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annotate skimage.xml @ 0:33e3d7e8283f draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
author imgteam
date Fri, 12 Dec 2025 22:22:02 +0000
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children a683c87ec261
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33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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1 <tool id="ridge_filter_skimage" name="Apply ridge filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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2 <description>with scikit-image</description>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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3 <macros>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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4 <import>creators.xml</import>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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5 <import>tests.xml</import>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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6 <token name="@TOOL_VERSION@">0.22.0</token>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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7 <token name="@VERSION_SUFFIX@">1</token>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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8 <xml name="base_params">
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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9 <param name="black_ridges" type="select" label="Mode of operation">
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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10 <option value="true" selected="true">Enhance dark ridges (low image intensities)</option>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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11 <option value="false">Enhance bright ridges (high image intensities)</option>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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12 </param>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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13 <param name="sigma_min" type="float" value="1" min="0.1" label="Minimum sigma" help="Lower bound of the scale for multi-scale analysis."/>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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14 <param name="sigma_max" type="float" value="3" min="0.1" label="Maximum sigma" help="Upper bound of the scale for multi-scale analysis."/>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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15 <param name="num_sigma" type="integer" value="10" min="2" label="Number of sigma steps for multi-scale analysis"/>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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16 </xml>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
imgteam
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17 <xml name="frangi_params">
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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18 <expand macro="base_params"/>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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19 <param name="alpha" type="float" min="0" value="0.5" label="Alpha"
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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20 help="Frangi correction constant that adjusts the filter's sensitivity to deviation from a plate-like structure."/>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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21 <param name="beta" type="float" min="0" value="0.5" label="Beta"
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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22 help="Frangi correction constant that adjusts the filter's sensitivity to deviation from a blob-like structure."/>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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23 </xml>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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24 </macros>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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25 <creator>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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26 <expand macro="creators/bmcv"/>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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27 <expand macro="creators/kostrykin"/>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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28 </creator>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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29 <edam_operations>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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30 <edam_operation>operation_3443</edam_operation>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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31 </edam_operations>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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32 <xrefs>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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33 <xref type="bio.tools">galaxy_image_analysis</xref>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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34 <xref type="bio.tools">scikit-image</xref>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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35 <xref type="biii">scikit-image</xref>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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36 </xrefs>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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37 <requirements>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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38 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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39 <requirement type="package" version="0.5.2">giatools</requirement>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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40 </requirements>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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41 <command detect_errors="aggressive"><![CDATA[
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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42
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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43 python '$__tool_directory__/filter_skimage.py'
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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44
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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45 '$input'
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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46 '$output'
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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47 '$params'
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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48
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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49 ]]></command>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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50 <configfiles>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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51 <configfile name="params"><![CDATA[
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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52 {
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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53
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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54 #if $filter.filter_type == "frangi" or $filter.filter_type == "hessian" or $filter.filter_type == "meijering" or $filter.filter_type == "sato"
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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55 "black_ridges": $filter.black_ridges,
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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56 "sigma_min": $filter.sigma_min,
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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57 "sigma_max": $filter.sigma_max,
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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58 "num_sigma": $filter.num_sigma,
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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59 #end if
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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60
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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61 #if $filter.filter_type == "frangi" or $filter.filter_type == "hessian"
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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62 "alpha": $filter.alpha,
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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63 "beta": $filter.beta,
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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64 #end if
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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65
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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66 #if $filter.filter_type == "laplace"
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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67 "ksize": $filter.ksize,
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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68 #end if
