ImageXd
ImageXd is the successor for image and image3d (which already replaces transform2). The software can be used for various applications. It can process 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 multicore 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 5.4.5
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)”.
//!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
//!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
//!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
see also image and image3d
Used for the ‘KIP.FasciaRG‘ project.
And used for these investigations:
Eigen L, Nyakatura JA (2021) Architectural properties of the musculoskeletal system in the shoulder of two callitrichid primate species derived from virtual dissection. Primates 62, 827–843. DOI:10.1007/s10329-021-00917-7
Sartori J, Stark H (2021) Tracking tendon fibers to their insertion – a 3D analysis of the Achilles tendon enthesis in mice. Acta Biomaterialia 120: 146-155. DOI:10.1016/j.actbio.2020.05.001 / ISSN:1742-7061
Nyakatura JA, Baumgarten R, Baum D, Stark H, Youlatos D (2019) Muscle internal structure revealed by contrast-enhanced µCT and fibre recognition: The hindlimb extensors of an arboreal and a fossorial squirrel. Mammalian Biology 99: 71-80. DOI:10.1016/j.mambio.2019.10.007 / ISSN:1616-5047
Dickinson E, Stark H, Kupczik K. (2018). Non-destructive determination of muscle architectural variables through the use of DiceCT. The Anatomical Record 301 (2): 363–377. DOI:10.1002/ar.23716 / ISSN:1932-8494
+ 1 Reference from image3d
+ 20 References from transform2.
If you want to send me a bug report or have some suggestions about what future versions of ‘image3d’ should support, you can contact me either by email (bugs[@]starkrats[dot]de).