Plugin

Track Processor Intensity Profile

Publication ID: ICY-L4L5K4

Short Description

A TrackProcessor that allows the user to monitor, visualize, and export, the intensity profile of tracks in time lapse sequences of 2D images.

Mean, max, min, median, sum and variance of the intensity are computed along time. Values are computed for pixels in a disk of user-defined diameter around each position of the track at each frame.

The plugin is accessible through the TrackManager plugin.

Documentation

A TrackProcessor that allows the user to monitor, visualize, and export, the intensity profile of tracks in time lapse sequences of 2D images.

Different methods for intensity computation are provided:

DISK

intensity is considered in a circular region around the center of mass of the detection at each frame. Works also in 3D for a sphere. The radius is user-defined.

Several indicators are available: Mean, max, min, median, sum and variance of the intensity are computed along time.

DISK_BACKGROUND_CORRECTED

same as above but every time a larger-radius (user-defined) disk is used for background estimation around each detection. The background pixels are those that fall within the large radius distance from the detection, while exceeding the small radius distance.

GAUSSIAN_FIT_2D

a gaussian shape is fitted at each detection location. The spatial position of the profile is fixed but the its optimal amplitude, as well as the background level, are estimated. The standard deviation of the Gaussian shape is user-defined and must be carefully chosen.

SPOT_MASK

when the ‘Spot Detector’ and the ‘Probabilistic particle tracker’ plugins are used in combination to generate some tracks, it is possible to use the mask provided by the spot detector to evaluate locally the target intensity.

Here, several indicators are available based on the particle mask: Mean, max, min, median, sum and variance of the intensity are computed along time.

For each method, multiple channels are handled separately.Results can be visualized directly in the plugin user interface and exported to Microsoft Excel format (xls) are in a text file (.txt). In the latter case two files are generated: one that contains the intensity values as a list, and the second that contains the line numbers corresponding to the start of a new track in the first file.

The plugin is accessible through the TrackManager plugin.

Resources needing this

3 reviews on “Track Processor Intensity Profile

  1. louiselaure
    Very useful plugin, but would be great if the value of the intensity of the object detected itself in 3D could be quantified over time (and not only the disk around it, because each object has a different shape and size)
  2. Institut Jacques Monod
    Great plugin! It would be really usefull and convenient to be able to export the data in a single text file, with columns corresponding to the number of the track computed, the time, and then the different data for the intensity (mean, var, etc...) Thanks!
  3. Debora Keller
    would be great to use this to filter spots of higher intensity - or set a threshold to select only given spots/tracks and get the stats on those

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Changelog

  • Version 0.0.1.8 • Released on: 2014-09-01 19:58:56
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    Description:

    Fixed xls export bug.

  • Version 0.0.1.7 • Released on: 2014-06-06 18:03:02
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    Description:

    Fixed bug with tracks longer than the image sequence.

  • Version 0.0.1.6 • Released on: 2014-06-06 06:37:52
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    Description:

    Fixed bug with detections outside of sequence bounds.

    Replaced deprecated functions for XLS output.

  • Version 0.0.1.5 • Released on: 2013-11-20 06:33:37
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    Description:

    Fixed minor bug with color images.

  • Version 0.0.1.4 • Released on: 2013-11-20 06:28:11
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    Description:

    Fixed minor bug for color image processing and compatibility issue with latest SpotTracking plugin.

  • Version 0.0.1.3 • Released on: 2013-10-11 00:25:47
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    Description:

    Gaussian fitting of detections (in 2D) and mask averaging (if the detection mask is provided) are now available.

    Disk averaging can also be used when subtracting the background value (average over a larger disk).

    Export can now be done in text files.

  • Version 0.0.1.2 • Released on: 2013-08-07 17:41:50
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    Description:

    Fixed median computation issue.

    Intensity profile based on Gaussian shape fit is also available.

  • Version 0.0.1.1 • Released on: 2012-11-03 23:43:06
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    Description:

    Initial commit

  • Version 0.0.1.0b • Released on: 2012-11-03 23:32:45
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