XNII application family

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xNII applications are designed for user guided registration (anchoring) of 2D experimental image data to 3D atlas reference space, thus facilitating data integration through standardized coordinate systems.

Current reference spaces in use:

  • Waxholm Space atlas of the Sprague Dawley rat brain version 2: T2* MRI, DTI, and delineation volumes are provided along with coordinate transformations and readings relative to Waxholm origin, Bregma and Lambda points. WHSv2
  • Allen Mouse Brain Atlas reference atlas version 2: grayscale Nissl volume and annotation volume are provided. ABAv2

A key feature of xNII applications is the capability to generate user defined cut planes through the atlas templates, matching the orientation of the cut plane of the 2D experimental image data, as a first step towards anchoring of images to the relevant atlas template. Cut plane location and orientation can be controlled both by means of interactive GUI and by providing numerical data.

xNII applications support multi-modality 3D atlas packages and one-click switching between image modalites (e.g., MRI and DTI) and structural parcellations. View location and UI settings in general are preserved while switching between modalities.
The applications have been tested extensively and are improved based on user feedback. A series of research projects are currently using the applications for registration of project data to standardized atlas space.

Application variants

There are three flavours of xNII applications available with varying capabilities and requirements.


Web-based version, running on Flash platform. Requires server-side storage system providing experimental images and a Web-server component for generating atlas slices. Because of the network access and operation in conventional browser environment, the storage system must be able to provide downscaled (close to display resolution) versions of the experimental images.
Current version of AligNII is integrated in the web-based Rodent Brain Navigator data system - a data system for internal use in HBP, developed and maintained in collaboration with the INCF Norwegian Node.
Access for partners in the Human Brain Project: contact Jan G. Bjaalie <j.g.bjaalie@medisin.uio.no>

Viewers accessible to anyone (require FlashPlayer):

  • WHSv2 Waxholm Space atlas of the Sprague Dawley rat brain version 2
  • ABAv2 Allen Mouse Brain Atlas reference atlas version 2


Standalone version, running on Microsoft Windows, 64-bit only. Application needs no installation or administrator rights. Both the atlas templates and the downscaled experimental images are brought to the user's computer.
QuickNII operates on image series and it provides estimated anchoring data for each image based on the work which has been done already. Diagrams showing stepping, scaling and rotation changes along the image series are provided in order to help review and curation work.

While QuickNII is a standalone application, in addition to the image files it requires a descriptor (XML) containing the sequence numbering and resolution of image files. As of now, automatic extraction of image series is provided for the Rodent Brain Navigator data system - a data system for internal use in HBP, developed and maintained in collaboration with the INCF Norwegian Node.

Access for partners in the Human Brain Project: contact Jan G. Bjaalie <j.g.bjaalie@medisin.uio.no>


Limited, standalone version of QuickNII. It also requires 64-bit Microsoft Windows (but no installation or administrator rights are necessary for use). CutNII is mainly a viewer for atlas packages and is capable of loading a single experimental image at a time.

CutNII is available for downloading from INCF Software Center: CutNII.

Basic operation

xNII applications maintain common look-and-feel, regardless of running in a browser (AligNII) or as standalone applications (QuickNII, CutNII).

Fixing the view

After resizing the application window, the layout can get really far from what users may want to have. Right-clicking mostly anywhere brings up a context-menu offering simple rearranging options, like tiling or cascading. Right-clicking on the gray background (you may have to use one of the generic rearranging options first) will bring up a version of the context-menu which offers a "Reset layout" option too. This will get as close to the initial layout (visible on the screenshot below) as possible using the current size of the application window.

Main View


Control bar

The control bar (or header) is always visible allowing direct access to most non-visual features all the time. Besides providing readings, the number boxes allow numeric input too.

1 Modality selection
Selection of template modality or segmentation
2 Store [only in AligNII and QuickNII]
Stores the current cutting plane descriptor for the current experimental image (local data for QuickNII, remote storage system in case of AligNII). Requires loading an experimental image first.
3 Restore [only in AligNII and QuickNII]
Restores the stored cutting plane descriptor for the current experimental image.
4 Undo
Undo the last transformation. Translation, rotation and scaling transformations are all recorded and can be undone up to the point of restoring the initial cut plane which was set on starting the application.
5 Redo
Redo undone transformation.
6 Pan stepping
Translation-steping resolution for the arrow controls (16), expressed in integer voxels
7 Rotation stepping
Rotation-steping resolution for the arrow controls (16), expressed in integer degrees
8 Width
Width of cut, expressed in integer voxels
9 Height
Height of cut, expressed in integer voxels
10 Rotation around the left-right axis
As seen in the Sagittal view
11 Rotation around the vertical axis
As seen in the Horizontal view
12 In-plane rotation
As seen in the Slice view
13 Data management (QuickNII only)
Launch data management window.

Windowed interface

The rest of the application interface is built from smaller windows. They can be resized (by grabbing edges and corners) and dragged (by grabbing the title bar) around, have minimize and maximize buttons (right end of the title bar).

14 Slice window
This is the main window, showing the current cut. Manipulations in this window all stay in the current cut plane. Besides using the button controls (16), users can simply drag the image in order to move around in the plane.
15 Cursor coordinates
Spacial coordinates of the mouse cursor. At the moment, file coordinates only, x-y-z coordinates increase towards RAS directions (right-anterior-superior). Note that the tool uses "Radiological" view configuration (see axis indicators, 19)
16 Step-wise controls
All views support moving and rotating the cut rectangle in their respective planes (static planes in the Sagittal-Coronal-Horizontal window, and the cut's own plane in the Slice window)
17 Projection of the cut rectangle
Drag anywhere (except the center point, 18) with the cursor to rotate the cut rectangle
18 Center of the cut rectangle
Drag with the cursor to translate the cut rectangle
19 Axis indicator
Shows the direction of coordinate growth for each axis
20 Values and control window
This window is minimized by default, offers functions which are presumably not needed all the time.

Values and control


21 Values and control window
Click on minimized windows to open them
22 Coordinate readings
Coordinate readings show the location of the midpoint (18) of the cut rectangle. When the focus (practically: the mouse) is in the Values and control window, a crosshair indicates this location in the Slice window. It also appears when the cut is dragged around in the Slice window and no experimental image is loaded. Numerical input is also supported, like entering zeroes into a row quickly jumps to the origin of the given coordinate system.
Mode settings
23 Direct RGB image (example
WHS Rat DTI modality)
There are no settings for RGB display
24 Intensity image (example
WHS Rat MRI modality)
Intensity images are displayed with grayscale representation. Contrast range can be adjusted using the two sliders below (26). See how the contrast has changed compared to the previous screenshot.
25 Segmentation image (example
WHS Rat segmentation version 2)
Segmentation can be viewed in outline (single color) and filled (using colors defined by the corresponding atlas) mode. Filled mode comes with a label popup displaying color and name of the structure under the mouse cursor. Set/clear the checkbox (27) in order to toggle the display mode.
26 Contrast range sliders for intensity images
Drag the sliders to set the intensity range of interest. Default settings range from the lowest occurring intensity level (bottom slider is in the leftmost position) to the highest occurring intensity level (top slider is in the rightmost position)
27 Segmentation display mode
Click on the checkbox to toggle display mode (25)

With support from the Human Brain Project through the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement no. 604102 (HBP).