Dataset Menu
Modify parameters such as voxel sizes and the bounding box for the dataset, start the Alignment tool, or do some other dataset related actions.
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Contents
Alignment tool...
Can be used to align the slices of the opened dataset or to align two separate datasets. Note the limitation! - area selected for the alignment should be present on both images completely. See more in the Alignment of datasets tutorial pages (html, pdf).
Description of the panels:
- Current dataset - shows details of the opened dataset.
- Mode - allows to select alignment mode to align either slices within the opened dataset or two separate datasets.
- Method - selection of method to be used for the alignment: either normalized cross-correlation or normalized sum of squared differences.
- Second stack - available only in the Align two stacks mode allows to select the second dataset as a stack of images in a single file, in a series of files in one directory, or import a variable with the dataset from the main Matlab workspace. When the automatic mode is selected the script will calculate the shifts. The shifts however can be provided manually, when the automatic check box is unchecked. In this case it is required to find the reference point on two images, take its X and Y coordinates and calculate the shifts as: shiftX = X1 - X2 and shiftY = Y1 - Y2.
- Parameters - mainly parameters of the search window that will be used for alignment. This window can be defined manually or uploaded from the Selection layer with the Get from Selection button. The shifts of images results in empty areas that can be filled with black, white or mean color of the image. In addition, if the Align the current dataset mode is used, it is possible to import and export the list of shifts between the images.
Crop dataset...
Crop the image and corresponding Selection, Mask, and Model layers. Cropping can be done in the Interactive, Manual or using ROI mode.
When the interactive mode is selected it is possible to draw (by pressing and holding left mouse button) a rectangle area a top of the image. This area can then be used for cropping.
The values for cropping may also be provided directly by enabling the Manual mode. It is also possible to do cropping based on the selected ROI. Use the ROI panel to make them.
The cropped datasets can be placed back to the original dataset using the Fuse into existing mode of the Chop image tool available at Menu->File->Chop images...->Import.... See more here.
Resample...
Resample image in any possible direction.
Transform
Transformation of dataset: image and all other layers. The following modes are possible
- Flip horizontally - flips dataset left to right, returns the dataset with columns flipped in the left-right direction, that is, about a vertical axis.
- Flip vertically - flips dataset up to down, returns the dataset with rows flipped in the up-down direction, that is, about a horizontal axis.
- Flip Z - flips dataset in the Z dimension, returns the dataset with slices flipped in the first-last direction, that is, about a central slice of the dataset.
- Rotate 90 degrees - rotates dataset 90 degrees clockwise diirection.
- Rotate -90 degrees - rotates dataset 90 degrees anti-clockwise diirection.
- Transpose XY -> ZX - physically transposes the dataset, so that the XY orienation, becomes ZX
- Transpose XY -> ZY - physically transposes the dataset, so that the XY orienation, becomes ZY
- Transpose ZX -> ZY - physically transposes the dataset, so that the ZX orienation, becomes ZY
Slice
Manipulations with individual slices of the dataset. The following actions are possible
- Delete slice... - removes desired slice(s) from the dataset. For example, type " 5:10 " to delete all slices from slice 5 to slice 10.
Scale bar
Scale bar is a tool that allows to use a scale bar printed on the image to calibrate physical size (X and Y) for pixels in MIB.
How to use:
Bounding Box...
Bounding Box defines position of the dataset in the 3D space; the bounding box information is important for positioning of datasets in the visualization software, such as Amira. The bounding box can be shifted based on its minimal or centeral coordinates. The current coordinates of the bounding box are shown under the Current Bounding Box text.
Attention! For 3D images the bounding box is calculated as the smallest box containing all voxel centers, but not all voxels as is! I.e. it's defined by the voxel centers, which means that a 1/2 voxel on both sides of the bounding box are subtracted, resulting in a bounding box that is 1 voxel smaller in all three directions.
- X, Y, Z, min - defines minimal coordinates of the bounding box
- X, Y, center - defines central coordinates of the dataset. When the central coordinates are used the X, min and Y, min coordinates are going to be recalculated.
- *X, Y, Z max - maximal values of the bounding box. When entered together with the X, Y, Z min coordinates - MIB recalculates the voxel sizes.
- Stage rotation bias, degrees - implemented only when entering X, Y center coordinates. Allows recalculation of the coordinates for the cases when the stage has some rotation bias, for example, Gatan 3View has 45 degrees stage bias.
- Import from Clipboard, parses text in the system clipboard and automatically extracts the following parameters (syntax: [ParameterName] = [ParameterValue]):
Parameter Name | Description |
ScaleX | The physical size of pixels in X |
ScaleY | The physical size of pixels in Y |
ScaleZ | The physical size of pixels in Z |
xPos | Central position of the dataset in the X plane |
yPos | Central position of the dataset in the Y plane |
Z Position | Minimal Z coordinate |
Rotation | Rotation BIAS Note! Since it is designed for Gatan 3View system MIB adds 45 degrees to the detected rotation value |
Example of text that can be copied to the system clipboard for automatic detection of paramters:
Parameters
Modifies parameters of the dataset: voxels sizes, frame rate for movies and units. Enter of new voxels results in recalculation of the bounding box.
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