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MOSAIC Plugins for ImageJ

This site is no longer maintained

The MOSAIC Group moved from ETH Zurich to the Max Planck Institute in Dresden (Germany) in summer 2012. This web site is no longer maintained and will be discontinued soon. Please visit our new site for all software downloads, publications, and information about our research and teaching.

>> http://mosaic.mpi-cbg.de ...

Several of the image-processing algorithms developed at the MOSAIC Group for fluorescence microscopy are available as plugins for the popular free image processing software ImageJ.

The first plugin was a popular 2D single-particle tracking tool. It can be used to track bright spots in 2D movies over time.

As more plugins have been added, we decided to provide them in a single, coherent package, which will also group them under a common menu point "MOSAIC" in ImageJ. The current version can be downloaded here

The current version of the package contains the following plugins:

3D tracking

The evolution of our classical 2D single-particle tracking tool. The tool now also supports 3D images (but still includes support also for 2D ones) and includes new and improved algorithms. The documentation consists of: (1) The user manual of the original 2D version, (2) a tutorial with example data, and (3) an addendum describing the additional functionality in the 3D version. More information, including a source code API reference, can be found here: https://weeman.inf.ethz.ch/ParticleTracker/.

Please use this version, even if you just plan to process 2D images. The old 2D plugin is no longer maintained.

November 2010: NEW VERSION!

The latest update of the 3D tracker plugin now supports:
- User-contributed function improvements (Many thanks to Dr. Kota Miura!)
- More robust detection algorithm
- Batch processing using ImageJ macros (output is written to disk)
- Number of detected particles is displayed
- Absolute threshold can be set instead of relative percentile
- The intensity momenta or order 0 to 4 are computed and output

The algorithm implemented in this plug-in is described in:

I. F. Sbalzarini and P. Koumoutsakos. Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology, Journal of Structural Biology 151(2):182-195, 2005. (PDF)

In order to ensure financial support for our project at ETH and allow further development of this software, please cite above publication in all your documents and manuscripts that made use of this software. Thanks a lot!

Background subtractor

This plugin implements a robust, histogram-based background subtractor, which is well suited to correct for inhomogeneous illumination artifacts. Please see the user manual for details and examples.

A PSF estimator

This plugin can be used to estimate the Point-Spread Function of the microscopy out of 2D fluorescence images. See the user manual for details.

3D PSF estimator

This plugin can be used to measure the 3D Point-Spread Function of a confocal microscope from an image stack. See the user manual for details.

Poisson noise

This plugin can be used to add synthetic Poisson-distributed noise to an image in order to simulate shot noise of various signal-to-noise ratios. It can be used to generate benchmark images in order to assess the accuracy and robustness of image processing algorithms as a function of the noise level present in images. See the user manual for details.

Bessel convolution

This plugin convolves an image with a Bessel function in order to simulate imaging with a microscope. The Bessel function is a model for a generic Point-Spread Function, depending on the wavelength and NA. This plugin can be used to generate synthetic images that mimic microscope output in order to benchmark the accuracy and robustness of image processing algorithms. See the user manual for details.

 

IN NO EVENT SHALL THE ETH BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF THE ETH HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. THE ETH SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND THE ETH HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

 

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© 2014 ETH Zurich | Imprint | Disclaimer | 6 December 2010
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