ctvox for ipad - bruker · ctvox for ipad 1.5 1 introduction the ctvox app brings 3d visualization...

CTvox for iPad

Version 1.5

Contents

Introduction .......................................................................................................................................... 1

Background ........................................................................................................................................... 1

Volume rendering ............................................................................................................................ 1

Multi-volume rendering................................................................................................................... 2

Transfer function ............................................................................................................................. 2

Installing CTvox ..................................................................................................................................... 3

Creating and transferring volume data ................................................................................................. 3

VXM file transfer using Dropbox ..................................................................................................... 4

VXM file transfer using iTunes ......................................................................................................... 6

Using CTvox ........................................................................................................................................... 7

Rendering view ................................................................................................................................ 7

Transfer function editor ................................................................................................................... 9

Multiple volumes ........................................................................................................................... 11

1 CTvox for iPad 1.5

Introduction

The CTvox app brings 3D visualization of volumetric data using direct volume rendering to your iPad.

Direct volume rendering is a visualization technique that allows intuitive and interactive exploration

of 3D voxel data by selectively introducing transparency and color. Examples of 3D voxel data

include (micro)CT and MRI scans and synthetic data resulting from numeric computations.

Central to volume rendering is the concept of the transfer function: it governs the mapping of the

original scalar data to a voxel's transparency and emission color, which are determining for the

rendering's appearance.

The following section offers a more detailed theoretical background on these concepts. To get

started right away, skip to the section on installing CTvox, on creating and transferring volume data

or on using CTvox.

Background

Volume rendering

Volume rendering is a 3D visualization technique that works directly on the volume data, rather than

relying on a geometric model built using this data as is the case in surface rendering. It allows to

interactively make selected portions of the data more or less transparent, providing a way to see

through the data and thus reveal complex 3D relationships in real-time.

In volume rendering, every voxel of the volume is assigned:

an emission color: the voxel emits light of a certain color and intensity. This color is

characterized by its red, green and blue components (or channels).

an opacity (opacity, also referred to as alpha, is the opposite of transparency.) The

transparency of a voxel determines how much of the light from more distant voxels (along

the same line of sight) passes through.

The so-called transfer function determines how the original volume data (in the case of CT,

representing X-ray attenuation) is mapped to emission and opacity. By adequately mapping to

emission color, distinct features can be color-highlighted (in the case of CT, e.g. different material

types). By tuning the opacity mapping, the degree to which more distant features shine through and

thus contribute to the final rendering can be modified (in real time). Specific features can even be

totally suppressed by mapping the corresponding data values to full transparency (= zero opacity).

The concept of imaging mode is also determining for the appearance of the rendering. The

supported imaging modes are:

Surface

This mode corresponds to the general emission-absorption model described above.


Maximum intensity projection

For every ray hitting the screen, only the most opaque voxel along the ray is retained.

Hence, this mode automatically highlights the structures of maximum intensity.

Attenuation

In this mode, the opacities for every voxel along a ray hitting the screen are integrated, mi-

micking the effect of a radiograph taken along the current viewing direction.

Multi-volume rendering

The technique of volume rendering can readily be extended to multiple volumes: every volume has

its own transfer function, yielding an emission color and opacity per volume. These emission colors

and opacities are then appropriately weighted to produce a combined emission color and combined

opacity.

A typical application for multi-volume rendering is multi-modality 3D imaging, in which distinct 3D

imaging techniques (CT, MRI, SPECT/PET, ...) provide multiple volumetric images (and typically

complementary information) of a single sample.

When working with multiple volumes, only the Surface imaging mode makes sense and is thus the

only imaging mode available.

Using the weight controls, the relative contribution of any volume to the rendering can be increased

or diminished; for instance, a volume can temporarily be made invisible.

Transfer function

In volume rendering, every voxel in the volume is assigned an emission color (the color the voxel

emits, determined by its red, green and blue components) as well as an opacity (opacity is the

opposite of transparency.) Both of course depend on the original volume data and the mapping is

governed by the so-called transfer function. The horizontal axis in the plot represents the original

scalar data (the x-ray attenuation), the vertical axis represents one of the transfer function

components (red, green, blue, luminance, opacity).

Modifying the opacity controls the visibility of the corresponding voxels and how much they obscure

more distant voxels. By setting the opacity for a given intensity range to zero (full transparency), the

corresponding voxels are effectively made invisible.

Two types of transfer functions exist:

The color channels are linked into a single intensity (or luminance) channel, which modulates

a user-specified base color. Only varying intensities of the specified base color or gray scales

(if the base color is white) will appear in the image.

