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MRI_Create_Synthetic_Spots_Tool

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Volker edited this page Jul 3, 2019 · 10 revisions

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.

| example image spot | example image ground truth |

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.

the create-synthetic-spots-tool toolset

  • 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

parameter dialog

  • 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.
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