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. See details here.

Crop dataset...

Crop the image and corresponding Selection, Mask, and Model layers. Cropping can be done in the Interactive, Manual or using ROI mode.

A brief demonstration is available in the following video:
https://youtu.be/PQtpYUuJwG8

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 dataset can be just cropped (the Crop button) or copied to another buffer and cropped (the Crop to button). The multiple buffer buttons buttons located at the top of the Directory Contents panel.

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.

A brief demonstration is available in the following video:
https://youtu.be/26-HROwg_JM

Transform

Transformation of dataset: image and all other layers. The following modes are possible

Add frame -> provide new width/height specify the frame by providing new width and height of the dataset.
Add frame -> provide dX/dY pads dataset in X (Frame width, px) and Y (Frame height, px) directions with a distinct number (Intensity pad value) or using various repetition methods:
  • replicate: pad by repeating border elements of array
  • circular: pad with circular repetition of elements within the dimension
  • symmetric: pad array with mirror reflections of itself
Position of the frame can be specified with the direction parameter:
  • both: pads before the first element and after the last array element along each dimension
  • pre: pad before the first array element along each dimension
  • post: pad after the last array element along each dimension
Flip horizontally - flip dataset left to right, returns the dataset with columns flipped in the left-right direction, that is, about a vertical axis
Flip vertically - flip dataset up to down, returns the dataset with rows flipped in the up-down direction, that is, about a horizontal axis
Flip Z - flip dataset in the Z dimension, returns the dataset with slices flipped in the first-last direction, that is, about a middle slice of the dataset
Flip Y - flip dataset in the T dimension, returns the dataset with time frames flipped in the first-last direction, that is, about a middle frame of the dataset
Rotate 90 degrees - rotate dataset 90 degrees clockwise diirection
Rotate -90 degrees - rotate dataset 90 degrees anti-clockwise diirection
Transpose XY -> ZX - physically transpose the dataset, so that the XY orienation, becomes ZX
Transpose XY -> ZY - physically transpose the dataset, so that the XY orienation, becomes ZY
Transpose ZX -> ZY - physically transpose the dataset, so that the ZX orienation, becomes ZY
Transpose Z <-> T - physically transpose the dataset, so that the Z orienation, becomes T
Transpose Z <-> C - physically transpose the dataset, so that the Z (depth) orienation, becomes C (color)
A brief demonstration is available in the following videos:
Flip: https://youtu.be/lGjhB-NJZMk
Rotate: https://youtu.be/WFbZn0rfb5I
Transpose: https://youtu.be/PyEXX7j6pnc

Slice

Manipulations with individual slices of the dataset. The following actions are possible

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.

A brief demonstration is available in the following video:
https://youtu.be/NZO0HG1d8ys

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.

A brief demonstration is available in the following video:
https://youtu.be/lY0XjNy4Dr8

Parameter NameDescription
ScaleXThe physical size of pixels in X
ScaleYThe physical size of pixels in Y
ScaleZThe physical size of pixels in Z
xPosCentral position of the dataset in the X plane
yPosCentral position of the dataset in the Y plane
Z PositionMinimal Z coordinate
RotationRotation 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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