Velocity Measurement Tool

The toolset allows to create kymograms and to measure the velocity of particles in the kymogram. The user can make a segmented line selection on the kymogram and the mean velocity for each segment will be measured. A synthetic example image can be found here: moving-particles-2.tif

Getting started

To install the tools, drag the link Velocity_Measurement_Tool.txt to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation and restart ImageJ.

Select the "Velocity Measurement Tool" toolset from the >> button of the ImageJ launcher.

  • the *?*-button opens this help page
  • the k-button creates a kymogram of the current image
  • the v-button measures the velocities corresponding to the line or segmented line selection on the kymogram

The measurement of the velocities is a modified version of code from (tsp050706.txt TimeSpacePlot (Kymograph)) by J. Rietdorf FMI Basel and A. Seitz EMBL Heidelberg.


Make a segmented line selection of the path of the particle for which you want to measure the velocity. You can use a z-projection (Image>Stacks>Z Project...) to create the selection and then transfer it to the time-series stack using ctrl+shift+e. Now press the k-button to get the kymogram. Now make a segmented line selection on the trace of the particle in the kymogram and press the v-button to get the speed measurements.


The input time series: The kymogram:

The kymogram with a segmented line selection:

The measurements in the results table:

  • dy sum - the sum of the distance travelled in y direction
  • dx sum - the sum of the distance travelled in x direction
  • dy now - the distance travelled on the current path segment in y direction
  • dx now - the distance travelled on the current path segment in x direction
  • actual speed - the speed on the current path segment
  • average speed - the average speed upto and including the current path segment

The x-axis represents the distance and the y-axis represents the time in the units set for the image for example pixel/time unit or micron/second.

Publications that use the tool

  1. Tsai, F.-C., Henderson, J.M., Jarin, Z., Kremneva, E., Senju, Y., Pernier, J., Mikhajlov, O., Manzi, J., Kogan, K., Le Clainche, C., et al. (2022). Activated I-BAR IRSp53 clustering controls the formation of VASP-actin–based membrane protrusions. Sci. Adv. 8, eabp8677. 10.1126/sciadv.abp8677.
  2. Hahn, I., Voelzmann, A., Parkin, J., Fülle, J.B., Slater, P.G., Lowery, L.A., Sanchez-Soriano, N., and Prokop, A. (2021). Tau, XMAP215/Msps and Eb1 co-operate interdependently to regulate microtubule polymerisation and bundle formation in axons. PLoS Genet 17, e1009647.
  3. Mahmood, I., Martinez-Hernandez, U., and Dehghani-Sanij, A.A. (2020). Evaluation of gait transitional phases using neuromechanical outputs and somatosensory inputs in an overground walk. Human Movement Science 69, 102558.
  4. Ali, M.F., Fatema, U., Peng, X., Hacker, S.W., Maruyama, D., Sun, M.-X., and Kawashima, T. (2020). ARP2/3-independent WAVE/SCAR pathway and class XI myosin control sperm nuclear migration in flowering plants. Proc. Natl. Acad. Sci. U.S.A. 117, 32757–32763. 10.1073/pnas.2015550117.
  5. Yu, S., Steuer Costa, W., Liewald, J.F., Shao, J., and Gottschalk, A. (2019). Synapsin is required for dense core vesicle capture and cAMP-dependent neuropeptide release (Neuroscience).
  6. Galiana, E., Cohen, C., Thomen, P., Etienne, C., and Noblin, X. (2019). Guidance of zoospores by potassium gradient sensing mediates aggregation. J. R. Soc. Interface 16, 20190367.
  7. Trigo, D., Goncalves, M.B., and Corcoran, J.P.T. (2019). The regulation of mitochondrial dynamics in neurite outgrowth by retinoic acid receptor β signaling. The FASEB Journal 33, 7225–7235.
  8. Nakos, K., Rosenberg, M., and Spiliotis, E.T. (2019). Regulation of microtubule plus end dynamics by septin 9. Cytoskeleton 76, 83–91.
  9. H. A. Ryan, S. Hirakawa, E. Yang, C. Zhou and S. Xiao, High-Voltage, Multiphasic, Nanosecond Pulses to Modulate Cellular Responses, in IEEE Transactions on Biomedical Circuits and Systems, vol. 12, no. 2, pp. 338-350, April 2018.
  10. Sawamiphak, S., Kontarakis, Z., Filosa, A., Reischauer, S., and Stainier, D.Y.R. (2017). Transient cardiomyocyte fusion regulates cardiac development in zebrafish. Nature Communications 8.
  11. Breznau, E.B., Murt, M., Blasius, T.L., Verhey, K.J., and Miller, A.L. (2017). The MgcRacGAP SxIP motif tethers Centralspindlin to microtubule plus ends in Xenopus laevis. Journal of Cell Science 130, 1809–1821.
  12. Elaina B. Breznau (2016). Regulation of epithelial cytokinesis and cell-cell junctions by MgcRacGAP. University of Michigan.
  13. Monteith, C.E., Brunner, M.E., Djagaeva, I., Bielecki, A.M., Deutsch, J.M., and Saxton, W.M. (2016). A Mechanism for Cytoplasmic Streaming: Kinesin-Driven Alignment of Microtubules and Fast Fluid Flows. Biophysical Journal 110, 2053–2065.

moving-particles-2.tif (2.32 MB) Volker Baecker, 04/03/2014 02:08 PM

toolset.png (701 Bytes) Volker Baecker, 04/03/2014 02:13 PM

moving-particles-2.gif (20.2 KB) Volker Baecker, 04/03/2014 02:19 PM

kymogram.png (191 Bytes) Volker Baecker, 04/03/2014 02:21 PM

kymogram-2.png (9.79 KB) Volker Baecker, 04/03/2014 02:25 PM

results.png (7.77 KB) Volker Baecker, 04/03/2014 02:29 PM