com.bitplane.xt.options

Interface ImarisAxesOptions<T>

All Superinterfaces:

org.scijava.optional.Options<T>

All Known Implementing Classes:

ImarisDatasetOptions

public interface ImarisAxesOptions<T>
extends org.scijava.optional.Options<T>

Option to specify which axes should be included (at least) when mapping an Imaris dataset to a ImgLib2 image.

Author:

Tobias Pietzsch

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	ImarisAxesOptions.Axis
static interface	ImarisAxesOptions.Val

Method Summary

Modifier and Type	Method and Description
default T	includeAxes(ImarisAxesOptions.Axis... axes) Specify which axes should be included (at least) when mapping an Imaris dataset to a ImgLib2 image.

Methods inherited from interface org.scijava.optional.Options

setValue

Method Detail

includeAxes

default T includeAxes(ImarisAxesOptions.Axis... axes)

Specify which axes should be included (at least) when mapping an Imaris dataset to a ImgLib2 image.

In Imaris, datasets are always 5D: for example, a 2D dataset (without channel or time) is represented as 5D with size=1 along Z, C, T axes. In ImgLib2, there is a distinction between a 2D image and a 5D image with size=1 along the 3rd, 4th, and 5th dimension. Therefore, there are several ways to represent such a dataset in ImgLib2.

By default, axes Z, C, and T are not represented in ImgLib2 if the dataset size along those axes is s=1. By specifying these axes as includeAxes() arguments, this can be overridden. For example, an Imaris dataset with size {100, 100, 1, 1, 1} would be represented as a 2D ImgLib2 image with size {100, 100}. Specifying includeAxes(Z, T), would result in a 4D ImgLib2 image with size {100,100,1,1}.

Parameters:

axes - the axes that should be included (at least) when mapping the Imaris dataset to ImgLib2 image.