@msdanalyzer

Description

Mean square displacement (MSD) analysis is a technique commonly used in colloidal studies and biophysics to determine what is the mode of displacement of particles followed over time. In particular, it can help determine whether the particle is:

  • freely diffusing;
  • transported;
  • bound and limited in its movement.

On top of this, it can also derive an estimate of the parameters of the movement, such as the diffusion coefficient.

@msdanalyzer is a MATLAB per-value class that helps performing this kind of analysis. The user provides several trajectories he measured, and the class can derive meaningful quantities for the determination of the movement modality, assuming that all particles follow the same movement model and sample the same environment.

has function
Examples of tracks to perform MSD analysis.

THOT

Description

Classification of trajectoire: need tracking results as input and will then classify the trajectories as  brownian motion, confined brownian or directed.

has function
thot

MicrotubuleTracker in FIJI

Description

MTrack is a tool, which detects, tracks, and measures the behavior of fluorescently labeled microtubules imaged by TIRF (total internal reflection fluorescence) microscopy. In such an in vitro reconstitution approach, stabilized, non-dynamic microtubule seeds serve as nucleation points for dynamically growing microtubules.

MTrack is a bi-modular tool. The first module detects and tracks the growing microtubule ends and creates trajectories. The second module uses these trajectories to fit models of dynamic behavior (polymerization and depolymerization velocities, catastrophe and rescue frequencies). It also computes statistics such as length and lifetime distributions when analyzing more than one movie (batch mode).

has topic
Track Filament shaped objects and analyze tracks using Ransac fits.

2D and 3D tracking based on global cost function optimization

Description

The workflow consists of firstly identifying spot (which can be also gravity center of cells identified by another method), and then secondly compute trajectories by linking these spots by global optimisation with a cost function. This method is part of the methods evaluated in Chanouard et al (2014) as "method 9" and is described in detail in its supplementary PDF (page 65).

Dependencies

Following plugins are required.

  1. JAR to be placed under IJ plugin directory
    1. A pdf file with instructions and output description is also available in the zip .
  2. MTrackJ : Used for visualization of tracks. Preinstalled in Fiji.
  3. Imagescience.jar: This library is used by MTrackJ. Use update site to install this plugin.
  4. jama.jar. Preinstalled in Fiji.

Advantages:

  • support blinking (with a parameters allowing it or not)
  • fast,
  • can be used in batch, some analysis results provided.
  • No dynamic model.
  • The tracking part is not dependent of ImageJ.

Pitfalls:

  • does not support division
  • the optimization algorithm used is a simulated annealing, so results can be slightly different between two runs.
  • No Dynamic model (so less good results but can be used for a first study of the kind of movements)

The sample data

The parameters used for this example data Beads, were

  1. detection: 150
  2. the max distance in pixels: 20
  3. max allowed disappearance in frame: 1