Documentation/Nightly/Extensions/IASEM

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Introduction and Acknowledgements

Acknowledgments: This work is supported by NLM, and the Slicer Community. Author: Bradley Lowekamp Contact: Bradley Lowekamp <email>blowekamp@mail.nih.gov</email> License: Apache License 2.0

The National Library of Medicine   National Alliance for Medical Image Computing (NA-MIC)

Extension Description

This extension is a compilation of modules which are useful for segmentation and processing of IASEM Electron Microscopy images. It adds modules which help in general with segmenting large data sets, and has components to deal with images in multi-resolutions.

IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).

• 

  Segmentation of Gold particles.

Modules

• BinShrink Image Filter
• SpacingAwareCurvatureDiffusion Image Filter
• DoubleThreshold Editor Effect
• BinaryWatershed Editor Effect

Use Cases

BinShrink Image Filter

Bin Shrink is one of the modules used to help ease the process of segmentation. By stipulating a neighborhood size, 5x5x5 for example, it will average the neighboring pixels within that 5x5x5 region and turn them into one pixel. Applying the Bin Shrink will result in reduced resolution and a less noisy image. Based on the features you want to segment, you can apply a more aggressive bin or a less aggressive bin based on the complexity of your features of interest. Binning the image does not significantly affect the quality of the image, it also reduces the amount of memory the computer needs to process the data, so the more an image is binned the faster slicer will work and the more free memory you will have.

Original gray scale image.

After running the BinShrink by a factor of 5x5x5.

Similar Extensions

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