The color channels vary independently (red, green and blue channels).

Multiple colors can be introduced in the image and are typically used to highlight various

elements of the volume data.

The following table illustrates both types of transfer functions:


Channels Rendering

luminance opacity

red green blue opacity

Installing CTvox

To install CTvox on your iPad, go through Apple’s App Store, in the usual fashion (the app is free of

charge.)

Creating and transferring volume data

Volume data for the CTvox app is stored in a VXM file. A VXM file contains both the volume data and

the associated transfer function(s).

VXM files are generated using the companion CTvox application for the Windows desktop, shown

below.

The desktop application can be downloaded free of charge from the Bruker microCT website, here.

http://www.bruker-microct.com/products/downloads.htm


To generate a VXM file from a dataset, select Export as VXM Data... from the Actions menu. All

currently visible volumes (up to four volumes) will be included in the exported dataset. The volume

data is adequately resized and saved as a single VXM file. The transfer function(s) (one per volume),

the scene's background color and the various labels are stored in the VXM file as well.

For full details on creating VXM files, we refer to the desktop application's online help on the Export

as VXM Data command.

The easiest way to transfer a VXM file to your iPad is to download it wirelessly using the device itself.

Any method will do: through the web browser, as an email attachment, using a cloud storage app

such as Dropbox, Google Drive or OneDrive. Next, open the downloaded file: this may be initiated

automatically after download or may require you tapping the Share button : CTvox will launch

and open the VXM file. From then on, the dataset is available for loading from CTvox's storage.

A set of example datasets is available here.

In the following sections, we’ll first cover in more detail how to use Dropbox to transfer VXM files,

then describe an alternative method using iTunes.

VXM file transfer using Dropbox

Dropbox is one of several free cloud storage and file synchronization services. Files can be uploaded

to Dropbox's servers and then shared between any number of computers and mobile devices. As

such, it's ideally suited to transfer VXM files generated on your Windows PC using CTvox to your

iPad.

Popular competitors offering a similar service include Google Drive and Microsoft's OneDrive.

Signing up for the service can be done through the Dropbox website, as part of the Windows

installation or from within the various mobile apps. To create an account, you'll need to specify your

first and last name and an email address as id.

Visit the Dropbox website to download the Windows version of the software. Installing Dropbox on

your PC creates a special Dropbox folder in the file system. Files placed in this folder will

automatically be synchronized with the cloud storage and thus be accessible from any computer or

device connected to internet that supports Dropbox.

To install Dropbox on your iPad, go through Apple's App Store, in the usual fashion.

https://www.dropbox.com/sh/u5b19yv5nzccsfm/TkUEAcz4sm

http://www.dropbox.com/


When installation has completed, launch the Dropbox app and sign up or sign in, depending on

whether you've already created your account. Navigate to the desired VXM files in your Dropbox.

The screenshot below shows a Dropbox subfolder containing VXM files.

Tap a VXM file to download it to your iPad. When downloading has completed, the app reports that

it cannot display the VXM file.

However, tapping the Share button , then selecting Open In… offers to open the downloaded file

using CTvox. As previously mentioned, this will copy the dataset to CTvox's dedicated storage and

launch CTvox to open it. From then on, the dataset is available in the Open dataset view.


VXM file transfer using iTunes

As an alternative method, you can use iTunes (9.1 or later) to transfer VXM files (and TF files, for that

matter) to an iPad connected to your computer. Here's how (the following screenshots were taken

using iTunes 12.2 on Windows):

1. Connect your iPad (physically) to your computer and launch iTunes.

2. Select your iPad.

3. Select the Apps tab and scroll to the bottom of the page.

4. The CTvox app should be listed under the File Sharing section. Select the CTvox app: the files

associated with CTvox on your iPad will appear in the Documents pane on the right.

5. Use the Add... button or drag and drop files onto the Documents pane to transfer them to

your iPad.

Transferred VXM and TF files will now appear in the Open dataset and Load transfer function views,

respectively.


Using CTvox

Rendering view

When launched, the app opens to an empty rendering view, waiting for a dataset to be opened.

Tapping the Open dataset button pops up a list of the datasets present in the app's storage.

Tapping the Edit button in the popover’s title bar allows you to delete datasets from the storage: tap

the button to the left of a dataset, then confirm by tapping .

Tap a listed dataset to open it.

The following gestures are available to adjust the scene:

Dragging with a single finger rotates the volume.

Pinching moves the camera closer or further.

Dragging with two fingers translates the volume.

A long press followed by dragging moves the faces of the clipping box.


