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