Need help or advice ? Come to the Icy club ! - Every Wenesday morning from 9h30 to 12h30 - Francois Jacob Building - Main hall - Pasteur
Register

User reviews

(4)
5 star
3
4 star
1
3 star
0
2 star
0
1 star
0
average rating: 4.75


Please log-in to post a review
Irina
30 Nov 2014 19:08
I use it often and it is very helpful to analyze our data. Thank you!
shaziza
29 Jul 2014 17:27
Nice updates!
IcyLyd
22 Jul 2014 11:18
update (2014-Jun22th):
Now you deserve the 5 stars: We can add many layers of filtering and export the results. The filtering is just ... perfect ! :)
Great update (2014-Jun20th): the available switch between displacement and speed is really usefull. Excel file export is clear and the scale is taken into account. I would love an update with filtering or sorting of the tracks inside the processor ! :)
Eric
20 Jun 2014 13:41
Fantastic update. Can retrieve datas from the tracks crossing a ROI !!!! Units are displayed !!!!

Motion Profiler

by Alexandre Dufour

Track manager plug-in measuring motion statistics in 2D/3D, including min/max/avg/total displacement (absolute & relative to origin), and displacement profiles along all spatial axes.

Publication Id
ICY-Y8S4C1
See technical details
View complete changelog

Documentation

"Motion Profiler" is a plug-in for the Track Manager that computes motion statistics and informative graphs describing the displacement of objects in the field. This plug-in also lets you filter selected tracks based on these statistics.

Computing & plotting statistics

Statistics and graphs are displayed either in pixel/frame units or in real units (in the latter case, make sure that the sequence on which the tracks are displayed has correct pixel size and time interval values).

They are presented in 3 (or 4) separate tabs containing one global summary plus specific statistics for each spatial direction X, Y (and Z if applicable). Such direction-specific information is particularly useful for directed migration experiments (e.g. chemotaxis), where one spatial direction is usually privileged over the others.

The following statistics are computed:

  • Duration: the length of a track, i.e. its number of detections minus one (NB: tracks with only onw time point will not appear as they have no duration; a track with two consecutive time points will have a duration of 1, etc.)
  • Total displacement: the sum of all consecutive displacements in each track, which corresponds to the total distance travelled by the object
  • Relative displacement: the distance between the starting and ending position of each track. It basically indicates if the object has returned to its initial position at the end of its path.
  • Min/Max/Avg displacement: the minimum/maximum/average displacement between any two consecutive time points throughout each track. NB: an option lets you display speed here instead of displacement.

These statistics can be exported as a .xls file for further processing in your favorite spreadsheet software.

In addition to quantitative statistics, this plug-in also plots a graph per sheet describing the displacement profiles over time. In the global case, the graph plots all tracks centered on the origin, which allows to visualise their degree (and direction) of spread. In each "directional" sheet, the tracks are not centered to the origin, and display the evolution of each spatial coordinate for each track over time. Note that the raw data for each graph is also available (click on the "table" icon on top of each graph to view and export them).

Filtering tracks

One of the great powers of the Track Manager is the ability to stack processors one after the other, in order to modify and/or filter tracks to build a powerful pipeline. "Motion Profiler" lets you do this as well: an option called "Filter tracks..." will basically replace the default statistics view by a filter view, where you can select on which criterion to filter, the operation and the threshold value (e.g. "Keep tracks where the duration is greater than 5 frames").

And because these processors can be stacked to infinity (or almost), you can add as many "Motion Profiler" instances to filter the right tracks and compute just the statistics you need. It's that simple.

Acknowledgments

The library used to create the graphs in 2D and 3D is called "jmathplot", it is written by Yann Richet and is released under a BSD license (available here).