By default, volume and clipping box will move as one. Setting Control to Clipping box in the Clipping

options will cause the clipping box to move independently from the volume. A double tap in the

rendering view will also switch control between volume and clipping box.

The remaining Clipping options include switching between clipping and cutting action for the clipping

box and showing/hiding the clipping box.

The Imaging mode specifies how light contributions from the various voxels are blended and thus

determining for the final appearance of the rendering (cfr. background item on volume rendering.)

Tapping the Reset scene button resets the scene (orientation and translation of both volume and

clipping box, size of the clipping box) as well as the Clipping options and Imaging mode settings.

The remainder of the settings are grouped under the Miscellaneous settings button .

The background color for the rendering can be modified: tapping the Background color row pops up

a color picker to select the new color.


Please note that loading a dataset changes the background color: when creating the VXM file using

the desktop application, the then active background color is stored in the file; the mobile app will

apply the stored background color when opening a dataset.

In the same vein, up to two text labels are included by the desktop application in the created VXM

file. These labels can be used to augment the dataset with information such as a description,

authoring information or copyright notice.

The visibility of the labels can be toggled (unless the content protection feature was checked during

export) and their size adjusted. The labels can be repositioned, too, simply by dragging them.

If the loaded dataset doesn't contain any label, the Miscellaneous settings button simplifies to a

Background color button.

The following table summarizes the controls for the rendering view.

Touch/gesture Effect

One finger drag Rotation

Two finger drag Translation

Pinch Camera distance

Long press + drag Move face clipping box

Single tap Show transfer function editor

Double tap Toggle volume/clipping box control

Transfer function editor

A single tap in the rendering view or tapping the button opens the transfer function editor: the

transfer function is overlaid on the rendering view and available for editing. As the transfer function

is modified, the rendering is updated in real time. A preview bar shows the resulting emission color.


Single tapping outside the plot or tapping the Done button closes the transfer function editor and

reverts to the rendering view.

The leftmost button selects and displays the active channel.

Switching the active channel may switch the transfer function's type (cfr. background item on

transfer functions.)

When the transfer function's type is luminance-opacity, tapping the Base color button pops up a

color picker to set the transfer function's base color.

Use the following touches/gestures to edit the active curve:

A single tap adds a marker or moves an existing one.

Drag a marker to move it.


Double tap a marker to remove it.

The curve mode specifies the type of curve interpolating the markers for the active channel: a jagged

polyline (useful to realize sharp transitions) or a smooth spline.

The Reset button allows you to reset the active channel, all channels or revert to the original

transfer function included with the dataset.

Transfer functions can be saved and subsequently reloaded. The file format used is the same as for

the desktop version (TF files), hence transfer functions can be exchanged. Use the button to

invoke the Load and Save transfer function popovers.

The TF file extension is registered with CTvox, which means that TF files can be transferred to the

app's dedicated storage by downloading them to the device and then requesting to open them in

CTvox (cfr. Creating and transferring volume data.) From then on, they will show up in the Load

transfer function popover.

Tapping the Edit button in the popover's title bar allows you to selectively delete transfer functions.

Multiple volumes

After opening a multi-volume dataset, the toolbar will show an additional button to invoke the

Multi-volume options.


A legend to identify the various volumes can be displayed. These volume labels are inserted by the

desktop application in the VXM file at the time of creation.

Like the text labels discussed earlier, the size of the volume labels can be adjusted and the legend

can be repositioned by dragging it.

The relative contribution of the various volumes to the rendering can be adjusted interactively by

enabling the volume weight controls: a set of sliders, one per volume, is overlaid on the rendering,

allowing adjustment of the relative weights.

The screenshot below shows the volume weight controls for a four-volume dataset.

The controls can be repositioned by dragging the translucent pane.

Tapping Reset weights will restore the volume weights to their initial values.

The following screenshot showcases an application of multi-volume datasets. The VXM dataset

consists of two volumes: a structural micro-CT scan of a core sample (a cylindrical rock section) and

the matching pore thickness information, obtained through post-processing of the micro-CT data.

The rock structure has been given a clay-like appearance and is augmented with the color-coded

pore thickness information. The legend, weight control and labels are all visible.


The transfer function editor, too, looks slightly different for a multi-volume dataset: since every

volume has its own transfer function, a volume selector appears leftmost in the toolbar, to allow

switching between the various transfer functions.

The Reset menu has some additional options:

Restore all initial TF

This will reset every volume's transfer function to its initial state, rather than just the one

currently selected.

Apply TF to all volumes

This option will apply the currently selected transfer function to the remaining volumes, i.e.

all volumes will have identical transfer functions.