Selection Panel

Selection panel contatins tools for manipulation with the Selection layer. The Selection is one of three main segmentation layers (Model, Selection, Mask) which can be used in combibation with other layer. See more about segmentation layers in the Data layers of Microscopy Image Browser section.

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Contents

 

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The A button

Press to add Selection layer to the selected Model or Mask layer, the destination layer is selected using Add to list box in the Segmentation panel.

Shortcuts

• A, do addition for the currently shown slice only
• ⇧ Shift + A, do addition for all slices of dataset
• ⇧ Shift+Alt + A, do addition for all slices of dataset including the time dimension

 

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The S button

Press to subtract Selection layer from the selected Model or Mask layer, the layer for subtraction is selected using Add to list box in the Segmentation panel.

Possible useage combinations

Select from	Add to	Fix Selection to Material	Masked area	Result of subtraction
Any	Mask	OFF	OFF	Mask - Selection
Nth Material	Mask	ON	OFF	Mask within selected material - Selection
Any	NOT Mask	OFF	OFF	All Materials - Selection
Nth Material	NOT Mask	ON	OFF	Selected material - Selection
Nth Material	NOT Mask	ON	ON	Selected material within the Mask - Selection

Shortcuts

• S, do subtraction for the current slice only
• ⇧ Shift+S, do subtraction for all slices of the dataset
• ⇧ Shift+Alt+S', do subtraction for all slices of dataset including the time dimension

 

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The R button

Press to replace the selected in the Add to list box material (that could be either marerial of the model or the Mask layer) with the contents of the Selection layer. The Add to list box is located in the Segmentation panel. Note! The Replace is sensitive to the state of the [✓] Masked area checkbox in the Segmentation panel.

Shortcuts

• R, do replacement for the current slice only
• ⇧ Shift+R, do replacement for all slices of the dataset
• ⇧ Shift+Alt+R, do replacement for all slices of dataset including the time dimension

 

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The C button

Press to clear the Selection layer.

Shortcuts

• C, clear the current slice only
• ⇧ Shift+C, clear Selection for all slices of the dataset
• ⇧ Shift+Alt+C, clear Selection for all slices of dataset including the time dimension

 

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The F button

Press to fill holes in the Selection layer. The operation can be triggered automatically when [✓] auto fill is checked.

Shortcuts

• F, fill holes for the current slice only
• ⇧ Shift+F, fill holes for all slices of the dataset
• ⇧ Shift+Alt+F, fill holes for all slices of dataset including the time dimension

 

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The Erode button

Press to perform binary erosion=shrinkage (imerode MATLAB function) of the Selection layer with the Strel size defined in the Strel edit box. The erotion works also in 3D, check the 3D check box. To get result as a difference between the current and the eroded selections check the [✓] difference checkbox.

Shortcuts

• Z, erode Selection for the current slice only
• ⇧ Shift+Z, erode Selection for all slices of the dataset
• ⇧ Shift+Alt+Z, erode Selection for all slices of dataset including the time dimension

 

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The Dilate button

Press to perform binary dilation (expansion) (imdilate MATLAB function) of the Selection layer with the Strel size defined in the Strel edit box. To dilate in 3D check the [✓] 3D checkbox in the Selection panel. To get result as a difference between the current and the dilated selections check the [✓] difference checkbox.

The dilation is also implemented in the Adaptive mode (switched ON with the [✓] Adapt checkbox), when the amount of expansion is limited by the image intensities in the expanded areas. The magnitude of the adaptation parameter is regulated with an edit box next to the Adapt. check box.

Shortcuts

• X, dilate Selection for the current slice only
• ⇧ Shift+X, dilate Selection for all slices of the dataset
• ⇧ Shift+Alt+X, dilate Selection for all slices of dataset including the time dimension

Color channel combo box

This combo box defines the color channel that will be used for the selection with the tools in the Segmentation panel.

The [✓] 3D checkbox

Check it to do some of the image and Mask/Model manipulations in 3D.

The [✓] auto fill checkbox

Check it to fill shapes drawn using the brush tool (and eraser) automatically after release of the left mouse button

The [✓] adapt. checkbox

Select to perform adaptive dilation or selection of the supervoxels when using the Brush tool. When the shapes are dilated or supervoxels are selected the function calculates mean intensity values and standard deviation within the original shape. During dilation/brush only pixels that have intensities mean+-standard deviation multiplied with Adapt. coefficients are taken.

The [✓] difference checkbox

When checked the results of Erosion and Dilation will be the differences between existing and eroded/dilated Selection layers.

The Strel edit box

Defines size of the structural element that is used during erosion (the Erode button) and dilation (the Dilate button). The size of the Strel element can be specified as a single number or as two semi-colon separated numbers. For example entering [ 3; 5 ] defines size of the Strel element as XY = 3 x 5 pixels for 2D, or as 3 x 3 x 5 pixels for 3D.

Right mouse click opens a dropdown menu

When clicking on an empty area of within this panel an additiona menu appears allowing to hide/show the following panels. This allows to increase space occupied by the Image view panel

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Published with MATLAB® R2023b and subsequently processed by prettify_MATLAB_html V6.8b2