Image Menu
Image processing functions
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Contents
Mode
Allows to change mode of the shown dataset, the following options are available:
- Grayscale, converts image to grayscale by removing any color information.
- RGB Color, converts image to the RGB color space.
- HSV Color, converts image to the HSV (hue, saturation, value) color space.
- Indexed, converts image to the indexed colors (not implemented for True Color images).
- 8 bit, convert dataset to the 8 bit format, the image intensities are scaled to preserve contrast of the original dataset.
- 16 bit, convert dataset to the 16 bit format, the image intensities are scaled to preserve contrast of the original dataset.
- 32 bit, convert dataset to the 32 bit format, the image intensities are scaled to preserve contrast of the original dataset.
Color Channels
Perform some actions with color channels of the image
- Swap channels..., allows to swap two color channels between each other
- Delete channel..., deletes specified color channel from the dataset.
It is also possible to delete color channel by pressing the Ctrl key and clicking on the desired color channel in the Colors table in the View settings panel.
Contrast
Adjust contrast of the dataset
- Linear contrast, linear contrast adjustment for current or all slices. It is however recommended to use the Display button in the View settings panel.
- Contrast-limited adaptive histogram equalization for current image only, CLAHE contrast equalization for the current slice. For details see documentation for Matlab function adapthisteq.
- Contrast-limited adaptive histogram equalization for all images, CLAHE contrast equalization for the whole dataset. For details see documentation for Matlab function adapthisteq.
- Normalize layers, normalization of image intensities between the slices. A) calculates mean intensity and standard deviation (std) for the whole dataset; B) calculates mean intensities and standard deviation for each image; C) shifts each image based on difference between mean values of that image and the whole dataset, plus stretches it based on ratio between standard deviation of the whole dataset and each image
- Normalize layers based on masked areas, essentially similar to the Normalize layers mode, except that all values are calculated from the masked areas only.
- Normalize based on masked background, normalizes image intensities between the slices using background areas that should be masked. A) calculates mean intensity for the masked area for the whole dataset; B) calculates mean intensities for the masked area for each image; C) shifts each image based on difference between mean values of the image and the whole dataset
Invert image
Invert image intensities, shortcut Ctrl+i.
Morphological operations
This section contains number of morphological operations that can be applied to images. The processed image may be also added or subtracted from the existing image (see the settings in the Additional action to the result panel).
List of available morphological operations
- Bottom-hat filtering (imbothat) computes the morphological closing of the image (using imclose`) and then subtracts the result from the original image
- Clear border (imclearborder) suppresses light structures connected to image border
- Morphological closing (imclose) morphologically closes the image: a dilation followed by an erosion
- Dilate image (imdilate)
- Erode image (imerode)
- Fill regions (imfill) fills holes in the image, where a hole is defined as an area of dark pixels surrounded by lighter pixels
- H-maxima transform (imhmax) suppresses all maxima in the image whose height is less than H
- H-mminima transform (imhmin) uppresses all minima in the image whose depth is less than H
- Morphological opening (imopen) morphologically opens image: an erosion followed by a dilation
- Top-hat filtering (imtophat) computes the morphological opening of the image (using imopen) and then subtracts the result from the original image
Intensity profile
Generate an intensity profile of the image data. The profiles can be obtained in two modes:
- Line
- Arbitrary
Histogram
Show histogram of image intensities, see details in imcontrast function of Matlab.
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