Star k ratS » ImageXd

ImageXd

ImageXd is the successor for image and image3d (which already replaces transform2). The software can be used for various applications. It can processes images (2d), image stacks (3d), vector fields, tensor fields (symmatrix), surface networks (meshes) and unstructured data (fibres, networks). Only the computer is the limit for the size of the data sets (64 Bit ~ 2^64 Bytes). Most functions are also optimized for multi-core processors.

New:
* Calculation of orientation tensors
* Analysis of tensor fields (FA, RA, Mean, …)
* For a possible visualization of your tensor data, I recommend the following paper: Leemans (2010) Visualization of Diffusion MRI Data
* Additional software tools: Slicer, OpenWalnut, MedInria, MRIcro, Trackvis, …

Major changes:
* namespace image -> scalar for image3d
* scalar.rgb & scalar.rgba -> vector.rgb & vector.rgba

Version 3.5.6

For command documentation, start the program for the first time. imageXd.macro is created with a complete list of commands.

This program is owned by Heiko Stark. It can be used free of charge for non-commercial use. For the common citations in publications please use the following entry “ImageXd software (Heiko Stark, Jena, Germany, URL: https://starkrats.de).

→ Download

An installer for Windows and Linux can be found here: Software

imagexd 64bit (Windows & Wine/Darwine)
imagexd 32bit (Windows, ReactOS & Wine/Darwine)
imagexd 32bit (Windows CE)
imagexd arm (Windows CE)

imagexd 64bit (MacOS X & Darling)
imagexd 32bit (MacOS X & Darling)

imagexd 64bit (Linux)
imagexd 32bit (Linux)

imagexd 64bit (FreeBSD)
imagexd 32bit (FreeBSD)

imagexd 64bit (Solaris)
imagexd 32bit (Solaris)

Note: Intel 32bit runs also on 64bit systems, but only with 4GB memory!
Note: Imagemagick works only for version 4-6. Please use the appropriate library.

→ Examples

→ Substack

//!imagexd
// This is a comment for the imagexd macro - you can use this macro like a programing language
// For more infos, please see https://stark-jena.de | imagexd
// Copyright (c) 2017 by Heiko Stark

// scalar.use default
scalar.load big.nii
new := scalar.substack <10,10,10> <20,20,20>
scalar.use new
scalar.save small.nii.gz

→ Statistics

//!imagexd
// This is a comment for the image3d macro - you can use this macro like a programing language
// For more infos, please see https://stark-jena.de | imagexd
// Copyright (c) 2017 by Heiko Stark

io.files *.nii
io.files *.nii.gz
io.files *.hdr
for io.files.length // runs for every file from list io.files
begin
     scalar.load io.files.getfile // load a file from list io.files
     
     newfile := io.files.getname . txt 
     scalar.info io.files.getfile newfile
     
     newfile := io.files.getname -h. ppm 
     scalar.histogram newfile
     //scalar.analysis newfile
     
     scalar.setrange
     scalar.setcrop
     
     newfile := io.files.getname -o. ppm
     scalar.gradient newfile
     
     new // clean memory
     io.files.next // go to next file from list io.files
end

→ Segment statistics

//!imagexd
// This is a comment for the imagexd macro - you can use this macro like a programing language
// For more infos, please see https://stark-jena.de | imagexd
// Copyright (c) 2017 by Heiko Stark

scalar.use image
scalar.load "stack.nii.gz"

scalar.use mask
scalar.load "labels.nii.gz"

output.store "stat.txt"
    for 0 scalar.labels.length

        scalar.use mask
        name := scalar.label for.count

        scalar.use image
        new := scalar.mask image mask for.count

        scalar.use new
        a := scalar.count 1 65535
        b := scalar.statistic 1 65535
        c := scalar.quantile 1 65535
        scalar.clean

        write for.count ": "
    
        writeln a " | " b " | " c

    end
end