Software Setup

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.

  1. Required Software
  2. Optional Software

Required Software

BioImage Suite is the only required software providing all the needed functionality for performing ISAS BioImage Suite.

BioImage Suite

BioImage Suite is a comprehensive, multi-platform image processing and analysis suite. BioImage Suite can be downloaded from here for Windows (XP,Vista,7), Linux, and Mac OSX.

Optional Software

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 SPM section of this website for more details on using these tools.


  1. 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
  2. To download this package visit the following site.
  3. Installation instructions are available here


  1. Download and install the ImageJ (Image Processing and Analysis in Java) software from the downloads section of the following site.
  2. Download the plugins "analyze reader" and "analyze writer" necessary for the analyze format from the ImageJ website. Save these in the ImageJ plugins directory.
  3. 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.
  4. 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.

Analyze Format

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.

  1. Open your reconstructed SPECT image in RView to check the voxel dimensions.
  2. Go to Scan Info in RView and note the voxel size (you will need this value later)
  3. Open ImageJ and go to File > Import > Raw… and select your .psm file.
  4. 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.
  5. 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.
  6. Go to File->Save As->Analyze and save your raw file into Analyze format (this should produce a .hdr and an .img file)
  7. 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.
  8. Click on the save header icon and replace your existing header with the corrected version.
  9. Display your new file in SPM to verify that it looks ok.

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