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The Volume Fusion module for Vision4D has been available since 2017. This article explains how it can be used.

Overview

Use Volume Fusion to merge images together that can't be merged using the Tile Sorter.

Registering the volumes for fusion using landmarks:

Add landmarks using markers to match specific pixels in both volumes.
You need 3 landmarks at a minimum, adding more is usually not necessary.
Add the landmarks always in the same order. This makes fusing the volumes much easier.

Registering the volumes for fusion by using surface transformation:

Extract an isosurface from the moving volume to use as a reference
Copy the surface over to the base volume and use the surface transformation tool to work out the translation, rotation, and scaling required (most easily done in VR)
Copy the transformation parameters into the Volume Fusion tool

Fused volumes can either merge equivalent channels or combine the volumes as different channels.

Volume Fusion maintains the resolution of the Base volume and matches that of the Moving volume. Take care when merging volumes of vastly different resolutions.

Volume Fusion was added to Vision4D as a tool to merge multiple image volumes that could not be merged otherwise. There are several reasons why two image volumes could not be merged:

They may not have the same orientation - Stitching using the Tile Sorter only works if the volumes have the same Z-axis direction
They may not have the same dimensions or resolution - this is also a pre-requisite for the Tile Sorter

Volume Fusion has been designed to work around these limitations.

This enables a few specific applications which would otherwise not be practically possible, including for example:

Merging images of a sample that cannot be imaged in a single acquisition because it extends beyond the range of the field of view or stage movement. In this case, we might capture as much of the sample as possible, maybe including tiling, repositioning the sample, and imaging another part of it.
Merging images of two parts of the same volume. This is an extension of the task above. If the sample is too large to fit in the imaging chamber, it may be possible to separate the sample into its constituent parts, image each of these individually, then merge them using Volume Fusion.
Merging images taken in different modalities. Multiple modalities are available for imaging samples, from light microscopy, whether widefield or fluorescence, to electron microscopy and topical spectral imaging (e.g. IR microscopes). Such acquisitions have different outputs and sample preparation steps and will often result in images of different sizes, calibrations, and channel colors.

In all of these cases, and more, Volume Fusion can be used to generate a single volume from two separate volumes, and that fused volume can be used for analysis and visualisation like any other dataset.

Fusing Volumes

Volume Fusion is essentially a two-step process. First, we need to establish registration parameters and then we can modify the moving image set according to those parameters so that it can be fused with the base image set. The registration is used to work out translation, rotation, and scaling and can be done in either one of two ways.

Landmark registration - Creating landmarks

Surface registration - extracting and transferring the surface

Surface registration - Transforming the surface in Vision4D

Surface registration - Transforming the surface in VisionVR

Additional considerations

Multimodal imaging

As mentioned above, Volume Fusion works by taking one image set that we define as the Base image set and another that we define as the Moving image set, and transforming the Moving set to match the Base. If both the base and moving image set are similar in size and channels, which is the base and which is the moving set is relatively unimportant. However, if combining images of vastly different resolutions, as one might if combining electron microscopy and light microscopy image, it is worth bearing in mind that the moving set will be scaled to match the base set. This will usually result in the moving set being either scaled up to gigantic proportions (if it is much lower resolution) or scaled down significantly (if it is much higher resolution). Because of this, Volume Fusion is only really useful for multimodal imaging if the two imaging modes produce images of similar resolution.

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Introduction to volume fusion

See also