BioImage Suite News

Shen 368 Region Parcellation

Xenophon Papademetris — Wed, 18 Dec 2019 2:32:21 GMT

We make available a 368-node functional parcellation based on Yale-acquired high-res fMRI data. For more information contact Xilin Shen (xilin dot shen at yale dot edu)

BioImage Suite 3.01 is released, forum is moved

Xenophon Papademetris — Fri, 25 Mar 2011 3:31:32 GMT

The BioImage Suite team is happy to announce the release of BioImage Suite 3.01. This is mostly a minor bugfix release to v3.0. The primary fix was in the diffSPECT tool which was broken in 3.0.

As of March 17th, 2011, the BioImage Suite forum was moved to a NITRC hosted site. The new link is http://www.nitrc.org/forum/?group_id=51 . Please use this for all new support questions for BioImage Suite.

Programming for Medical Image Analysis with VTK

Xenophon Papademetris — Mon, 16 Nov 2009 5:30:57 GMT

We are happy to make available the second edition of the online book "An introduction to Programming for Medical Image Analysis With the Visualization Toolkit" (283 pages). This book is an edited and expanded collection of class notes that we wrote for the graduate seminar ``Programming for Medical Image Analysis'' (ENAS 920a) that was taught at Yale University, Department of Biomedical Engineering, in the Spring of 2009. It is currently in draft version but it is made available in the hope that it will be useful as a (self-)teaching tool for researchers in this area. Please be warned that the book is still in preparation -- in particular the references section is still incomplete.

This is available from the Yale BioImage Suite Webpage http://www.bioimagesuite.org.

(Direct Link: http://bioimagesuite.org/vtkbook5/)

BioImage Suite - Slicer Integration

Alark Joshi — Fri, 21 Aug 2009 9:13:14 GMT

BioImage Suite and Slicer can use each other's functionality using new features in BioImage Suite.

Take a look here http://www.slicer.org/slicerWiki/index.php/Slicer3:VisualBlog

This is coming up in the next beta release 3.0b2, hopefully in the next 2-3 weeks.

BioImage Suite 2.6b2 Released

Alark Joshi — Thu, 28 Aug 2008 7:12:21 GMT

The BioImage Suite team is pleased to announce the release of the second
beta (testing) version of BioImage Suite 2.6. This release contains
everything that will be in the official 2.6 release projected to be
released early next month. BioImage Suite v2.6 is an update of version
2.6b1 release in July 2008. The main features of this release are:

* Improvements of the DTI tools to better integrate with the viewers

* New Multi-b value tensor fitting tool (in experimental mode, enable by
setting the EnableBetaFeatures flag under Advanced/Miscellaneous to
on). Any feedback on this module will be particularly appreciated

* Explore mode in Fiber Tracking where if enabled simply pressing the mouse
button somewhere in the three orthogonal slices will quickly initiate
a new fiber tracking. This enables better exploration of the data

* Updates to our FSL interface to account for changes as part of FSL
release 4.1.

* As an additional tool we provide a custom windows version of FSL bet that
can be used with BioImage Suite under Windows. Download from <url>
http://bioimagesuite.org/download/2.6/bis_bet/</url> -- to get this
download
<url>http://bioimagesuite.org/download/2.6/bis_bet/bet_bis.zip</url> and
unzip in c:\yale\bioimagesuite_extra\bin or somewhere else in your path.

* Small modifications to the build system for compilation under Debian 5.0.

* A small number of little fixes in various places.

We anticipate that this is will be the final beta release for this version and that
the official release of BioImage Suite 2.6 will be made early next
month. Work is also progressing on BioImage Suite 3.0 -- we anticipate a
first alpha release later in 2008.

BioImage Suite is supported in part by the National Institutes of Health
(NIH)/National Institute of Biomedical Imaging and Bioengineering (NIBIB)
under grant R01 EB006494. It is made available under the terms of the GNU
General Public License (GPL) v2.

