Short Description

Extrudes ROI along time, depth and/or channels to simplify manual segmentation and tracking


This plugin takes all ROI from an input sequence, and extrudes them either to all slices (Z), frames (T) or channels (C) of the sequence.

Typical use case - 3D segmentation: By default, 2D ROI created from the user interface are assigned an undefined Z position ("all"). This plugin will replace such ROI by duplicating it on all slices of the sequence, and assiging each copy to the corresponding Z slice, allowing manual adjustment of the ROI on each slice. The final 3D segmentation can then be obtained by combining a selection of 2D ROI from the ROI panel.

The same remark applies to manual tracking, where "Z" and "slice" are replaced by "T" and "frame" respectively.

Response to comments/ratings:

  • The Z/T/C position for each created ROI is available in the ROI panel, though it might not be visible by default. This value can be made visible by ticking the corresponding column via the upper right-hand corner button of the ROI panel (the column selector).
  • Accessing the corresponding plane/frame when clicking on such a ROI is a general feature that is curently not available in Icy, and is not related to this plugin in particular. This plugin merely generates and adds ROI onto the sequence, and is not reponsible for their interaction with the display. This feature should be requested on the user forum to the developer team.

One review on “Extrude ROI

  1. S
    My mistake... indications are correct when the right option is ticked!! For the 2nd question, I posted it on the forum. Best.

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  • Version • Released on: 2013-12-12 00:37:35