Segmentation Tools

This panel hosts different tools that are used for the image segmentation.

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Contents

General info

This panel consists of two parts. The left hand side of the panel has two combo boxes (Selection type and Materials) that are always seen. The view of the right hand side of the panel may be different depending on the Selection type.

The segmentation tools can be selected using the Selection type combo box.

Note! Combination of Ctrl + the mouse scroll wheel allows modificaton of brush size and other segmentation tools.

The Materials combo box defines type of the visualization for models. The models may be shown either as a filled or as outlined structure. The transparency of the Model layer can be adjusted via the Transparency slider in the View Settings panel.

1. The 3D ball

Makes selection as a spherical object in the 3D space with a radius taken from the Radius, px edit box.

Note! The 3D shape of the ball is defined by the pixel dimensions, see Dataset Parameters in Menu->Dataset->Parameters.

Selection modifiers
  • None / Shift+left mouse click, will add selection with the existing one
  • Ctrl + left mouse click, will remove selection from the current
A brief demonstration is available in the following video:
https://youtu.be/ZcJQb59YzUA?t=1s

2. Annotations

A brief demonstration is available in the following video:
https://youtu.be/3lARjx9dPi0
A set of tools to add/remove annotations.

When the Annotation tool is selected the mouse click above the image adds annotation to the model. The annotations can be removed by using Ctrl + left mouse click combination.
  • The Annotation list button starts a window with the list of existing annotations. It is possible to load and save annotations to the main Matlab workspace or to a file (matlab and excel formats). See more below.
  • The Show only marker checkbox - when selected the annotation text is not displayed and the marker cross is only seen.

  • The List of labels table shows a list of annotations. The right mouse button click calls an additional popup menu that allows to add, delete or jump to the highlighted annotation
  • The Auto jump checkbox - when enabled, the image in the Image View panel is automatically shifted, thereby placing the selected annotation at the center of the image
  • The Load button imports annotations from the main Matlab workspace or load them from a file
  • The Save button exports annotations to the main Matlab workspace or to save them as a file in Matlab or Excel formats
  • The Refresh table button updates the list of annotations
  • The Delete all button removes all annotations

3. The Brush tool

Use brush to make selection. The brush size is regulated with the Radius, px edit box
A brief demonstration is available in the following video:
https://youtu.be/ZcJQb59YzUA?t=37s


Objects from different image slices may be connected using the Interpolation function (shortcut i or via Menu->Selection->Interpolate), see more in the Selection menu section.

Size of the Brush can be regulated using Ctrl + Mouse wheel.

Selection modifiers
  • None / Shift + left mouse click, will add selection with the existing one
  • Ctrl + left mouse click, will remove selection from the current, i.e. eraser mode
  • The radius of the brush in the eraser mode could be amplifier using the Eraser, x edit box.

Superpixels with the Brush tool

The Superpixels mode can be initiated by selecting the Watershed or SLIC checkbox. In the Superpixels mode the brush tool selects not individual pixels but rather groups of pixels (superpixels). While drawing the selection of the last superpixel can be undone by pressiong the Ctrl+Z shortcut.

The superpixels are calculated using the

The two additional edit boxed (N, Compact/Invert) offer possibility to modify the size of generated superpixels (see below). The values in the N edit box can be changed using the Ctrl+Alt + mouse wheel or Ctrl+Alt+Shift + mouse wheel shortcuts.

References:

The set of superpixels is individual for each magnification (especially in the SLIC mode). It is possible to define size of superpixels (the N edit box, default value 220 for SLIC, for Watershed use lower numbers) and compactness (the Compact edit box; higher compactness gives more rectangularly shaped superpixels). In the Watershed mode the Compact edit box is called Invert; when objects have dark boundaries over bright backround number in the Invert edit box should be 1 (or higher), if the objects have bright boundaries over dark background this number should be 0.

During drawing the boundaries of the superpixels for the SLIC mode are shown using the drawregionboundaries.m function written by Peter Kovesi Centre for Exploration Targeting, School of Earth and Environment, The University of Western Australia.

Note 1! The Superpixels mode is sensitive to the Adapt. checkbox in the Selection panel. When the Adapt. checkbox is selected the superpixels are selected based on the mean value of the initial selection plus/minus standard deviation within the same area multiplied by the factor specified in the Adapt. editbox of the Selection panel.

Note 2! While drawing the value in the Adapt. editbox may be changed using the mouse wheel.

Note 3! The function relies on slicmex.c that should be compiled for your operating system. Please refer to the Microscopy Image Browser System Requirements section for details.