Installation Instructions

There are two types of binary installers provided:

1. Complete: This is a complete package and includes all necessary files to run BioImage Suite (including VTK, ITK, Tcl/Tk etc.)
2. Upgrade: This assumes that BioImage Suite 2.5 is already installed on your computer and does not include any other common files

To download follow the instructions at
http://research.yale.edu/bioimagesuite/forum/index.php?topic=173.0. The
direct link to the beta download side is
http://bioimagesuite.org/download/Install_beta.html.

BioImage Suite 2.6 beta 1 has been released

Alark Joshi — Wed, 16 Jul 2008 2:48:14 GMT

---------------------------------------------------------------------------------------------------------------------------------------------------------------

BioImage Suite 2.6 is an update of version 2.5 released in January 2008. The main features of this release are:

* Lots of little improvements and bug fixes including improved NIFTI format handling for better data interexchange with other software.
* First release of the complete BioImage Suite manual in both pdf (325 pages) and html formats. See http://bioimagesuite.org/public/Intro.html and http://bioimagesuite.org/doc/.
* Inclusion of Broadmann Areas atlas defined on the MNI T1 Template (Colin 27) Brain at 1 mm resolution. This work was presented in HBM 08.
* Improved Objectmap Editing tool with new objectmap regularization option to smooth manually defined regions. This was used in the creation of the Broadmann Areas atlas.
* New optimized fMRI GLM Tool for single subject fMRI analysis -- this complements already available multisubject analysis tools. This includes a user-friendly graphical user interface for defining activation tasks/blocks. Ability to leverage AFNI for single subject GLM analysis in addition to internal code (results are identical).
* New Manual Registration Tool which complements existing automated linear and nonlinear methods already available.
* Substantially improved Colormap Editor with additional presets and graphical transfer function editing. The resulting improvements are particularly useful for obtaining optimal volume rendering displays.
* New Diff-SPECT tool for detecting statistically significant blood flow changes between ictal and interictal SPECT in Epilepsy.
* Improved "bookmark" tools for marking favorite images/directories and setup files in various viewers and controls.
* Revamp of build system to make it more standards compliant. Update to CMake 2.4.x. A user should now be able to install from source using simply "make install". BioImage Suite should also compile with CMake 2.6
* Packages on Linux/Mac OS X are now in .sh format (built with CPack)
* Improved integration with the Windows shell with the ability to automatically detect and execute the appropriate version of VTK when a .tcl script is invoked (either on the console or via double-clicking). This is in preparation for the peaceful coexistence of BioImage Suite 2.x (based on VTK 4.4) with the upcoming BioImage Suite 3.0 (based on VTK 5.2).

BioImage Suite is supported in part by the National Institutes of Health (NIH)/National Institute of Biomedical Imaging and Bioengineering (NIBIB) under grant R01 EB006494. It is made available under the terms of the GNU General Public License (GPL) v2.

Installation Innstuctions

There are two types of binary installers provided:

1. Complete: This is a complete package and includes all necessary files to run BioImage Suite (including VTK, ITK, Tcl/Tk etc.)
2. Upgrade: This assumes that BioImage Suite 2.5 is already installed on your computer and does not include any other common files

To download follow the instructions at http://research.yale.edu/bioimagesuite/forum/index.php?topic=173.0. The direct link to the beta download side is http://bioimagesuite.org/download/Install_beta.html.

MICCAI 2008

David Kennedy — Tue, 22 Jan 2008 8:31:04 GMT

11th International Conference on Medical Image Computing and Computer Assisted Intervention, will be held from September 6 to 10, 2008 in New York City, USA. MICCAI typically attracts over 600 world leading scientists, engineers and clinicians from a wide range of disciplines associated with medical imaging and computer assisted surgery.

See the conference website at: http://miccai2008.rutgers.edu/index.html

BioImage Suite 2.5RC2 Released/Course to Begin Jan 24th

Xenophon Papademetris — Tue, 15 Jan 2008 3:11:32 GMT

See http://research.yale.edu/bioimagesuite/forum/index.php?topic=190.0

for the complete release announcement.

There will be a BioImage Suite training course to be taught at Yale University beginning on Thursday, Jan 24th. This will consist of a number of weekly sessions and all notes/examples/test-data from this course will be made available through the following webpage

http://research.yale.edu/bioimagesuite/course/