The tool creates images of 2D-spots for the evaluation and benchmarking of spot detection tools. Two populations of spots with different means and variations of the size can be created in the same image.

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The source code in git-hub can be found here.

Getting Started

To install the tool save the file create_synthetic_spots_tool.ijm into the folder macros/toolsets of your FIJI installation.

Select the ''Create synthetic spots tool'' toolset from the >> button of the ImageJ launcher.

• A left-click on the first button runs the tool with the current parameters
• A right-click on the first button allows to modify the current parameter-set.
• the n-button allows to create a new parameter-set.
• the o-button allows to open a previously stored parameter-set.

Options

• The name of the current parameter-set is displayed. When no other parameter-set has been opened the parameter-set ''default'' is used.
• type: The type of the image, 8-bit, 16-bit or 32-bit.
• image size: the width and height of the image in pixel.
• background level: the basic background intensity.
• background noise: the standard deviation of the background.
• add gradient: if checked an intensity gradient is added to the image.
• gradient: to create a gradient, the sum of the x- and y-positions is multiplied by the given factor.
• number population 1: the number of spots in population 1
• number population 2: the number of spots in population 2
• mean diameter 1: the average diameter of the spots in population 1.
• mean diameter 2: the average diameter of the spots in population 2.
• stdDev diameter 1: the standard-deviation of the diameter of the spots in population 1.
• stdDev diameter 2: the standard-deviation of the diameter of the spots in population 2.
• intensity: the mean intensity of the spots.
• sigma convolution: the standard deviation of the Gaussian kernel with which the image is convolved.
• foreground noise: the standard deviation of the intensity of the spots.
• do not touch edges: if checked the created spots will not touch the borders of the image.
• create image: if checked the ground-truth image is created in addition to the spots-image.

Managing parameter-sets

When the parameters are modified they are automatically saved to a file in the folder csst in the ImageJ-base folder. When a new parameter-set is created with the n-button, it is saved to a new file. This new parameter-set will initially contain the values of the current parameter-set. You can open saved parameter-sets with the o-button.

Results

Running the tool will create three items:

1. The spots image
2. The ground-truth image This is a two-channel image. Channel 1 contains an indexed mask of the spots of population 1 and channel 2 an indexed mask of the spots of population 2.
3. A table containing the following data:

• Class: the population to which the spot belongs
• XC, YC: the centre point of the spot
• Diameter: the diameter of the spot
• Radius: the radius of the spot
• Area: the area of the spot

Limitations

• The created images are 2D
• The creation will be slow for big images
• No PSF is used for the convolution, only a Gaussian
• Spots are created independently and the overlap can not be controlled

See also

• MRI_Count_Spot_Populations_Tool