Dataset Menu

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Overview

Modify parameters such as voxel sizes and the bounding box for the dataset, start the Alignment tool, or do other dataset-related actions.

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Alignment tool

Can be used to align the slices of the opened dataset or to align two separate datasets. See details here.

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Crop dataset

Crop the image and corresponding Selection, Mask, and Model layers. Cropping can be done in

• Interactive
• Manual
• ROI mode

Demonstration

• Crop dataset demonstration

Click to see details

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Resample

Resample image in any possible direction.

Demonstration

• Resample demonstration

Click to see details

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Transform

Transformation of dataset: image and all other layers.

Demonstration

• Flip demonstration
• Rotate demonstration
• Transpose demonstration

Click to see details

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Slice

Manipulations with individual slices of the dataset.

Click to see details

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Scale bar

Scale bar is a tool that allows using a scale bar printed on the image to calibrate physical size (X and Y) for pixels in MIB.

Demonstration

• Scale bar demonstration

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Bounding Box

Bounding Box defines the position of the dataset in 3D space, important for positioning in visualization software like Amira.

The bounding box can be shifted based on its minimal or central coordinates.

Demonstration

• Bounding Box demonstration

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Parameters

Modify dataset parameters: voxel sizes, frame rate for movies, and units. Entering new voxel sizes recalculates the bounding box.

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