Matlab

u-Track is a client-side OMERO MATLAB application implementing the sophisticated multiple-particle tracking algorithm of Jaqaman et al. . It works on data previously imported into an OMERO server, and produces results in the form of MATLAB data structures as well as providing functionality to visualise these results.

CellX is an open-source software package of workflow template for cell segmentation, intensity quantification, and cell tracking on a variety of microscopy images with distinguishable cell boundary.

Installation and step-by-step usage details are described in Mayer et al (2013). 

After users provide a few annotations of cell sizes and cell boundary profiles, it tries to match boundary profile pattern on cells thus provide segmentation and further tracking. It works the best on cells without extreme shapes and with a rather homogeneous boundary pattern. It may not work well on images with cells of sizes only a few pixels. Its output comprises control images for visual validation, text files for post-processing statistics, and MATLAB objects for advanced subsequent analysis.

Oufti (previously named MicrobeTracker) is a MATLAB application / suite of tools for analysing fluorescent spots inside microbes. MicrobeTracker can identify cell outlines and fluorescent foci, and generate plots and statistics based on positions and intensity (kymographs, histograms etc.) The MATLAB code is easy to modify and extend to add additional plots and statistics: see e.g. Lesterlin et al. (2014).

The Outfi Forum is quite active.

If your images are corrupted by a strong dominant Gaussian noise you can try this simple filter. It is based on thresholding in the DCT domain and is usually vastly superior to typical Gaussian filtering in term of detail preservation / noise reduction trade-off. The filter unfortunately introduces some block like artifacts that can be mitigated by averaging out overlaping shifted windows (as implemented in the Matlab version) and performing maximum intensity projection after the filtering: As such the filter is way more adapted to process 3D stacks that you plan to maximum intensity project than to process single z slice images.

The quantification is explained in detail in chapter 8 "Cell Polarity - Focal Adhesion and Actin Dynamics in Migrating Cells" in "Bioimage Data Analysis Book" downloadable from here.

For codes and sample images, download the zipped archive (linked under "Download").