The ISAS BioImage Suite method primarily relies on the BioImage Suite image processing software package.
We also provide a list of recommended software to complement BioImage Suite.
- Required Software
- Optional Software
BioImage Suite is the only required software providing all the needed functionality for performing ISAS BioImage Suite.
BioImage Suite is a comprehensive, multi-platform image processing and analysis suite. BioImage Suite can be downloaded from
for Windows (XP,Vista,7), Linux, and Mac OSX.
The following software packages are optional complements to ISAS BioImage Suite.
Matlab & SPM2
While we recommend ISAS BioImage Suite, the original implementation of ISAS using Matlab
and SPM2 remains an option for those more familar with these tools.
Please see the
of this website for more details on using these tools.
- RView is software intended for volume image registration/segmentation and display.
"This software integrates a number of 3D/4D data display and fusion routines together with 3D rigid volume registration using Normalised Mutual information.
It also contains many interactive volume segmentation and painting functions for structural data analysis." - Colin Studholme
- To download this package visit the following site.
- Installation instructions are available here
Download and install the ImageJ (Image Processing and Analysis in Java) software
from the downloads section of the
Download the plugins "analyze reader" and "analyze writer"
necessary for the analyze format from the
ImageJ website. Save these in the ImageJ plugins directory.
Start up the ImageJ program and navigate to
Plugins->Shortcuts->Install Plugin... to create a
shortcut so that the analyze reader and writer plugins
will become new menu items.
Put the analyze reader in the Import menu and set the
command to Analyze.
Software that Converts Scans to Analyze Format
For scans to be analyzed by SPM2 they must be in Analyze format; however, if you are starting with
a different file format (ie. Dicom) then follow the steps below.
If you are starting with scans that are not in Analyze format,
there are a number of ways to convert them to the appropriate
format, and this will vary somewhat depending on what scanner
and reconstruction methods were used.
Open your reconstructed SPECT image in RView to check the
Go to Scan Info in RView and note the voxel size (you will
need this value later)
Open ImageJ and go to File > Import > Raw… and select your
Now you must enter some parameters to open the image:
Image type: 16 bit unsigned
Width and Height: 128 (the matrix dimension)
Offset to first image: 2048 (this is the header length)
Number of Images: 128
Gap b/w images: 0
Leave the other boxes unchecked and click Ok.
You should be able to view your picker image at this point.
Go to Image->Rotate->Flip Horizontally so that converted
images will be in the same orientation as the SPECT template.
Go to File->Save As->Analyze and save your raw file into
Analyze format (this should produce a .hdr and an .img file)
The voxel dimensions of your new image have been set to the
default value (which is 1). In order to change it to the appropriate
value as determined in Step 2, you can edit the header using
MRIcro. Initialize MRIcro, and
Open the header file of the scan.
On the top left, there is a header information box and the
voxel sizes (mm) are listed for X, Y and Z. Change these
values to the appropriate values obtained from RView.
Click on the save header icon and replace your existing
header with the corrected version.
Display your new file in SPM to verify that it looks ok.
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