Segmentation Tools
This panel hosts different tools that are used for the image segmentation.
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Contents
The 3D ball
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Makes selection as a spherical object in the 3D space with a radius taken from the
Radius, px edit box. The Eraser, x edit box modifies
increse of the 3D ball eraser, when holding the Clrl key. A brief demonstration is available in the following video: ![]() Note! The 3D shape of the ball is defined by the pixel dimensions, see Dataset Parameters in Menu->Dataset->Parameters. Selection modifiers
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The 3D lines
A demonstration is available on youtube:
https://youtu.be/DNRUePJiCbE
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The 3D lines tool can be used to draw lines in 3D and arrange them as
graphs or skeletons. The 3D lines composed of Nodes (Vertices)
connected with Edges (a line that connect two nodes). Separated from each
other sets of 3D lines organized into separate trees.
Modification of nodes is possible using mouse clicks. To increase flexibility, the clicks can be extended with key-modifiers, such as Shift, Control, Alt. Each action can be configured depending on needs. Please refer to a table below for various options: Available actions
Press the Table view button to start a window which tables that describe the 3D lines (see below). |
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Table with the list of trees The upper table shows the list of trees and number of nodes that compose each tree. Each tree should have an unique name! Right mouse click starts a popup menu with various options:
Space between the tables
Nodes table The table shows list of nodes and offers multiple actions via a popup menu:
Edges table The table shows list of edges; certain actions available via a popup menu:
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Annotations
A brief demonstration is available in the following videos:
https://youtu.be/3lARjx9dPi0
https://youtu.be/6otBey1eJ0U
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A set of tools to add/remove annotations. Each annotation allows to mark specific location in the dataset, assign a label and a value to it 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.
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List of annotations window
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The Brush tool
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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: ![]() 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
Interpolation settings, press to start a dialog that allows to modify the interpolation settings. The settings can also be modified from the Preference dialog and the type can be switched using a dedicated button in the toolbar. ![]() |
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
- SLIC (Simple Linear Iterative Clustering, good for objects with distinct intensities) algorithm written by Radhakrishna Achanta et al., 2015 , Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland.
- Watershed (good for objects with distinct boundaries).
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:
- Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine S?sstrunk, SLIC Superpixels Compared to State-of-the-art Superpixel Methods, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274 - 2282, May 2012.
- Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine S?sstrunk, SLIC Superpixels, EPFL Technical Report no. 149300, June 2010.
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.
The Black and White Thresholding tool
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Makes black and white thresholding of the current image slice or the
whole dataset (depending on status of the 3D and 4D checkboxes).
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. The Adaptive checkbox starts adaptive threshoding with the 'Sensitivity' and 'Width' parameters modified by the scroll bars. |

Drag & Drop materials
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Shift MIB layers (selection, mask, model) to left/right/up/down
direction. The tool allows to move individual 2D/3D objects as well as
complete contents of the layers in 2D and 3D.
A combobox offers possibility to choose the layer to be moved. Mouse click or use of the buttons in the panel move the selected layer left/right/up/down by the specified number of pixels. A brief demonstration is available in the following video: ![]() |
Start by | Modifier | 3D checkbox | Action |
Mouse click over an object | Control | Unchecked | Move the selected object in 2D |
Mouse click over an object | Control | Checked | Move the selected 3D object. Note! Only for Matlab version 2017b and newer |
Mouse click | Shift | Unchecked | Move all objects on the shown slice, i.e. 2D movement |
Mouse click | Shift | Checked | Move all objects on all slices, i.e. 3D movement |
Left/Right/Up/Down buttons | - | Unchecked | Move all objects on the shown slice by the specified number of pixels, i.e. 2D movement |
Left/Right/Up/Down buttons | - | Checked | Move all objects on all slices by the specified number of pixels, i.e. 3D movement |
The Lasso tool
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Selection with a lasso, rectangle, ellipse or polyline tools.
A brief demonstration is available in the following video: ![]() How to use:
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The Lasso tool works also in 3D.
The Magic Wand+Region Growing 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 Variation edit boxes.
A brief demonstration is available in the following video:
https://youtu.be/ZcJQb59YzUA?t=1m50s
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The Magic Wand works also in the 3D mode (the 3D switch in the Selection panel).
Selection modifiers for the Magic wand tool:
- None + left mouse click, will replace the existing selection with the new one.
- Shift + left mouse click, will add new selection to the existing one.
- Ctrl + left mouse click, will remove new selection from the current.
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
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How to use:
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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:
- The Scale edit box - during the tracing the image gets enhanced by taking into account intensities of the starting and ending points img(img>min([val1 val2])-diff([val1 val2])*options.scaleFactor) = maxIntensity;
- The Width edit box - defines a width of the resulting trace
- The BlackSignal checkbox defines whether the signal is Black on White, or White on Black
- The Straight line checkbox - when checked, the points are connected with a straight line
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).
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
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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:
- 1. Mouse click: selects object from the Mask/Model layers with mouse click. Note 1! Separation of objects is sensitive to the connected neighbourhood connectivity parameter from the Magic Wand tool; Note 2! In the 3D mode the function uses object statistics that is generated by pressing the |Recalc. Stats| button. If the Mask/Model layers have been changed press the |Recalc. Stats| button again.
- 2. Lasso: selects object with lasso tool (Press first [None/Shift/Ctrl] + Right mouse button, then hold the left mouse button while moving mouse around). Can also make selection for the whole dataset if the |3D| checkbox in the Selection panel is checked.
- 3. Rectangle or Ellipse: these tools work in similar to the lasso tool manner but give rectangle or ellipsoid selection. Works also in 3D.
- 4. With the Polyline option the selection is done by drawing a polygon shape point by point. Start drawing with right mouse button and finish with a double click or right mouse click. Works also in 3D.
- 5. Use Brush to select some of the masked/model areas. Size of the Brush is defined in the Brush edit box.
- 6. Mask within selection with mouse click on the image makes a new selection that is an intersection of the existing selection and the mask/model layer. With Ctrl+mouse click the new selection is Selection -minus- Mask. This action is sensitive to the 3D checkbox state in the Selection panel.
Selection modifiers:
- None / Shift + left mouse click, will add selection with the existing one.
- Ctrl + left mouse click, will remove selection from the current.
The Spot tool
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Adds a spot - a circular object with a mouse click A brief demonstration is available in the following video: ![]() Use the Radius, px edit box to specify the radius of the spot. Works also in 3D. Selection modifiers
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