Image Menu

Image processing functions

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Mode

Allows to change mode of the shown dataset, the following options are available:

Color Channels

Perform some actions with color channels of the image

A brief demonstration is available in the following video:
https://youtu.be/gT-c8TiLcuY

It is also possible to do color channel operations from the Colors table in the View settings panel.

Contrast

Adjust contrast of the dataset. For the linear contrast stretching it is recommended to use Image Adjustment dialog available via the Display button in the View Settings panel.

A tutorial on image normalization is available in the following video:
https://youtu.be/MmBmdGtuUdM

Invert image

Invert image intensities, shortcut Ctrl+i.

A brief demonstration is available in the following video:
https://youtu.be/1DG2w5XYA18

Tools for images

In this section, MIB has tools that are targeted for manipulation of the image layer.

Image arithmetics
A brief demonstration is available in the following video:
https://youtu.be/-puVxiNYGsI
    Parameters and options:

  • Input A, specify index of the MIB container with the source image. The image in the specified container will be referenced as "A"
  • Destination class, the result of the operation will be stored in one of these classes
  • Destination buffer, the result of the operation will be stored in this container
  • Input B, an optional input to specify a second MIB container to use. The image in the specified container will be referenced as "B"
  • Input C, an optional input to specify a third MIB container to use. The image in the specified container will be referenced as "C"
  • Convert via uint32, use this checkbox to ensure that before the operations images are converted to unit32 container and highlights are not clipped away
  • Expression, an expression with arithmetic operation to perform, see below for some examples

    Examples:
  • A=A+100, increase intensity of all pixels in image A by 100
  • A=A*2, increase intensity of all pixels in image A in 2 times
  • A=A+B-C, add image B to image A and subtract image C from the result
  • A=A+mean(B(:)), add mean value of image B to image A
  • A=A-min(B(:)), subtract the min-value of image B from image A
  • A(:,:,2,:)=A(:,:,2,:)*1.4, increase image intensity of the second color channel in 1.4 times


Intensity projection
A brief demonstration is available in the following video:
https://youtu.be/hwFpS_3eP9U
    Calculate one of the following intensity projections:
  • maximum intensity projection, project the voxel with the highest value on every view throughout the volume onto a 2D image
  • minimum intensity projection, project the voxel with the smallest value on every view throughout the volume onto a 2D image
  • mean intensity projection, project the mean value of voxels on every view throughout the volume onto a 2D image
  • median intensity projection, project the median value of voxels on every view throughout the volume onto a 2D image


Select image frame
A brief demonstration is available in the following video:
https://youtu.be/sWjipmeU5eA
Detects the frame (which is an area of the same intensity that touches edge of the image) of the image. The detected area can be assinged to the Selection or Mask layers, or that area can be replaced with another color for the Image layer.

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).

A brief demonstration is available in the following video:
https://youtu.be/itbVLFm0FKQ

List of available morphological operations

Intensity profile

Generate an intensity profile of the image data. The profiles can be obtained in two modes:

For intensity profiles it is recommended to use the Measure length tool.

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