlas
    2. Hide atlas structures
    3. Load experimental data
    4. Improve NIfTI dataset visualization
    5. Clipping
    6. Build a slice
    7. Spatially transform the clipping plane
    8. Spatially transform experimental data
    9. Change background color
    10. Navigate the camera
    11. Find atlas coordinates for a point of interest
    12. Select an atlas structure(s)
    13. Identify an object in 3-D viewer
    14. Exit Atlas3D

1. Introduction

Atlas3D is an advanced visualization tool which allows combined visualization of experimental image data within the 3-D atlas space together with 3-D viewing and user-defined slicing of selected atlas structures. The tool uses Java 3D application programming interface for the rendering and handling atlas structures hierarchy.

1.1 First run

On the first run only two windows will be shown: Main Atlas3D containing the main menus and the 3-D viewer Atlas3D. Please resize/move them for your convenience. The location/size will be stored and used when you run the tool next time. It also applies to any newly opened window. Please follow the HOWTO section in order to quickly try out the tool's features.

2. Menus and controls

2.1 Main Atlas3D window

Main Atlas3D window contains the following menus:

2.1.1 File

  • Import File(s)... - imports data from files. Supported formats are VRML, NIfTI, PNG, XYZ coordinate list, ATLAS package.
  • Import URL... - imports data from URL
  • Save Screenshot... - saves current 3-D viewer picture to a file
  • Exit - shuts down the tool

2.1.2 Edit

  • Load data - loads the data for the selected node(s)
  • Show - makes all selected nodes visible
  • Hide - makes all selected nodes invisible
  • Delete - deletes all selected nodes from the scene

2.1.3 Visual

  • Appearance - changes visual attributes of a selected object
  • Background colour - changes background color

2.1.4 Tools

  • Camera - advanced camera control
  • Transformations - selected object traslate/scale/rotate
  • NIfTI - NIfTI visualization parameters
  • Task Monitor - opens Task Monitor window

2.1.5 Atlases

  • 32 mouse brain structures 3-D reconstructed from “The Mouse Brain in Stereotaxic Coordinates” by Paxinos & Franklin (2001) - loads Mouse Atlas
  • 62 rat brain structures 3-D reconstructed from “The Rat Brain in Stereotaxic Coordinates” by Paxinos & Watson (2005) - loads Rat Atlas

2.1.6 Objects

  • Cube 1000x1000x1000 - creates a cube with W=D=H=1000 µm
  • Color 3D grid - creates coordinate 3D grid represended by 3 planes (x=0, y=0 and z=0)
  • Sphere R=100 - creates a sphere with radius 100 µm
  • Axis 1000x1000x1000 Unit=100 - creates 3 axis (0x, 0y, 0z) with 100 µm units.

2.1.7 Help

  • Manual - opens Help window
  • Current Java3D configuration - opens system information panel
  • About Atlas3D

2.2 Atlas3D 3-D viewer window

  • View All button - places the camera in the position where all objects in the scene are visible while the camera's oribting point is set to the common geometric center of all objects in the scene
  • View Selected button - places the camera in the position where all selected objects are visible while the camera's oribting point is set to the common geometric center of all selected objects
  • None|Box|Highlight|Box&Highlight combobox - defines how selected objects will be marked:None - no marking, Box - red bounding box (default), Highlight - red wireframe, Box&Highlight- bounding box and wireframe
  • Perspective|Orthograpic combobox - sets the projection type, Perspective is default
  • Pick toggle button - enables/disables object mouse picking mode
  • XYZ - enables/disables coordinate mouse picking mode


3.1 Load an atlas

To load an atlas go to Atlases menu in Main Atlas3D window and select the atlas you would like to load.

Only default structures of the atlas will be loaded. If you want to load other atlas structures you have to select them in main Atlas3D window (the tree) and click "Load data" from the popup menu or from the main menu bar. To monitor the loading progress a Task Monitor window will be automatically opened (you might need to resize the window if you have not used that window before).

