Getting started
Before you run the plugin, let's see what kind of input it expects.
As an input, the CurveMorph takes:
- a stack opened in Fiji;
- list of ROIs in ROI Manager.
It uses the currently active image of Fiji, it should be a stack
(contain more than one slice or frame or both).
It can be multi-color composite image.
Large images can be opened as Virtual stacks.
It works with 8-, 16- and 32-bit images.
RGB stacks can be made composite using Image -> Color -> Make Composite Fiji command,
processed and re-assembled to RGB.
The ROI Manager must contain at least two (or more) ROIs assigned
at different slice or frame positions of the image stack.
The ROI must be of line (Straight Line), polyline (Segmented Line),
or freeline (Freehand Line) type, and they can have an arbitrary thickness (Line Width).
ROIs of other types can be present, but will be ignored.
You can check ROI's position in a stack by selecting it in ROI Manager
and pressing the "Properties" button, in the "Position" field.
Depending on your image (hyperstack or "regular", simple Z or T stack),
FIJI/ImageJ will display position either as a (C, Z, T) format,
or as a single (N) digit. These two notations cannot be mixed,
so if they are (in very rare cases), you need to correct to one of them.
Once these two are prepared, you can run the plugin and adjust parameters in the dialog.
There are two options:
- Shape morphing will interpolate ROIs width, length, and angles between segments;
-
XY interpolation will interpolate ROIs width and XY centerline coordinates (sampled equidistantly),
without length/angle preservation.
To illustrate the difference between the two methods, take a look at the (intentionally exaggerated) interpolation examples below:
