medical image analysis / Blog: Recent posts

Release 2.2.5

A new release has been prepared that includes a lot of changes: new programs for doing a fuzzy cmeans classification on sparse input data, combining an abitrary number of images with an comutative operation, estimating a bounding box around the data in an image, applying a deformabale model to a mesh, and evaluating statistics in a masked area of an 3d image.
New mesh and image filters are provided, amongst them a 2D max-flow/min-cut segmentation filter. ... read more

Posted by Gert Wollny 2015-09-29

STACOM 2014 MoCo Challange (2)

The article comparing the cardiac motion compensation algorithms implemented in MIA when applied to the STACOM challenge data is now available from Springer or as preprint.

Posted by Gert Wollny 2015-01-16

Release 2.2.3

Apart from some bug fixes this release provides support for NiPyPe, i.e. most command line tools can now easily be integrated into NiPy workflows. For some basic examples see [MIA and NiPyPe].

Posted by Gert Wollny 2015-01-09

MIA plays the software part in a new Open Research publication

Cardiac image processing continues to be a main factor that drives the development of MIA. With the GigaScience Journal we now published a data paper that focuses on the reproducibility by making the data, the software, and all the scripts needed to run publicly available. For the lazy all is shaped into a virtual hard drive that contains a minimalist Ubuntu Linux installation, and everything installed ready to run the published experiments, play with the parameters, add new data. ... read more

Posted by Gert Wollny 2014-11-12

Bugfix release 2.2.2 available

This release comprises fixes to issues that surfaced by the latest Coverity analysis and minor issues with the linking to VTK and warnings issued by the Debian lintian tool.

This version will most likely be the one that makes into the next stable Debian GNU/Linux release.

Posted by Gert Wollny 2014-10-22

STACOM 2014 MoCo Challange

MIA was used in the STACOM 2014 Motion Compensation challenge. The results can be browsed and compared here.

Posted by Gert Wollny 2014-09-15

Version 2.2.0 released

The new version comes with lots of enhancements. Highlights are

  • Support for NIFTI-1 image files
  • Basic support for HDF5 image files
  • Support VTK >= 6 data IO
  • Cost functions with mask support in voxel based image registration
  • Filter chains can now contain combiners, load and store intermediate results.
  • 3D orientations are better tracked
  • More C++11
Posted by Gert Wollny 2014-09-05

Release of version 2.0.12

The new release is, essentially, a bug fix release that resolves the issues found through Coverty and corrects some minor issues.

Posted by Gert Wollny 2013-11-27

Bugfix release imminent.

Coverty detected a total of 184 defects in the code, of which 37 could be dismissed as false positives or intentional. The remainder of 147 defects was fixed and this makes an update of the stable package worthy. If the Debian package does not show new errors, the new tarball will be uploaded soon.

Of course all these defects were also fixed in the master tree.

Posted by Gert Wollny 2013-11-22

MIA paper available

Something I completely forgot to mention: a paper describing the software has been accepted for publication in Source Code for Biology and Medicine of BioMed Central. It is published as Open Access and can be downloaded here

Posted by Gert Wollny 2013-11-14

Ohloh and Coverty

In order to make the project a bit more visible, and also to do more code checking I've connected this Sourceforge project to Ohloh and Coverty.

Unfortunately, in order to display the bragging-widgets Ohloh requires scripts that can not be embedded in this markup based forum. So, if you want to have a look at them, you will have to follow this link. ... read more

Posted by Gert Wollny 2013-11-14

Bug fixing with 2.0.11

Version 2.0.11 has now been released to fix some minor bug. Especially the fix for [tickets:#123] needed to get out there in order to make it easy to run the perfusion analysis of the data now publicly available. Currently, not all data sets are segmented, but I'm working on it. To describe this data, I also submitted a data paper has been submitted to ISBI 2014. Let's see if it gets accepted. ... read more

Posted by Gert Wollny 2013-10-15

2.0.10 released

Now that version 2.0.10 has been released work will begin to overhaul the API to allow for new features, amongst these

  • full support for orientation in 3D data sets
  • support for IO of images and vector field stored in HDF5 and Nifti1
  • diffeomorphic registration
  • proper handling of voxel and pixel sizes in registration algorithms

Meanwhile, the mia-viewit program will be prepared for Debian and the python interface package created. Most likely the minimum compiler to be used will be changed to g++-4.7 and clang++-3.3 in order to make use of more C++11 features. Limiting factor is currently support for Ubuntu 12.04 since it does only provide g++-4.6. ... read more

Posted by Gert Wollny 2013-07-02

Up to the next version ...

