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StructureTensor2D

by Pierre Weiss

This plugin allows visualizing the output of the structure tensor in 2D as a field of ellipses. This can be useful to analyze geometrical configurations of cells/nuclei in dense tissues for instance. Ellipses are displayed on a regular grid with step size fixed by the user. The user can set an ROI to specify where the ellipses should be displayed.

The plugin should be used with Java 7 or above since there are multi-threaded pieces of codes (JTransforms of Piotr Wendykier).

This plugin was developed mostly by Guillaume De Brito during an internship in 2015. It is maintained by Pierre Weiss.

In case you use this plugin for a publication, please cite:
Structure tensor based analysis of cells and nuclei organization in tissues.
W. Zhang, J. Fehrenbach, A. Desmaison, V. Lobjois, B. Ducommun, P. Weiss*,
B. Kovac, A. Le Guelvouit IEEE TMI (2015).

Publication Id
ICY-T6U2R1
See technical details
View complete changelog

Documentation

General documentation

 

This plugin allows visualizing the output of the structure tensor in 2D as a field of ellipses, segments or both. This can be useful to analyze geometrical configurations of cells/nuclei in dense tissues for instance. Ellipses are displayed on a regular grid with step size fixed by the user. The user can set an ROI to specify where the ellipses should be displayed.

The plugin should be used with Java 7 or above since there are multi-threaded pieces of codes (JTransforms of Piotr Wendykier).
This plugin was developed mostly by Guillaume De Brito during an internship in 2015. It is maintained by Pierre Weiss.

In case you use this plugin for a publication, please cite:
Structure tensor based analysis of cells and nuclei organization in tissues.
W. Zhang, J. Fehrenbach, A. Desmaison, V. Lobjois, B. Ducommun, P. Weiss*,
B. Kovac, A. Le Guelvouit IEEE TMI (2015).


How to use it

The plugin needs an opened image with dimensions Z, T and C equal to 1 to work properly.

  • Input Sequence : Choose one of your opened sequences to use the plugin with.
  • ROI? : Check this box to display the result only on the selected ROIs.
  • Type : Check the type of result you want to display. If you select multiple types, one image will be displayed for each
    • Ellipse
    • Segment
    • Both
  • Display anisotropy image : This option will display an additional image reprenting the anisotropy of the image.
  • Sigma : The value of Sigma represents the characteristic size of the ellipses, or segment, to analyze
  • Delta : The value of Delta represents the step size between each ellipse or segment

Examples

Here you can see the comparison between one original image (Note the deformations around the cells, and their repercussion in the resulting image), and its result with segments, and with Sigma = 15 and Delta = 30.

Original ImageResulting Image

We can also zoom in the resulting image to get a closer look to the segments orientation. Here we also used a ROI so we can avoid displaying segments in the black part of the image. We also reduced Delta to a value of 10, so the segments are much shorter and closer to each other.

Closer look on the results