Hop over to PeerJ to read about the algoritm implemented in MIA that can be used for the segmentation of paleoantological material. The tool you are looking for is mia-3dsegment-local-cmeans. Many thanks to Chris J. Dunmore and Dr. Matthew M Skinner at the School of Anthropology & Consservation at the University of Kent, UK, for getting me involved in this research.
This release brings just two small changes, one one hand a bug was fixed in mia-3dsegment-local-cmeans, and mia now compiled against boost version 1.65.
The new version provides a tool for symmetric fluid dynamic registration, some local-cmeans based segmentation tool, new image filters, and it adds compatibility for VTK-7 data IO.
The new version can also be run from a docker image.
In addition the new version fixes a number of issues:
For the latest release now a Docker image is now available. This makes running mia-tools of the latest stable release on non-linux operating systems easy,
In order to run the tools by using this image, Docker must be installed accordingly.
On MS Windows, the disk on which the data is located that you want to process needs to be enabled for sharing. ... read more
The paper summarizing the results of the cardiac motion compensation challange from STACOM 2014, in which the MIA software package took part, has been accepted for publication:
Beau Pontre, Brett R. Cowan, Edward DiBella, Sancgeetha Kulaseharan, Devavrat Likhite, Nils Noorman, Lennart Tautz, Nicholas Tustison, Gert Wollny, Alistair A. Young, and Avan Suinesiaputra, An Open Benchmark Challenge for Motion Correction of Myocardial Perfusion MRI , IEEE Journal of Biomedical and Health Informatics, DOI: 10.1109/JBHI.2016.2597145
The development of MIA has reached a new milestone with the release of the version 2.4. One of the major changes is that MIA can now rely fully on the C++11 facilities for multi-threading, making it possible to remove it's dependencies on the Intel threading building blocks. As a result MIA can now be compiled and run on many more architectures, specifically, it can now be build on all Debian release architectures.
The last few days I have been busy to get MIA to compile on FreeBSD, mostly because this seems to be the closest one can get to Mac OS X, and for the latter a MIA user requested help.
The git HEAD now compiles properly with clang-3.7 and using libc++. Most problems arose from a different behaviour in the explicit instaciation of template, but according to this bug report this might change in newer versions of clang. ... read more
Thanks to the integration of github with Travis-CI and Coveralls, it has now become possible to get a up-to-date information about the amount the unit tests cover the library code base.
Currently, my work on mia focuses on crancking up this coverage by adding more tests.
All the MIA software packages as well as some other image processing related tools and libraries are now made availabe to Gentoo via the imaging overlay. To enable it just run as root
layman -a imaging
From the backlog of things that have been done with MIA comes a publication about motion compensation in prostate perfusion imageing.
In order to facilitate coolaboration with people who do not use sourceforge, but github, the master branch of MIA-2 is now mirrored on GitHub.
Since this mirroring is done manually expect some delays in the syncronisation.
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
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.
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].
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
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.
MIA was used in the STACOM 2014 Motion Compensation challenge. The results can be browsed and compared here.
The new version comes with lots of enhancements. Highlights are
The new release is, essentially, a bug fix release that resolves the issues found through Coverty and corrects some minor issues.
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.
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
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
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
Now that version 2.0.10 has been released work will begin to overhaul the API to allow for new features, amongst these
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
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.