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GREG Graphical Random Ellipsoids Generator

by Biomedical Imaging Group

This plugin generates 2D or 3D time sequences with elliptical objects moving over time in them. Use it to test your cell tracking algorithms.

Publication Id
ICY-B7R6O6
See technical details
View complete changelog

Documentation

GREG Icon

GREG:
Graphical Random Ellipsoids Generator

1. Cells Properties

Cells Count

Number of cells to generate.

Cells Radius Range Average radius of the cells.
Cells Velocity Range Initial speed of the cells. Cells have a brownian behaviour.
Cells Eccentricity Range 1 Describes the aspect of the cell. A value close to 0 leads to a circle and a value close to 1 leads to an ellongated cell.
Cells Eccentricity Range 2 Same as above. This parameter only makes sense in 3D.
Cells Blur Radius Standard deviation of the Gaussian blur applied to the cells.

 

2. Noise Properties

The background of the image is generated using an accumulation of noisy images (the noise follows the distribution given by the user) at different scales. It is then mixed with the cells using some blending mode  (the usual blending modes are available).

Remark: Icy auto-scales the image levels. Therefore, some parameters, like noise intensity, may seem to not work properly. In this case, just uncheck the "Auto bounds" button in the "Lookup Table", and manually reset the bounds.

Noise Levels Number of layers of noise to generate.
Noise Intensity Intensity of the background. A value of 0 means no noise at all.
Blending Mode Specifies the method used to add the noise to the cells.
Noise Profile Distribution of the noise used to generate each level.
A left click adds a control point. A right click removes a control point. Just drag a point to move it.

 

Noise Example Noise Example Noise Example
  Some noisy background examples  

 

3. Sequence Properties

Background Value Gray level of the background (without noise). 0 means black and 1 white.
Foreground Value Range Gray level of the cells.
Image Width -
Image Height -

Image Depth

A 3D image is a an image with a depth greater than 1.
Sequence Duration Number of frames in the generated sequence.
Add cells ROI If checked, adds the cells ROI to the sequence.
Use Track Manager If checked, creates tracks for the Track Manager plugin.

 

Output Example

Output Example