next up previous contents
Next: Bibliography Up: 9 Appendices Previous: B. Compiling BioImage Suite   Contents

Subsections

C. Bioimagesuite FAQ

This is a list of questions that are frequently asked on either the BioImageSuite Forum at
http://research.yale.edu/bioimagesuite/forum/index.php or in person.

C.1 Working with DICOM data

BioImage Suite uses as a default the "old" Mayo Analyze format in which each image is stored in a pair of files

.hdr = 348 byte header .img = raw image data

See http://bioimagesuite.org/public/FileFormats.html.

We can do some basic DICOM to Analyze conversion using the File Import tool, provide that as stated in the manual "DICOM import is limited to reading images in which the whole series is placed in its own directory in which there are no other files.".

A quick Google search will reveal that there a number of tools out there for the DICOM->Analyze Conversion, this web page
http://www.sph.sc.edu/comd/rorden/dicom.html is a good start. Internally we have a set of linux scripts to do this with, if you are using Linux, we can provide some of these tools as well.

There is a very nice DICOM viewer called ezDICOM which will be happy to do the conversion you need. You only need to ask it to convert to Analyze, point it to your DICOM file and presto, there is a .hdr and .img file sitting next to your .dcm file.

Find it here: 

http://www.sph.sc.edu/comd/rorden/ezdicom.html#intro

Some other nice DICOM tools to be found at David Clunie's site http://www.dclunie.com/ Have a look at dicom3tools http://www.dclunie.com/dicom3tools.html and also his PixelMed toolkit 

http://www.pixelmed.com/index.html#PixelMedJavaDICOMToolkit

C.2 How to install BIS on Debian

For running BioImage Suite 2.5 on Debian you first have to install VTK and ITK manually.

  1. Prerequisites - You need to install following packages: 

    # apt-get install g++ make cmake xlibmesa-gl-dev tcl8.4-dev tk8.4-dev iwidgets4 tcllib \\
dpkg-dev cdbs patchutils debhelper zlib1g-dev libpng12-dev libtiff4-dev lapack3-dev

  2. Download and Install VTK-4.4.2 from source 

      $ wget --http-user=USERNAME --http-password=PASSWORD \\
 http://bioimagesuite.org/download/src/dependencies/VTK_4.4.2_patched.zip
  $ unzip VTK_4.4.2_patched.zip
  $ cd VTK
  $ ccmake .
With
 - VTK_USE_HYBRID              ON
 - VTK_WRAP_TCL                 ON
 - VTK_USE_PARALLEL          ON
 - BUILD_TESTING                  OFF

 $ make
 # make install (as root, install path is /usr/local/)

  3. Backport ITK 3.4

    Add the Debian-Sid sources to your /etc/apt/sources.list 

      # pico /etc/apt/sources.list (deb-src http://ftp.de.debian.org/debian/ sid main)
  # apt-get update

    To auto-build the package when it's been downloaded, just add -b to the command line, like this: 

      # apt-get -b source libinsighttoolkit-dev

    If you decide not to create the .deb at the time of the download, you can create it later by running: 

      # dpkg-buildpackage -rfakeroot -uc -b

    Install the packages 

      # dpkg -i libinsighttoolkit3.4_3.4.0-1_i386.deb
  # dpkg -i libinsighttoolkit-dev_3.4.0-1_i386.deb

    Remove the Debian-Sid sources from your /etc/apt/sources.list 

      # pico /etc/apt/sources.list (deb-src http://ftp.de.debian.org/debian/ sid main)

  4. Download and Install BioImageSuite 2.5 (http://bioimagesuite.org/download/src/) 
      $ unzip bioimagesuite_2.5_01_29_2008_src_2366.zip

    Change into BIS main directory 

      $ cd bioimagesuite_src/

    uncomment clapack 

      $ pico CMakeOptions.cmake

  $ ccmake .
With
  - BUILD_SHARED_LIBS                            ON
  - BIOIMAGESUITE_USE_SYSTEM_LIBS     ON
  $ make

    Set the BASE variable in file setpath.sh 

      $ pico bioimagesuite_src/bioimagesuite/setpaths.sh
 (in my case: BASE=/home/guest/bioimagesuite/bioimagesuite-2.5.0/bioimagesuite_src/bioimagesuite )

   $ source bioimagesuite_src/bioimagesuite/setpaths.sh

    Start the Program 

       $ bis.tcl

  5. To ``install'' simply type ``make install''.

  6. A couple of additional comments

    • Download and Install VTK-4.4.2 from source - please use the slightly patched version from the BioImage Suite webpage, this fixes a nasty bug -

      See: http://bioimagesuite.org/download/src/dependencies/. Otherwise the software will crash if the image you are using has more than 4 frames!

    • You will also need to install "lapack" 
      Set BIOIMAGESUITE_USE_SYSTEM_LIBS to ON to use this.

C.3 Working with TIFF images

If these are ordinary tiffs. You should be able to import these into BioImage Suite more or less directly. Alternatively consider using one of the many conversion tools available to convert the tiffs to Analyze (7.5) format. Possible tools include

While we can support a variety of formats internally, it might be better to use a tool specialized for format coversion prior to moving the images into BioImage Suite.

BioImage Suite prefers grayscale images, color would be most likely interpreted as time frame (i.e. multi-component images e.g. red,green and blue are typically dealt with as multiframe images). You are better off converting them to grayscale.

C.4 How can I obtain Bioimagesuite?

Instructions for downloading BioImage Suite can be found at: http://bioimagesuite.org/public/Downloads.html.

Basically you need to

Register on this forum and log in. Follow this link http://research.yale.edu/bioimagesuite/forum/index.php?topic=88.0 to a message in the forum that specifies the username/password you will need to use to download the Software. This link is not accessible to non-members of the forum.

Please note:The username/password required to download BioImage Suite is not your forum username/password but rather the common username/password given in the thread pointed to by the previous link (http://research.yale.edu/bioimagesuite/forum/index.php?topic=88.0)

The only reason for this is so that we can keep track of who and how many are downloading the software. The process of registering on the forum is completely automated and mostly instantaneous.

C.5 Is there any documentation for Bioimagesuite?

Other than this manual, which can also be found online at http://www.bioimagesuite.org/public/Intro.html, we have also taught a course on using Bioimagesuite for image analysis. The handouts for the course and some test data can be found at http://research.yale.edu/bioimagesuite/course/

C.6 How do I convert matlab format (.mat) into .hdr ?

Take a look at this toolkit 

http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=8797&objectType=FILE

(See also notes here http://www.rotman-baycrest.on.ca/ jimmy/NIFTI/examples.txt)

BioImage Suite can read both NIFTI and Analyze just fine.

next up previous contents
Next: Bibliography Up: 9 Appendices Previous: B. Compiling BioImage Suite   Contents