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
'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
'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 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
'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
'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
'F' button
Press to fill holes in the Selection layer.
Shortcuts:
- 'F', fill holes for the current slice only
- Shift+'F', fill holes for all slices of the dataset
'Er' 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
'Di' 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
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 Er button) and dilation (the Di 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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