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Slice menu

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Slice Dataset Dialog

Manipulate individual slices or frames of the dataset, including the image and corresponding Selection, Mask, and Model layers.

Demonstration:

Select an action from Menu->Dataset->Slice to perform operations such as copying, inserting, swapping, or deleting slices or frames.

Copy Slice

Copy Slice

This action copies a slice from one position to another within the same dataset:

  • Replace or insert slice at the destination choose the operation mode from the dropdown:
  • Replace overwrite the destination slice with the source slice.
  • Insert insert the source slice at the destination position, shifting subsequent slices forward.

  • Swap swap positions of the two specified slices

  • Source Slice enter the slice number to copy (e.g., 5 for the fifth slice).

  • Destination Slice enter the target slice number, use 0 to insert the slice at the end of the dataset

This is useful for duplicating a slice to correct errors (e.g., replacing a corrupted slice) or rearranging data (e.g., inserting a reference slice). The image and all layers are copied, maintaining alignment across the dataset.

Insert Empty Slice(s)

Insert Empty Slice(s)

This action inserts one or more uniformly colored slices at a specified position:

  • Dimension dimension where an empty slice needs to be inserted
  • Destination slice index enter the slice number where the new slice(s) will be inserted (e.g., 10 to insert at position 10, 0 to insert at the end of the dataset).
  • Number of Slices to Insert specify how many slices to insert in the field (e.g., 1 for a single slice).
  • Intensity of background define the intensity or color of the new slice(s) (e.g., 0 for black, 255 for white in grayscale).

Inserting empty slices is ideal for adding placeholders, creating gaps for manual annotations, or preparing datasets for further processing. The inserted slices are applied to the image and all layers, shifting existing slices as needed to accommodate the new ones.

Interval Slicing

Interval Slicing

This action extracts every N-th slice to create a new dataset:

  • Dimensions select re-slicing dimension: depth, height, width**
  • Slice index(es) to keep provide the step size (e.g., 1:2:end to keep every second slice, 1:5:end to keep every fifth slice).

The current dataset is replaced with the selected slices, reducing the selected dimension. This is useful for downsampling a stack to reduce data size, focusing on key slices, or preparing data for preparation of dataset for training of CNNs. The image and layers are updated to include only the extracted slices, preserving their content.

Swap Slices

Swap Slice

This action swaps the positions of two or more slices within the dataset: see Copy Slice for details

Delete Slice(s)

Delete Slice

This action removes one or more slices from the dataset:

  • Dimensions select dataset dimension: depth, height, width, time**
  • Slice index(es) to delete specify indices of slices to delete.

Deleting slices reduces the dataset’s Z-dimension, which is helpful for removing defective slices (e.g., blurry or empty ones) or trimming irrelevant data. The image and layers are updated, with remaining slices renumbered to close the gaps created by deletion.

Delete Frame(s)

This action removes one or more frames from a time series. See Delete Slice(s) for details.

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