Segmentation Panel¶

Overview¶

The segmentation panel is the main panel used for segmentation. It allows creating models, modifying materials, and selecting different segmentation tools.

What are the models¶

A model is a matrix with dimensions equal to those of the opened image dataset:
[1:imageHeight, 1:imageWidth, 1:imageThickness].
The model consists of materials, and each element of the model matrix (pixel) can belong only to a single material (having indices: 1, 2, 3, etc) or to an exterior (with index 0). Therefore, it is not possible to have several materials overlapping above the same pixel of the image.
Each material in the model matrix is encoded with its own index.

Model = \[1 1 0 0; 1 1 0 0; 0 0 2 2; 0 0 2 2\]

[   1 1 0 0
    1 1 0 0
    0 0 2 2
    0 0 2 2   ]

New button¶

The New button is used to start a new model. When clicked, the existing model layer will be removed.

Whenever possible, it is recommended to use models with 63 materials. If you need to work with materials exceeding 255, see this video:

• MIB 2.1: Compatible with models with more than 255 materials

For more information about different types of models visit

• Ribbon → Model → Convert type

Load button¶

The Load button is used to load a model from disk. The following formats are accepted:

• MATLAB (*.MAT): default and recommended format.
• Amira Mesh binary (*.AM): for models saved in Amira format.
• Hierarchical Data Format (*.H5): for data exchange with Ilastik.
• Medical Research Council format (*.MRC): for data exchange with IMOD.
• NRRD format (*.NRRD): for models saved in 3D Slicer format.
• TIF format (*.TIF).
• Hierarchical Data Format with XML header (*.XML).
• All standard file formats when selecting All files(*.*).

Alternatively, use Ribbon → Model → Load model or drag-and-drop a *.model file to the Image document view.

[+], [-], [>|], [Squeeze], [Recolor] buttons¶

These buttons are located in the Segmentation panel above the segmentation table and depending on the model type do different operations.

• + add a new material to the model (only for models with 63 and 255 materials).
• - delete the selected material(s) from the model (only for models with 63 and 255 materials).
• find and select the next empty index in the model (only for models with more than 255 materials). With 3D unchecked, the index is the next one free on the shown slice.
• squeeze the model—remove all empty indices and select the next available empty index (only for models with more than 255 materials). With 3D unchecked, only the shown slice is renumbered.
• 3D tick when each index is one object through the whole volume, as after stitching; untick when the numbering restarts on every slice (only for models with more than 255 materials). The setting is saved with the model; when a model saved without it is opened, MIB asks.
• regenerate colors of materials: for random colors (prompts for the random seed), Ctrl + for random colors without the prompt, for a context menu with additional settings:

• update the visualization settings Filled or Contour for both models and mask. Note! Filled visualization is more efficient.

Segmentation table¶

The Segmentation table displays the list of materials in the model.

• MIB in brief: Segmentation Table

• C: shows colors for each material. over the color box to open a color selection dialog.
• Material: lists all model materials. Right-click () to open a context menu with additional options (see below).
• Add to: defines the destination material for the Selection layer during Add (A) and Replace (R) actions.
  Linked to the selected material by default, but can be unlinked with Restrict to material or the context menu Unlink material from Add to.

• Show selected material only toggle to show only the selected material in the Image View panel.
• Rename (F2) rename the selected material, use F2 key shortcut. For models with more than 255 materials the table offers only two material slots and the name of each slot is the index of the material shown in it; renaming such a slot switches it to another material index.
• Set color change the color of the selected material (same as on the color box in the first column of the table)
• Quantify material... calculate properties for objects of the selected material. See Ribbon → Model → Model/Mask quantify.

• Materials: direct operations available for materials of the model ( Materials menu demo)

• Material to Selection: copy the selected materials to the Selection layer.

• Material to Mask copy the selected material to the Mask layer.

• Mask to Material copy the Mask layer to the selected material.

• Render render the model using variety of methods

• Unlink material from Add to prevent the Add to column from changing with material selection.

• Ctrl + A: highlight the selected material in the Selection layer for the current slice.
• Alt + A: highlight for the selected material on all slices of the dataset.

Segmentation tools dropdown¶

The Segmentation tools dropdown provides tools to separate and identify regions or objects within an image.

• 3D ball
• 3D lines
• Annotations
• Brush
• BW Thresholding
• Drag & Drop materials
• Lasso
• MagicWand-RegionGrowing
• Membrane ClickTracker
• Object Picker
• Segment-anything model
• Spot

Restrict to material checkbox¶

The Restrict to material checkbox ensures segmentation tools apply only to pixels that already belong to the material selected in the Material column of the table. Pixels belonging to any other material are not touched, even if the tool passes over them.

Restrict to mask checkbox¶

The Restrict to mask checkbox limits segmentation tools to pixels that lie inside the Mask layer. Any selection or segmentation action outside the masked area is silently ignored, making it easy to confine automated tools to a hand-drawn region of interest.

Favorite tool (D) checkbox¶

The Favorite tool (D) checkbox marks favorite selection tools for quick access with the D key.

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