biswebnode/bin/bw_clusterthreshold.xml

A node.js implementation of BioImage Suite Web command line tools in Javascript and WebAssembly

<?xml version="1.0" encoding="utf-8"?>
<executable>
	<category>BisWEB</category>
	<title>Cluster Threshold</title>
	<description>This element will separate an image into clusters and apply binary thresholding. The image is first thresholded using a threshold. Then it is filtered to remove binary blobs that smaller than the cluster size selected.</description>
	<version>1.3.0b2</version>
	<documentation-url>https://bioimagesuiteweb.github.io/bisweb-manual</documentation-url>
	<license>GPL v2</license>
	<contributor>Zach Saltzman and Xenios Papademetris</contributor>

<acknowledgements>Funding for this work was provided by the NIH Brain Initiative under grant R24 MH114805.</acknowledgements>
	<parameters>
		<label>Standard</label>
		<description>Standard Parameters</description>
		<double>
			<name>Threshold</name>
			<label>Threshold</label>
			<description>The value to threshold at (zero out voxels below threshold)</description>
			<longflag>--threshold</longflag>
			<default>1</default>
		</double>
		<integer>
			<name>Cluster Size</name>
			<label>Cluster Size</label>
			<description>Size of clusters to form</description>
			<longflag>--size</longflag>
			<default>1000</default>
			<constraints>
				<minimum>2</minimum>
				<maximum>1000000</maximum>
			</constraints>
		</integer>
		<string-enumeration>
			<name>OutputClusterNo</name>
			<label>OutputClusterNo</label>
			<description>It true the output image is filled with the cluster number instead of the actual image values</description>
			<longflag>--outclustno</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<string>
			<name>One Connected</name>
			<label>One Connected</label>
			<description>Whether to use 6 or 26 neighbors</description>
			<longflag>--oneconnected</longflag>
			<default>true</default>
		</string>
		<string>
			<name>Keep Largest Only</name>
			<label>Keep Largest Only</label>
			<description>If true return only largest cluster</description>
			<longflag>--keeplargest</longflag>
			<default>false</default>
		</string>
		<integer>
			<name>Frame</name>
			<label>Frame</label>
			<description>Which frame from the time series to cluster (fourth dimension)</description>
			<longflag>--frame</longflag>
			<default>0</default>
		</integer>
		<integer>
			<name>Component</name>
			<label>Component</label>
			<description>Which component to take a frame from (fifth dimension)</description>
			<longflag>--component</longflag>
			<default>0</default>
		</integer>
		<string-enumeration>
			<name>Debug</name>
			<label>Debug</label>
			<description>Toggles debug logging</description>
			<longflag>--debug</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>SlicerProgress</name>
			<label>SlicerProgress</label>
			<description>Enables progress xml outputs for Slicer</description>
			<longflag>--slicerprogress</longflag>
			<default>true</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
	</parameters>
	<parameters>
		<label>Inputs</label>
		<description>Input Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>Input Image</name>
			<label>Input Image</label>
			<description>The filename for the image to be processed</description>
			<longflag>--input</longflag>
    			<channel>input</channel>
		</image>
	</parameters>
	<parameters>
		<label>Outputs</label>
		<description>Output Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>Output Image</name>
			<label>Output Image</label>
			<description>The output image</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</image>
	</parameters>

</executable>