Description

Adds overlay contour lines (and optional labels) to an image. Lines correspond to contours of constant intensity in the input image.

Parameters

Input image: Image onto which overlay will be rendered. Input image will only be updated if "Apply to input image" is enabled, otherwise the image containing the overlay will be stored as a new image with name specified by "Output image".

Apply to input image: Determines if the modifications made to the input image (added overlay elements) will be applied to that image or directed to a new image. When selected, the input image will be updated.

Add output image to workspace: If the modifications (overlay) aren't being applied directly to the input image, this control will determine if a separate image containing the overlay should be saved to the workspace.

Output image: The name of the new image to be saved to the workspace (if not applying the changes directly to the input image).

Minimum intensity: Minimum contour magnitude to display.

Maximum intensity: Maximum contour magnitude to display.

Number of contours: Number of different contour magnitudes to display. Contour lines are equally spaced in magnitude between "Minimum intensity" and "Maximum intensity".

Contour colour mode: Determines the colour look-up table to use when rendering the contours. Colour corresponds to the magnitude of that contour line:

- "Black fire" Standard ImageJ "Fire" look-up table. Values taken from "https://github.com/imagej/ImageJA/blob/master/src/main/java/ij/LookUpTable.java".

- "Ice" Standard ImageJ "Ice" look-up table. Values taken from "https://github.com/imagej/ImageJA/blob/master/src/main/java/ij/LookUpTable.java".

- "Jet" Look-up table with colour progression blue > cyan > green > yellow > orange > red.

- "Physics" Standard Fiji "Physics" look-up table. Values taken from "https://github.com/fiji/fiji/tree/master/luts/physics.lut".

- "Random" Random sequence of colours.

- "Single colour" All contour lines have the same colour, determined by the "Contour colour" parameter.

- "Single colour gradient" Single colour gradient from the colour determined by the "Contour colour" parameter (lowest magnitude contour line) and white (highest magnitude contour line).

- "Spectrum" Standard ImageJ "Spectrum" look-up table. Values taken from "https://github.com/imagej/ImageJA/blob/master/src/main/java/ij/LookUpTable.java".

- "Thermal" Standard Fiji "Thermal" look-up table. Values taken from "https://github.com/fiji/fiji/tree/master/luts/Thermal.lut".

Contour colour: Contour colour used when "Contour colour mode" is set to either "Single colour" or "Single colour gradient". Choices are: White, Black, Red, Orange, Yellow, Green, Cyan, Blue, Violet, Magenta.

Line width: Width of the rendered lines. Specified in pixel units.

Draw every N points: Specifies the interval between plotted points on the contour line. This is useful when there are a lot of contour lines in an image and where a reduction in line precision isn't problematic. Plotting fewer points will reduce the memory required to store/display overlays.

Show labels: Display magnitude values as text on each contour line. Labels are placed randomly on each contour and are oriented in line with the local contour line.

Decimal places: Number of decimal places to use when displaying numeric values.

Use scientific notation: When enabled, numeric values will be displayed in the format 1.23E-3. Otherwise, the same value would appear as 0.00123.

Label colour mode: Determines the colour look-up table to use when rendering the contour labels. Colour corresponds to the magnitude of that contour line:

- "Black fire" Standard ImageJ "Fire" look-up table. Values taken from "https://github.com/imagej/ImageJA/blob/master/src/main/java/ij/LookUpTable.java".

- "Ice" Standard ImageJ "Ice" look-up table. Values taken from "https://github.com/imagej/ImageJA/blob/master/src/main/java/ij/LookUpTable.java".

- "Jet" Look-up table with colour progression blue > cyan > green > yellow > orange > red.

- "Physics" Standard Fiji "Physics" look-up table. Values taken from "https://github.com/fiji/fiji/tree/master/luts/physics.lut".

- "Random" Random sequence of colours.

- "Single colour" All contour line labels have the same colour, determined by the "Contour colour" parameter.

- "Single colour gradient" Single colour gradient from the colour determined by the "Contour colour" parameter (lowest magnitude contour line label) and white (highest magnitude contour line label).

- "Spectrum" Standard ImageJ "Spectrum" look-up table. Values taken from "https://github.com/imagej/ImageJA/blob/master/src/main/java/ij/LookUpTable.java".

- "Thermal" Standard Fiji "Thermal" look-up table. Values taken from "https://github.com/fiji/fiji/tree/master/luts/Thermal.lut".

Label colour: Contour line label colour used when "Contour colour mode" is set to either "Single colour" or "Single colour gradient". Choices are: White, Black, Red, Orange, Yellow, Green, Cyan, Blue, Violet, Magenta.

Label size: Font size of the text label.