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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69
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70 "dtype": "$dtype",
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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71 "filter_type": "$filter.filter_type"
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72
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73 }
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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74 ]]></configfile>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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75 </configfiles>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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76 <inputs>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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77 <param name="input" type="data" format="tiff,png" label="Input image"/>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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78 <param name="dtype" type="select" label="Output pixel type"
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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79 help="Data type used to store the pixel values in the output image.">
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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80 <option value="float64" selected="True">64-bit floating point</option>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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81 <option value="float32">32-bit floating point</option>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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82 <option value="float16">16-bit floating point</option>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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83 </param>
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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84 <conditional name="filter">
33e3d7e8283f planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/ridge_filter/ commit 85b0f6afacb8933db19e03682559cc4d71031cf1
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85 <param name="filter_type" type="select" label="Filter">
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86 <option value="frangi" selected="True">Frangi vesselness filter</option>
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87 <option value="hessian">Hybrid Hessian filter</option>
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88 <option value="laplace">Laplace filter</option>
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89 <option value="meijering">Meijering neuriteness filter</option>
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90 <option value="sato">Sato tubeness filter</option>
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91 </param>
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92 <when value="frangi">
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93 <expand macro="frangi_params"/>
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94 </when>
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95 <when value="hessian">
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96 <expand macro="frangi_params"/>
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97 </when>
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98 <when value="laplace">
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99 <param name="ksize" type="integer" value="3" label="Kernel size"
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100 help="Define the size of the discrete Laplacian operator such that it will have the size of a hypercube with this edge length (in pixels)."/>
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101 </when>
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102 <when value="meijering">
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103 <expand macro="base_params"/>
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104 </when>
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105 <when value="sato">
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106 <expand macro="base_params"/>
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107 </when>
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108 </conditional>
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109 </inputs>
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110 <outputs>
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111 <data format="tiff" name="output"/>
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112 </outputs>
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113 <tests>
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114 <!-- Single-image (Q), Single-frame (T), Single-slice (Z), multi-channel (C), Frangi (dark) -->
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115 <test>
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116 <param name="input" value="scikit-image/retina.png"/>
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117 <param name="dtype" value="float16"/>
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118 <conditional name="filter">
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119 <param name="filter_type" value="frangi"/>
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120 <param name="black_ridges" value="true"/>
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121 <param name="sigma_min" value="0.5"/>
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122 <param name="sigma_max" value="20"/>
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123 <param name="num_sigma" value="10"/>
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124 <param name="alpha" value="0.5"/>
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125 <param name="beta" value="0.5"/>
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126 </conditional>
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127 <expand macro="tests/intensity_image_diff" name="output" value="retina_frangi.tiff" ftype="tiff"/>
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128 <assert_stdout>
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129 <has_line line='Applying filter: "frangi"'/>
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130 <has_line line="Performing 2-D filtering"/>
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131 </assert_stdout>
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132 </test>
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133 <!-- Single-image (Q), Single-frame (T), Single-slice (Z), single-channel (C), Hessian (dark) -->
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134 <test>
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135 <param name="input" value="retina_0c_0z_0t_0q.tiff"/>
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136 <param name="dtype" value="float16"/>
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137 <conditional name="filter">
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138 <param name="filter_type" value="hessian"/>
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139 <param name="black_ridges" value="true"/>
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140 <param name="sigma_min" value="0.5"/>
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141 <param name="sigma_max" value="20"/>
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142 <param name="num_sigma" value="10"/>
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143 <param name="alpha" value="0.5"/>
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144 <param name="beta" value="0.5"/>
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145 </conditional>
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146 <expand macro="tests/intensity_image_diff" name="output" value="retina_0c_0z_0t_0q_hessian.tiff" ftype="tiff"/>
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147 <assert_stdout>
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148 <has_line line='Applying filter: "hessian"'/>
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149 <has_line line="Performing 2-D filtering"/>
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150 </assert_stdout>
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151 </test>
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152 <!-- Single-image (Q), Multi-frame (T), Single-slice (Z), single-channel (C), Meijering (dark) -->
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153 <test>
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154 <param name="input" value="retina_0c_0z_3t_0q.tiff"/>
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155 <param name="dtype" value="float16"/>
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156 <conditional name="filter">
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157 <param name="filter_type" value="meijering"/>
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158 <param name="black_ridges" value="true"/>
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159 <param name="sigma_min" value="0.5"/>
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160 <param name="sigma_max" value="20"/>
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161 <param name="num_sigma" value="10"/>
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162 </conditional>
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163 <expand macro="tests/intensity_image_diff" name="output" value="retina_0c_0z_3t_0q_meijering.tiff" ftype="tiff"/>
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164 <assert_stdout>
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165 <has_line line='Applying filter: "meijering"'/>
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166 <has_line line="Performing 2-D filtering"/>
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167 </assert_stdout>
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168 </test>
