Image3d

Image3d is a command line tool to process and evaluate spatial data (such as CT or MRI data). Additionally, it can process the resulting vector fields, point-vector-lines clouds (see cloud2) and mesh data (see transform2).

Alternatively, you can also use Nipype (AFNI, ANTs, FSL) for spatial data analysis.
Or with a GUI – MRIcro, MRIcron or MRIcroGL and also commercial tools like Imaris and Amira.

Version 4.6.13

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 “Image3d software (Heiko Stark, Jena, Germany, URL: http://starkrats.de).


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

image3d 64bit (Windows & Wine/Darwine)
image3d 32bit (Windows, ReactOS & Wine/Darwine)
image3d 32bit (Windows CE)
image3d arm (Windows CE)

image3d 64bit (MacOS X & Darling)
image3d 32bit (MacOS X & Darling)

image3d 64bit (Linux)
image3d 32bit (Linux)

image3d 64bit (FreeBSD)
image3d 32bit (FreeBSD)

image3d 64bit (Solaris)
image3d 32bit (Solaris)

Note: Intel 32bit runs also on 64bit systems, but only with 4GB memory!

//!image3d
// This is a comment for the image3d macro - you can use this macro like a programing language
// For more infos, please see http://stark-jena.de | image3d
// Copyright (c) 2013-2014 by Heiko Stark

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

//!image3d
// This is a comment for the image3d macro - you can use this macro like a programing language
// For more infos, please see http://stark-jena.de | image3d
// Copyright (c) 2013-2014 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
     image.load io.files.getfile // load a file from list io.files
     
     newfile := io.files.getname . txt 
     image.info io.files.getfile newfile
     
     newfile := io.files.getname -h. ppm 
     image.histogram newfile
     //image.analysis newfile
     
     image.setrange
     image.setcrop
     
     newfile := io.files.getname -o. ppm
     image.gradient newfile
     
     new // clean memory
     io.files.next // go to next file from list io.files
end

Used for the ‘Wirbelkörperstabilisierung‘ project.


And used for these investigations:

Kupczik K, Stark H, Mundry R, Neininger F, Heidlauf T, Röhrle O (2015). Reconstruction of muscle fascicle architecture from iodine-enhanced microCT images: a combined texture mapping and streamline approach. Journal of Theoretical Biology 382 (7): 34–43. DOI:10.1016/j.jtbi.2015.06.034 / ISSN:0022-5193


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).