Documentation/Nightly/Extensions/IASEM - Revision history

Blowekamp at 16:55, 6 November 2014

2014-11-06T16:55:06Z

2014-11-06T16:51:11Z

2014-01-09T23:26:40Z

2014-01-09T23:18:41Z

2013-08-29T19:25:43Z

2013-08-07T17:38:28Z

2013-08-06T18:27:08Z

Image Size Reduction

2013-08-06T18:23:15Z

Image Size Reduction

2013-08-06T18:19:12Z

BinShrink Image Filter

2013-08-06T18:18:07Z

BinShrink Image Filter

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 After an area of interest is visually  determine the ROI tool can be used to define a region of interest, which can be specified as the "Image ROI" and a sub-volume can be loaded at a higher resolution.
 ===DoubleThreshold Editor Effect===
 ===BinaryWatershed Editor Effect===

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 * SpacingAwareCurvatureDiffusion Image Filter
 * IASEM Import
 * DoubleThreshold Editor Effect
 * BinaryWatershed Editor Effect

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 ===SpacingAwareCurvatureDiffusion Image Filter===
 ===DoubleThreshold Editor Effect===
 ===BinaryWatershed Editor Effect===

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 * BinShrink Image Filter
 * SpacingAwareCurvatureDiffusion Image Filter
 * DoubleThreshold Editor Effect
 * BinaryWatershed Editor Effect
 <!-- ---------------------------- -->

← Older revision		Revision as of 19:25, 29 August 2013
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	IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).		IASEM stands for ion-abrasion scanning electron microscopy, some times also call dual-beam or focused ion-beam scanning electron microscopy (FIBSEM).
		+
		+	Sample data can be downloaded from http://placid.nlm.nih.gov/community/22, in particular the dateset below is the [http://placid.nlm.nih.gov/community/22 GoldBeads].

	<gallery widths="200px" perrow="4">		<gallery widths="200px" perrow="4">

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 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Walk Through}}
-===Image Size Reduction===
+===Multi-Resolution Label Map Segmentation===
 When a data set is too large we can use a combination of tools and modules to help speed things up. We can BinShrink the gray scale to reduce resolution and size, and we can crop the region of interest. Cropping, however distorts the dimensions of the volume and we must resample it to match the original gray scale when putting them back together.
 {|

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 #Apply the BinShrink Image Filter.
 #Create a Region of Interest (ROI) using the Fiducial Module in the Slicer Toolbar.
-#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop the region of interest.
+#Use the [[Documentation/{{documentation/version}}/Modules/CropVolume|Crop Volume]] module to crop the region of interest. '''Make sure to check the box for Voxel based cropping, since this is a gray scale and not a label map.'''
 #Apply  [[Documentation/{{documentation/version}}/Modules/Editor#Threshold|Threshold Effect]], or any other editing technique, to your gray scale image to create a label map.
 #[[Documentation/{{documentation/version}}/Modules/BRAINSResample|Resample]] the label map so its dimensions match those of the gray scale image.

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 {{documentation/{{documentation/version}}/extension-section|Walk Through}}
 ===BinShrink Image Filter===
 {|
 |[[Image:OriginalGoldGrayscale.png|thumb|Step 1: Original gray scale image.]]