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169 <!-- Multi-image (Q), Single-frame (T), Single-slice (Z), single-channel (C), Sato (dark) -->
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170 <test>
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171 <param name="input" value="retina_0c_0z_0t_2q.tiff"/>
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172 <param name="dtype" value="float16"/>
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173 <conditional name="filter">
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174 <param name="filter_type" value="sato"/>
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175 <param name="black_ridges" value="true"/>
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176 <param name="sigma_min" value="0.5"/>
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177 <param name="sigma_max" value="20"/>
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178 <param name="num_sigma" value="10"/>
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179 </conditional>
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180 <expand macro="tests/intensity_image_diff" name="output" value="retina_0c_0z_0t_2q_sato.tiff" ftype="tiff"/>
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181 <assert_stdout>
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182 <has_line line='Applying filter: "sato"'/>
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183 <has_line line="Performing 2-D filtering"/>
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184 </assert_stdout>
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185 </test>
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186 <!-- Single-image (Q), Single-frame (T), Multi-slice (Z), single-channel (C), Laplace -->
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187 <test>
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188 <param name="input" value="retina_0c_5z_0t_0q.tiff"/>
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189 <param name="dtype" value="float16"/>
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190 <conditional name="filter">
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191 <param name="filter_type" value="laplace"/>
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192 <param name="ksize" value="5"/>
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193 </conditional>
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194 <expand macro="tests/intensity_image_diff" name="output" value="retina_0c_5z_0t_0q_laplace.tiff" ftype="tiff"/>
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195 <assert_stdout>
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196 <has_line line='Applying filter: "laplace"'/>
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197 <has_line line="Performing 3-D filtering"/>
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198 </assert_stdout>
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199 </test>
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200 <!-- Bright ridges, Single-image (Q), Single-frame (T), Multi-slice (Z), single-channel (C), Frangi (bright) -->
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201 <test>
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202 <param name="input" value="retina_inv_0c_0z_0t_0q.tiff"/>
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203 <param name="dtype" value="float16"/>
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204 <conditional name="filter">
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205 <param name="filter_type" value="frangi"/>
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206 <param name="black_ridges" value="false"/>
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207 <param name="sigma_min" value="0.5"/>
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208 <param name="sigma_max" value="20"/>
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209 <param name="num_sigma" value="10"/>
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210 <param name="alpha" value="0.5"/>
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211 <param name="beta" value="0.5"/>
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212 </conditional>
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213 <expand macro="tests/intensity_image_diff" name="output" value="retina_inv_0c_0z_0t_0q_frangi.tiff" ftype="tiff"/>
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214 <assert_stdout>
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215 <has_line line='Applying filter: "frangi"'/>
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216 <has_line line="Performing 2-D filtering"/>
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217 </assert_stdout>
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218 </test>
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219 </tests>
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220 <help>
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221
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222 **Applies a ridge filter to an image.**
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223
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224 Ridge filters can be used to detect ridge-like structures, such as neurites, tubes, vessels, wrinkles, or rivers. Different
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225 ridge filters may be suited for detecting different structures, e.g., depending on contrast or noise level. 2-D and 3-D
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226 images are supported. For multi-channel images, the filter is applied to all channels of the image. For time-series images,
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227 the filter is also applied for all time steps.
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228
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229 Frangi vesselness filter
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230 ========================
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231
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232 Filter an image with the Frangi vesselness filter. This filter can be used to detect continuous ridges, e.g. vessels,
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233 wrinkles, rivers. It can be used to calculate the fraction of the whole image containing such objects. Calculates the
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234 eigenvalues of the Hessian to compute the similarity of an image region to vessels, according to the method described in
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235 Frangi et al. (1998).
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236
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237 Hybrid Hessian filter
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238 =====================
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239
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240 Filter an image with the Hybrid Hessian filter (Schrijver 2001, Kroon 2009). This filter can be used to detect continuous
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241 edges, e.g. vessels, wrinkles, rivers. It can be used to calculate the fraction of the whole image containing such objects.
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242 Almost equal to Frangi filter, but uses alternative method of smoothing.
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243
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244 Laplace filter
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245 ==============
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246
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247 Find the edges of an image using the Laplace operator.
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248
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249 Meijering neuriteness filter
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250 ============================
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251
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252 Filter an image with the Meijering neuriteness filter. This filter can be used to detect continuous ridges, e.g. neurites,
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253 wrinkles, rivers. It can be used to calculate the fraction of the whole image containing such objects. Calculates the
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254 eigenvalues of the Hessian to compute the similarity of an image region to neurites, according to the method described in
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255 Meijering et al. (2004).
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256
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257 Sato tubeness filter
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258 ====================
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259
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260 Filter an image with the Sato tubeness filter. This filter can be used to detect continuous ridges, e.g. tubes, wrinkles,
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261 rivers. It can be used to calculate the fraction of the whole image containing such objects. Calculates the eigenvalues of
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262 the Hessian to compute the similarity of an image region to tubes, according to the method described in Sato et al. (1998).
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263
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264 </help>
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265 <citations>
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266 <citation type="doi">10.1007/BFb0056195</citation>
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267 <citation type="doi">10.1002/cyto.a.20022</citation>
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268 <citation type="doi">10.1016/S1361-8415(98)80009-1</citation>
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269 </citations>
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270 </tool>