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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'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.

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'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.

Select fromAdd toFix Selection to MaterialMasked areaResult of subtraction
AnyMaskOFFOFFMask - Selection
Nth MaterialMaskONOFFMask within selected material - Selection
AnyNOT MaskOFFOFFAll Materials - Selection
Nth MaterialNOT MaskONOFFSelected material - Selection
Nth MaterialNOT MaskONONSelected material within the Mask - Selection

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'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.

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'C' button

Press to clear the Selection layer.

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'F' button

Press to fill holes in the Selection layer.

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'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.

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'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.

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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.

'3D' checkbox

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

'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.

'difference' checkbox

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

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.

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