An empty Task Monitor window signifies that the loading process is finished. If you did not touch any controls during the loading (which you can do - the loading is a background process) you should see something similar to the picture below.

The atlas is loaded.

3.2 Hide atlas structures

Select the atlas structure(s) you want to hide as described in 3.12 Select an atlas structure(s). Hiding of atlas structure(s) can be performed in 3 different ways:

  1. Perform a middle-click (wheel-click) with the mouse on the selected structures in the Main Atlas3D window. This action inverses visibility for the selected nodes.
  2. Open Edit menu in Main Atlas3D window and select Hide.
  3. Right-click on the selected structures in the Main Atlas3D window to make the pop-up menu appear and then click on the Hide menu item.

Note that all hidden structures are displayed as grayed items in the main tree. On the example picture above Ventricular system and septum structures are hidden.

To make the structures visible again select the Show menu item either from the Edit menu in the Main Atlas3D window or from the pop-up menu. You can also permanently (for the session) delete the structures by selecting the Delete menu item.

3.3 Load experimental data

Click on File menu in the Main Atlas3D window. Select Import File(s)... and the Import Files(s)window will be shown.

Select which type of the file(s) you want to import from Files of Type: combo box, then select the file(s) to import from the directory panel. Click the Import selected file(s) button to perform the loading. TheTask Monitor window will appear automatically to display the progress. For each imported dataset a new node will be created in the tree in the Main Atlas3D window. Your visualized data should appear in the Atlas3D 3-D viewer window. If your data is not displayed in the 3-D viewer but listed in the tree inMain Atlas3D window try one of the following:

  • Click the View All button in the Atlas3D 3-D viewer window. This will change the camera parameters to envelop all the objects in the 3-D scene.
  • Select the newly created node in the tree in Main Atlas3D window and click View Selected button in Atlas3D 3-D viewer window. This will focus the camera on the "location" of your data.

Currently supported file types are XYZ, PA, VRML, m3d VRML, NIfTI, PNG

3.4 Improve NIfTI dataset visualization

When you load a NIfTI image file the visualized data might look like this:

To improve the visualization click on the Tools menu and select NIfTI menu item.

It will open NIfTI window. If the controls in the window are disabled you need to select the NIfTI node in the tree in Main Atlas3D window first. In the version 2.1a there is one extra slider to build an isosurface for a certain value.

Adjust the Min Value and Max Value parameters in the NIfTI window to obtain better visualization results. The pictures below show the data before and after adjusting the Min Value parameter.

You might also try to adjust the color using Appearance window.

3.5 Clipping

First you need to create a clipping planes (you can have several clipping planes, but there are some limitations). Open Clipping planes window by clicking Clipping planes menu item in Tools menu.

Clipping planes window will appear.

Create clipping planes by clicking on Create clipping planes at the root node button. Select the clipping planes in the tree in Main Atlas3D window.

Once you selected the Clipping planes 20000x20000 node Clipping planes window will be updated with the information about this clipping planes.

Select the structures you want to clip from Available list and move them to Currently in the scope list using the buttons between the lists.

Brain and corpus callosum become clipped.

3.6 Build a slice

To build a slice(s) (custom atlas diagrams) you need to clip the objects first (see 3.5 Clipping). Then click on Build Slice button in Clipping planes window. As this operation might be time consuming, the Task Monitor will be shown automatically. The resulting slices will be displayed in a new folder in the Main Atlas3D window.

This new folder contains the resulting slices - one per structure/object. Note that the slices inherit the properties of their parents - if the parent was transparent the resulting slice will be transparent too. Visibility of the slices can be controlled in the same manner as any other structure/object. The pictures below show the initial sliced structures and the resulting atlas slice (the camera position is preserved, the atlas is hidden).

The resulting slice can be displayed at standard angles by adjusting the camera (see 3.10 Navigate the camera). The screenshot below is taken from such camera position.

3.7 Spatially transform the clipping plane

Choose Transformations from the Tools menu in the Main Atlas3D window.

