Publication list of Dr. Daniel L. Belavy - ROIanalyser (original) (raw)

This website contains the most recent stable version of the ROIanalyzer plugin developed by Dr. Timo Rantalainen and A/Prof. Daniel Belavy. The current jar file can be downloaded from here. The source code for this plugin can be found on Github here.

First usage: Setup ImageJ

If you are using this for the first time, follow the following steps.

macro "ROIanalyse...[k]" {

run("ROI subregions");

run("ROI Export");

run("Draw", "slice");

run("Next Slice [>]");

run("Select None");

}

Sub-region Rows: 1

Sub-region Columns: 5

Root Directory: c:/Output (note: for a Mac, use /Output)

Results Sub-directory: NAMEOFYOURDIR_Results [this is an example, this is the directory name where the output text files with the measurements will be stored]

Roi results directory: NAMEOFYOURDIR_ROIs

Visualise Sub-regions: 0 [if set to 1, this will generate a new image for you to visualise the segmentation]

ROI to read: [no need to change this one. Only used when reloading ROIs into ImageJ for reanalysis]

Stack path: [no need change this one. Only used when reloading ROIs into ImageJ for reanalysis]

Rotation: 0 [0=uses all pixels to rotate the ROI to the horizontal, 1=top row of pixels, 2=bottom row of pixels, 4=no rotation

Erode ROIs: 0 [1 or more erodes one or more layer(s) of pixels from the outside of the ROI before conducting the analysis

Print Widths: 1 [0 means the widths of the individual subregions are not included in the results]

PolyFit: 0 [0 means there is no polynomial fitting to flatten the ROI. 1, 2, 3, 4... means a line, 2nd order polynomial (quadratic), 3rd order polynomial (cubic), 4th order polynomial is fitted to the ROI to flatten the ROI. Note: the ROI is flattened such that the topmost end of the ROI (in the image) ends up at the left side of the flatted ROI]

Settings for analysis of different structures

Sub-region Columns: 2

... we have implemented in the plugin a process that takes the region of interest traced and fits a polynomial to "flatten it" (the following image is a flattened internal oblique):

... and then the plugin pulls out the data of interest. The settings to tweak are:

Sub-region Rows: 1

Sub-region Columns: 3

Rotation: [no need to change this as when PolyFit is not 0, this is automatically set as setting "4", for no rotation]

PolyFit: 4 [this means a 4th order polynomial is fitted. A 3rd order probably suffices, a 2nd order generally won't]

For the data that gets outputted here, the "width" data will give you how long the muscle is (from left to right on the "flattened" image above; i.e. so if want to look at shortening) and the "height" data will give you the thickness of the muscle.

...

Macros for different image types

// DIXON Analyser Macro (for muscle)

macro "DIXON_Muscle_ROIanalyse... [j]" {

run("ROI subregions");

run("ROI Export");

run("Draw", "slice");

run("Next Slice [>]");

run("ROI subregions");

run("ROI Export");

run("Next Slice [>]");

run("ROI subregions");

run("ROI Export");

run("Next Slice [>]");

run("ROI subregions");

run("ROI Export");

run("Next Slice [>]");

run("Select None");

}

// DIXON Analyser VB Axial DIXON. start with 04O

macro "DIXON_AxVB_start with 04O.. [j]" {

run("ROI subregions");

run("ROI Export");

run("Draw", "slice");

run("Previous Slice [<]");

run("ROI subregions");

run("ROI Export");

run("Previous Slice [<]");

run("ROI subregions");

run("ROI Export");

run("Previous Slice [<]");

run("ROI subregions");

run("ROI Export");

run("Next Slice [>]");

run("Next Slice [>]");

run("Next Slice [>]");

run("Next Slice [>]");

run("Next Slice [>]");

run("Next Slice [>]");

run("Next Slice [>]");

run("Select None");

}

Batch re-processing of DICOM images using existing ROIs