biswebnode/bin/bw_projectreslicemask.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>ProjectReslice Mask</title>
	<description>Reslices and projects a 3D mask to a 2d optical image</description>
	<version>1.3.0b2</version>
	<documentation-url>https://bioimagesuiteweb.github.io/bisweb-manual</documentation-url>
	<license>GPL v2</license>
	<contributor>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>
		<string-enumeration>
			<name>Flip</name>
			<label>Flip</label>
			<description>It true project along the increasing axis</description>
			<longflag>--flip</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<string-enumeration>
			<name>Axis</name>
			<label>Axis</label>
			<description>Which axis to project along ('x', 'y', 'z', 'auto')</description>
			<longflag>--axis</longflag>
			<default>y</default>
			<element>x</element>
			<element>y</element>
			<element>z</element>
			<element>auto</element>
		</string-enumeration>
	</parameters>
	<parameters advanced="true">
		<label>Advanced</label>
		<description>Advanced Parameters</description>
		<string-enumeration>
			<name>VFlip</name>
			<label>VFlip</label>
			<description>It true flip the vertical  axis</description>
			<longflag>--flipy</longflag>
			<default>true</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<double>
			<name>Threshold</name>
			<label>Threshold</label>
			<description>The intensity threshold to detect background in shaded projection</description>
			<longflag>--threshold</longflag>
			<default>1</default>
			<constraints>
				<minimum>0</minimum>
				<maximum>100000</maximum>
			</constraints>
		</double>
		<string-enumeration>
			<name>Objectmap</name>
			<label>Objectmap</label>
			<description>If set treat image as object map and do not interpolate</description>
			<longflag>--isobjectmap</longflag>
			<default>false</default>
			<element>true</element>
			<element>false</element>
		</string-enumeration>
		<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>reference</name>
			<label>reference</label>
			<description>The 2D optical image to project mask to</description>
			<longflag>--reference</longflag>
    			<channel>input</channel>
		</image>
		<image fileExtensions=".nii.gz,.nii">
			<name>Mask</name>
			<label>Mask</label>
			<description>The 3D image or mask (thresholded at 1)</description>
			<longflag>--mask</longflag>
    			<channel>input</channel>
		</image>
		<image fileExtensions=".nii.gz,.nii">
			<name>Angio Image</name>
			<label>Angio Image</label>
			<description>Load the 3D angio image</description>
			<longflag>--angio</longflag>
    			<channel>input</channel>
		</image>
		<file>
			<name>3D Transformation 2</name>
			<label>3D Transformation 2</label>
			<description>Thetransformation used to map 3D Image to 3D optical image of individual mouse</description>
			<longflag>--angioxform</longflag>
    			<channel>input</channel>
		</file>
		<file>
			<name>2D Rotation</name>
			<label>2D Rotation</label>
			<description>The mapping from projected angio to the optical image</description>
			<longflag>--rotxform</longflag>
    			<channel>input</channel>
		</file>
	</parameters>
	<parameters>
		<label>Outputs</label>
		<description>Output Objects</description>
		<image fileExtensions=".nii.gz,.nii">
			<name>Output mask</name>
			<label>Output mask</label>
			<description>Save the projectResliced mask</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</image>
	</parameters>

</executable>