The Transformations window will be opened.

In order to spatially transform the clipping plane, the clipping plane object must be selected in the Main Atlas3D window.

Translate/scale/rotate the Clipping planes by moving the sliders or manually set the transformation values in the Transformations window. If the range is not wide enough the limits can be adjusted by typing !<left_limit> or <right_limit>! and hitting Enter in the corresponding textfield. Example: 15000! <Enter> - will set the right limit to 15000 microns.

3.8 Spatially transform experimental data

Choose Transformations from the Tools menu in the Main Atlas3D window.

The Transformations window will be opened.


Select the image data node in the Main Atlas3D window.

Translate/scale/rotate the node by moving the sliders or manually set the transformation values in theTransformations window. If the range is not wide enough the limits can be adjusted by typing !<left_limit> or <right_limit>! and hitting Enter in the corresponding textfield. Example: 15000! <Enter> - will set the right limit to 15000 microns.

3.9 Change background color

The background color can be changed by choosing the color in Background color window. To open this window click Background colour menu item in Visual menu.

3.10 Navigate the camera

There are to ways to navigate the camera:

  1. Drag the mouse in the Atlas3D 3-D viewer (left mouse button - orbiting, right mouse button - panning, middle mouse button - zoom).
  2. Using the Camera window, which can be activated by selecting Camera from the Tools menu.

    Camera window will be shown.

    Note that Predefined camera positions are sensitive to a selected object(s). When you press one of the buttons the camera axes will be aligned to the axes depicted on the icon and the camera will be directed to the center of the selected object(s). Also, the distance from the camera to the center will be set to envelop all the selected object(s).
    Also you can control the camera position by adjustng the orbiting parameters:

3.11 Find atlas coordinates for a point of interest

In the Atlas3D 3-D viewer select XYZ toggle button. This enables coordinate picking mode.

Click on the point of interest in the Atlas3D 3-D viewer. A small sphere will be created identifying the location you clicked as it is shown on the pictures below.

In the main tree in the Main Atlas3D window the corresponding node will be created. Its name displays X, Y and Z atlas coordinates of the clicked point (center of the sphere). In this example the coordinates are X=+2481,5; Y=-2311,4; Z=+20,0.

The sphere's visibility can be manipulated same way as an atlas structure (see 3.2 Hide atlas structures).

3.12 Select an atlas structure(s)

Selecting an atlas structure(s) can be performed in 2 different ways:

  1. By clicking on the nodes in the main tree in Main Atlas3D window. Hold Shift key to select the range on the nodes or hold Control key to select individual nodes.
  2. By clicking on the structures in the 3-D viewer in Atlas3D window. For that you need to enable the picking mode by selecting Pick toggle button in the 3-D viewer in the Atlas3D window.

    Hold the Shift key to add the structure to the list of already selected structures. If you click on a already selected structure it will be deselected (removed from the list).

The methods described above can be also used on any objects including the slices and the coordinate picking spheres.

Selection visualization has 4 different modes: NoneBox(Default), HighlightBox&Highlight. It can be controlled from the combobox in Atlas3D window.

Selection visualization modes:

  1. None. Selected structures will not be marked.
  2. Box. This is default mode. The selected structures will be marked with red bounding boxes (one box per structure). The bounding box is formed using the bounds of the structure plus the bounds of all its children.
  3. Highlight. The selected structures and their children will be marked with red wireframe appearance.
  4. Box&Highlight. Combination of 2 and 3. 

3.13 Identify an object in 3-D viewer

An object in 3-D viewer can be identified by selecting it with the mouse in the Atlas3D 3-D viewer (see3.12 Select an atlas structure(s)). Corresponding node in the main tree will be highlighted showing the object's name and position in the hierarchy.

3.16 Exit Atlas3D

Close Main Atlas3D window or click on Exit menu item in the File menu. The confirmation dialog will be shown. Click Yes button.

Atlas3D reference
Neural Systems and Graphics Computing Laboratory www.NeSys.uio.no