biswebnode/bin/bw_projectresliceimage.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 Image</title>
	<description>Project Reslices a 2D optical image via 3D to a new 2D atlas space 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>
		<integer>
			<name>Depth</name>
			<label>Depth</label>
			<description>Number of voxels to go below the brain surface</description>
			<longflag>--depth</longflag>
			<default>1</default>
			<constraints>
				<minimum>1</minimum>
				<maximum>10</maximum>
			</constraints>
		</integer>
	</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>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>Image to Reslice</name>
			<label>Image to Reslice</label>
			<description>Load the 2D image to projectReslice</description>
			<longflag>--input</longflag>
    			<channel>input</channel>
		</image>
		<image fileExtensions=".nii.gz,.nii">
			<name>Reference Image</name>
			<label>Reference Image</label>
			<description>Load the 3D reference image</description>
			<longflag>--reference</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 Transform 1</name>
			<label>3D Transform 1</label>
			<description>Load the transformation used to map Atlas to 3D Image of individual mouse</description>
			<longflag>--xform</longflag>
    			<channel>input</channel>
		</file>
		<file>
			<name>3D Transformation 2</name>
			<label>3D Transformation 2</label>
			<description>The second transformation 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 Image</name>
			<label>Output Image</label>
			<description>Save the projectResliced image</description>
			<longflag>--output</longflag>
    			<channel>output</channel>
		</image>
		<image fileExtensions=".nii.gz,.nii">
			<name>Output 2D Atlas Image</name>
			<label>Output 2D Atlas Image</label>
			<description>Save the projected 2D (from ref) image</description>
			<longflag>--ref2d</longflag>
    			<channel>output</channel>
		</image>
	</parameters>

</executable>