4. The Black and White Thresholding tool

Makes black and white thresholding of the current image slice or the whole dataset (depending on status of the all checkbox).

Use the Low Lim and High Lim sliders and edit boxes to provide the threshold values.

If the Masked area check box is selected the thresholding is performed only for the masked areas of the image, which is very convenient for local black and white thresholding.

The right mouse click above the threshold sliders opens a popup menu that allows to set the step for slider movement.
A brief demonstration is available in the following video:
https://youtu.be/ZcJQb59YzUA?t=4m37s

5. The Lasso tool

Selection with a lasso, rectangle, ellipse or polyline tools.
A brief demonstration is available in the following video:
https://youtu.be/OHFdGj9uBro
How to use:
  • Press and release the selection mouse key (default: left mouse button) above the image to initialize the lasso tool
  • Press the left mouse button to start selection of areas
  • Release the left mouse button to accept selection
  • When working in the Polyline mode selection is finished using a double click of the left mouse button
When the Ctrl key is pressed during step 1, the selected area is subtracted from the existing selection.

The Lasso tool works also in 3D.

Selection modifiers:

6. The Magic Wand tool

Selection of pixels with the mouse button based on their intensities. The intensity variation is calculated from the intensity of the selected pixel and two threshold values from the Threshold edit boxes.

A brief demonstration is available in the following video:
https://youtu.be/ZcJQb59YzUA?t=1m50s
  • Connect 8 specifies the 8 (26 for 3D) connected neighbourhood connectivity
  • Connect 4 specifies the 4 (6 for 3D) connected neighbourhood connectivity
  • Radius allows defining an effective range for the magic wand

The Magic Wand works also in the 3D mode (the 3D switch in the Selection panel).

Selection modifiers for the Magic wand tool:

7. The Membrane Click Tracker tool

This tool tracks membrane-type objects by using 2 mouse clicks that define start and end point of the membrane domain.

A brief demonstration for 2D is available in the following video:
https://youtu.be/ZcJQb59YzUA?t=3m14s
A brief demonstration for 3D is available in the following video:
https://youtu.be/ZcJQb59YzUA?t=2m22s
How to use:
  • Shift + left mouse click to define the starting point of a membrane fragment
  • mouse click to trace the membrane from the starting point to the clicked point

The membrane is traced with help of Accurate Fast Marching function http://www.mathworks.se/matlabcentral/fileexchange/24531-accurate-fast-marching by Dirk-Jan Kroon, 2011, University of Twente.

Note! It is highly recommended to compile the corresponding function (see details in the Membrane Click Tracker section of the System Requirements page ), otherwise the function is very slow!

Extra parameters:

Note! When the 3D switch in the Selection panel is enabled the Membrane Click Tracker tool connects points (linearly) in the 3D space (this may be very usefull for tracing microtubules).

8. Object Picker

This mode allows fast selection of objects from the Mask or Model layers. When the Mask and Model radio buttons define the target layer for selection.

A brief demonstration is available in the following video:
https://youtu.be/mzILHpbg89E
Works also in 3D (select the 3D check box in the Selection panel).

Note! The 3D mode requires calculating statistics for the objects. Please select the material in the Select from list box and press the Recalc. Stats button (the button becomes available when the Mask->Mask statistics... or Menu->Models->Model statistics....

Possible Object Picker selection modes are:

Selection modifiers:

9. Smart Watershed

This is a simplified version of the watershed image segmentation. Please see details in the Menu->Tools->Watershed segmentation section.

In brief: a model with 2 materials is needed. One material labels the background while another labels the object of interest. The labels can be drawn using the brush tool which is activated during the Smart Watershed. Use the Ctrl+mouse wheel to change size of the brush.

  • The material that labels the background should be selected in the Background combobox
  • The material that labels the object should be selected in the Object combobox
  • Type of images should be selected in the lowest combobox. Select the Black-on-white option for electron microscopy data or White-on-black for light microscopy data
How to use:

Note 1: for multi-colored images the color channel should be selecrted in the Color channel combobox of the Selection panel.

Note 2: this tool is compatible with the ROI mode and the block mode.

10. The Spot tool

Adds a spot - a circular object with a mouse click

A brief demonstration is available in the following video:
https://youtu.be/AlCzjKuyJww
Use the Radius, px edit box to specify the radius of the spot.

Works also in 3D.

Selection modifiers
  • None / Shift + left mouse click, will add new spot to the existing ones
  • Ctrl + left mouse click, will remove selection from the current

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