Right now the pre-release of 2.0.10 is compiling in the Ubuntu Launchpad servers, and I've updated the Changelog for the new release that I will probably make available by the end of the week. Hopefully by then the Debian bug #709554 will be fixed by then so that mia-viewitgui can be uploaded without workarounds.

After this all goes forward to version 2.2, which means API changes and ABI breaks. The biggest issue to be tackled is proper orientation and scaling handling.

Posted by Gert Wollny 2013-06-17

Debian release

As of version 2.0.9, MIA is now an official Debian package availabe in unstable.
The command line tools are named mia-tools and the development files package is called libmia-2.0-dev. This means there is a good chance that MIA will it make into the next Ubuntu release. For now, Ubuntu 12.04 packages for version are provided via the MIA-PPA. ... read more

Posted by Gert Wollny 2013-05-23

Cleaning up with hotfixes.

Version 2.0.8 has been released but unfortunately it was not really tested on i386, so if you run MIA on a 32 bit installation, some tests will fail because of lack of floating point accuracy. I guess this is because on Intel 32 bit the processor has less floating point registers and has to store, and hence, truncate intermediate results. Interestingly, this problem doesn't appear on 33 bit PowerPC (i.e. the G4). In addition, if you want to develop with MIA, the miacore.pc file has a bug so that pkg-config will not provide the proper C-flags.
Both issues have been fixed in git head, and a hotfix patch to the source code is provided. ... read more

Posted by Gert Wollny 2013-03-08

ABI change for 2.0.8

The Debian package was rejected in the first round because of some licencing documentation issues. For that reason I will take the chance to apply some ABI changes that would otherwise be postponed for more time. Among these are removing some unused parameters [tickets:#70], and preparing the new interface for the transformation penalty terms.

Posted by Gert Wollny 2013-02-18

Working the website

The MIA Debian packages are still stuck in the NEW pipeline of ftpmaster, which means apart from the odd minor fixes and enhancements to the code, I'm currently focusing on improving the documentation of the web site:

The ticket system is now split into trackers for the different sub-projects and a tracker for the web site itself has been add, and some [wiki:Tutorials] are now available.... read more

Posted by Gert Wollny 2013-01-25

A new release

Finally, MIA has seen a new release (2.0.6) that might be considered "stable". The code has seen a lot of cleanups and added functionality since the 2.0.3 release, and therefore, it is binary incompatible. Nevertheless, from now on the 2.0 releases will no longer see updates that may break binary compatibility.

The next milestone is to get the software accepted into Debian-med. There exists already an Ubuntu PPA. ... read more

Posted by Gert Wollny 2012-11-23

Big file name cleanup

In order to get rid of the useless duplication of dimension specifiers a big cleanup of the file names has now been pushed to origin/master.

To change the file names dependent projects the following script should be helpful (assuming your header files are named ".hh" and cour implementation files ".cc", if you should adjust the script accordingly.):

files=$(grep -l "<mia/2d/2[dD].*>" $(find . -name "*.hh" -o -name "*.cc"))

for f in $files; do 
    sed -ie "s/\(<mia\/2d\/\)2[dD]/\1/g" $f ; echo $f; 
done... [read more](/p/mia/blog/2012/11/big-file-name-cleanup/)
Posted by Gert Wollny 2012-11-02

More automatic documentation

Latest changes to the auto-documentation is the linking of String command line tools with plug-in handlers. With this addition, now all programs should print the supported file types in their help output, and the man pages and on-line help is also updated accordingly.

What is still missing is that help also informs the user what pixel types a file type supports and whether multiple images can be stored in one file. ... read more

Posted by Gert Wollny 2012-10-26

Towards a new release

Finally, I got the issues with the viewer resolved and the lightning is correct now. Next thing is to get all the test data running that is planned for a paper in Source Code in Biology and Medicine. When the paper gets submitted, the new version will be released and the visualization tool will also see a revival as proper release.

Posted by Gert Wollny 2012-10-02

Cleaning the code

With C++11 a lot of constructs have become obsolete and can now be replaced by cleaner implementations. One example is the THROW macro that used a construct of strings and values added together by the "<<" operator to form the actual message to be passed to the exception.
With variadic templates, this construct has become obsolete and one can now use the template function create_execption to construct an exception of any type with a constructor that expects a std::string as argument. ... read more

Posted by Gert Wollny 2012-09-05

Starting with Allura

As you can see, MIA switched to the new sourceforge backend Allure. In the context of this transitition the organisation of the SCM repositories of MIA will be reviewed and old code will be droppend from the repositories.

If you where using code from the repositories, you might want to reconfigure the origin of your code base. For git repositories this can be done by using

git remote set-url origin <newurl> <oldurl>... [read more](/p/mia/blog/2012/08/starting-with-allura/)
Posted by Gert Wollny 2012-08-27