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TED The Ellipsoid Detector

by Biomedical Imaging Group

This plugin is the first stage of a cell tracking pipeline using parametric snakes. See the plugin snake tracker for more details, and to download the whole pipeline in one click.

Publication Id
ICY-T9X5X3
See technical details
View complete changelog

Documentation

TED Icon

TED:
The Ellipsoid Detector

Presentation

TED is a plugin for ICY detecting ellipsoidal shapes in 2D and 3D images. It outputs a list of ROI.

TED was designed to work with the Active Cells and Active Cells Tracker plugins and can be used in a Protocols pipeline (see PACT: a Pipeline for Automated Cell Tracking).

Parameters

Radius Range
Expected radius range of the cells to detect.
Target Brightness Indicates if the the cells are darker than the background (Dark) or the opposite (Bright).
Threshold Controls the segmentation step. A small value leads to the detection of less contrasted objects.
Optimize Descriptors Indicates if the descriptors of the detected cells have to be optimized.
Maximum number of iterations Maximum number of iterations during the optimization process.

 

Remark: The preview checkbox allows the user to see the result of the segmentation step. It could be a good idea to use that in order to play with the threshold parameter, before starting the whole process.

 

TED Result

Final output