Kymoquant

Description

Measurement of kymograph generally deals with slanted streaks in kymograph to measure velocity of movements. This is a pretty much manual procedure that needs hands-on work. Kymoquant analyzes kymograph by treating patterns appearing in kymograph as texture: for a specified area in kymograph, it detects the most likely orientation of streaks and outputs this result as velocity. This workflow was created to ease the situation when it is difficult to find major direction of streaks only with eyes.

Oufti

Description

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.

KymographTracker

Description

Generation of Kymographs using 2D+t images. In the generated kymographs, objects can be tracked and the results are visualized.

has function

Multi Kymograph

Description

This macro and plugins suite for ImageJ (and Fiji) serves to measure the velocity of moving structures and visualize them, from image time series (2D over time).

The module can be installed in ImageJ as a Macro Menu and each function/component can be called separately. The full workflow consists in calling some, or all, the functions sequentially in order to get from the image preparation (e.g. filtering and visualization of tracks) to the production of the kymographs (time vs. distance plot) and their analysis (retrieving the velocities).

Here is the full workflow sequence:

  • Load image sequence
  • Crop and time-filter the image sequence ("Walking average" plugin)
  • Generate tracks by z-projection ("Stack difference" plugin)
  • Select tracks and restore them in the original stack.
  • execute plugin "multiple kymograph"
  • Analyse: select edges of moving tracks graphically and quantify movement in a table.

input: 8-bit, 16-bit stacks, 2D in time. Calibrated is better for meaningful velocity measurements.

ouput: the kymograph image, the velocity measurements tables.

Requires ImageJ version: 1.33.n minimum.

Example of applications:

  • velocity of moving objects/ structures with sharp edges, incl. the velocity of microtubules (and their plus ends),
  • the velocity of vesicles or particles along a 2D path
  • the velocity of migration of the edge of a cell or a multicellular group
  • retraction velocity of contractile bundles (e.g. actin fibers) or multicellular tissues after mechanical disruption (e.g. laser surgery)