## Prerequisites

Before starting this lesson, you should be familiar with:

## Learning Objectives

After completing this lesson, learners should be able to:
• Create slice views of volumetric image data

• Master different ways of dealing with anisotropic voxels

## Motivation

Volumetric data is intrinsically difficult to visualise, especially on a 2D computer monitor. Various volume rendering techniques, including VR, exist, however for quantitative image inspection, where it is critical to access the gray value of individual voxels, extracting one 2-D slice of a volume is the method of choice. Thus, such volume slicing is implemented in almost all image analysis software packages. A conceptual challenge is that microscopes often produce anisotropic data, where the voxel spacing along the z-axis is typically larger than in the x and y axes. Thus, creating a slice, e.g., in the zy plane needs to be done with special care.

## Concept map

graph TD V["Volume data"] --> S("Slicing") V --- A["Anisotropic"] S --> M["2D image"] M -.- A

## Activities

#### Create slice views of a 3D image

• Open a 3D image, e.g.,
• Create slice views of the 3D volume in XY, XZ, and YZ planes
• Appreciate and deal with anisotropic voxels sizes
• Optionally also create slice views at non-orthogonal planes

Show activity for:

## ImageJ GUI

• Open a 3D image
• Use `Image > Properties` to check for anisotropic voxel sizes
• Use `Image > Stacks > Orthogonal views` to view the data in XY, XZ and YZ planes
• Understand how the anisotropy is dealt with
• Use `Image > Stacks > Reslice` to resample the data, exploring the below options for dealing with anisotropy
• `Output spacing`
• `[ ] avoid interpolation`, if this is checked, `Output spacing` is ignored
• Use the line tool to draw a line ROI and again use `Image > Stacks > Reslice` to resample along this line
• Slice the data at arbitrary angles using `Plugins > BigDataViewer > Open Current Image]`
• `Shift-X/Y/Z`: slice along x,y,z.
• `Left button drag`: slice along arbitray plane
• `I`: toggle interpolation

## Assessment

### Fill in the blanks

1. A set of 2D ____ placed on top of each other form a 3D ____.
2. An ____ voxel size can cause the image to appear ____ when viewing it at an angle.
3. Rendering anisotropic voxels can be done in various ways, such as ____, ____, or ____.

## Solution

1. 2D slices placed on top of each other from a 3D stack.
2. An anisotropic voxel size can cause the image to appear deformed when viewing at a certain angle.
3. One can render anisotropic voxels, by (i) isotropic resampling, (ii) just showing them as a square anyway, (iii) showing them as a rectangle.

### True or False

1. Isotropic image data has voxels of equal XYZ dimensions.
2. Slicing is the process of sectioning the data, that has more than two dimensions, along defined axes and dimensions.
3. Reslicing is a term used to indicate repeated slicing.

## Solution

1. True
2. True
3. False - Typically, the term reslicing refers to resampling volumetric data from a different direction, such that the resulting image stack is a rotated version of the original stack.

## Explanations

The word ‘slice’ is often used in different ways. The different ‘layers’ in the z-dimension are referred to as z-slices. Slicing (or subsetting) image data means that part of the image data is selected and ‘sliced out’ to form a new image. This can include selecting one or more dimensions, or just part of a dimension, for example selecting slice 6-12 of the Z-dimension. You can also rotate the data in one of the spatial dimensions and resample the data set to see that data from a different angle, which is sometimes referred to as ‘reslicing’.

## Follow-up material

Recommended follow-up modules: