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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
author imgteam
date Thu, 06 Mar 2025 18:12:27 +0000
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1 <tool id="ip_color_deconvolution" name="Perform color decomposition" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="ip_color_deconvolution" name="Perform color deconvolution or transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <import>creators.xml</import> 4 <import>creators.xml</import>
5 <import>tests.xml</import> 5 <import>tests.xml</import>
6 <token name="@TOOL_VERSION@">0.8</token> 6 <token name="@TOOL_VERSION@">0.9</token>
7 <token name="@VERSION_SUFFIX@">2</token> 7 <token name="@VERSION_SUFFIX@">0</token>
8 </macros> 8 </macros>
9 <creator> 9 <creator>
10 <expand macro="creators/bmcv"/> 10 <expand macro="creators/bmcv"/>
11 </creator> 11 </creator>
12 <edam_operations> 12 <edam_operations>
19 <requirement type="package" version="0.24.0">scikit-image</requirement> 19 <requirement type="package" version="0.24.0">scikit-image</requirement>
20 <requirement type="package" version="11.0.0">pillow</requirement> 20 <requirement type="package" version="11.0.0">pillow</requirement>
21 <requirement type="package" version="1.5.2">scikit-learn</requirement> 21 <requirement type="package" version="1.5.2">scikit-learn</requirement>
22 <requirement type="package" version="2.1.2">numpy</requirement> 22 <requirement type="package" version="2.1.2">numpy</requirement>
23 <requirement type="package" version="2024.9.20">tifffile</requirement> 23 <requirement type="package" version="2024.9.20">tifffile</requirement>
24 <requirement type="package" version="0.3.1">giatools</requirement>
24 </requirements> 25 </requirements>
25 <command detect_errors="aggressive"> 26 <command detect_errors="aggressive">
26 <![CDATA[ 27 <![CDATA[
27 python '$__tool_directory__/color_deconvolution.py' '$input' '$output' '$convtype' 28
29 python '$__tool_directory__/color_deconvolution.py'
30
31 '$input'
32 '$output'
33 '$convtype'
34
35 #if str($isolate_channel) != '':
36 --isolate_channel '${isolate_channel}'
37 #end if
38
28 ]]> 39 ]]>
29 </command> 40 </command>
30 <inputs> 41 <inputs>
31 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Image file with 3 channels"/> 42 <param name="input" type="data" format="tiff,png,jpg,bmp" label="Input image" help="The input image must have 3 axes and 3 channels. The channels must correspond to the last axis."/>
32 <param name="convtype" type="select" label="Transformation type"> 43 <param name="convtype" type="select" label="Transformation type">
33 <option value="ica" selected="True">ica</option> 44
34 <option value="pca">pca</option> 45 <!-- Color deconvolution and recomposition operations -->
35 <option value="nmf">nmf</option> 46 <option value="he_from_rgb">Deconvolve RGB into H&#38;E (Hematoxylin + Eosin)</option>
36 <option value="fa">fa</option> 47 <option value="rgb_from_he">Recompose RGB from H&#38;E (Hematoxylin + Eosin)</option>
37 <option value="xyz2rgb">xyz2rgb</option> 48 <option value="hdx_from_rgb">Deconvolve RGB into Hematoxylin + DAB</option>
38 <option value="rgb_from_rbd">rgb_from_rbd</option> 49 <option value="rgb_from_hdx">Recompose RGB from Hematoxylin + DAB</option>
39 <option value="rgb_from_hdx">rgb_from_hdx</option> 50 <option value="rgb2hed">Deconvolve RGB into Hematoxylin + Eosin + DAB</option>
40 <option value="rgb2hsv">rgb2hsv</option> 51 <option value="hed2rgb">Recompose RGB from Hematoxylin + Eosin + DAB</option>
41 <option value="rgb_from_bro">rgb_from_bro</option> 52 <option value="hpx_from_rgb">Deconvolve RGB into Hematoxylin + PAS</option>
42 <option value="bpx_from_rgb">bpx_from_rgb</option> 53 <option value="rgb_from_hpx">Recompose RGB from Hematoxylin + PAS</option>
43 <option value="hed_from_rgb">hed_from_rgb</option> 54 <option value="hax_from_rgb">Deconvolve RGB into Hematoxylin + AEC</option>
44 <option value="rgbcie2rgb">rgbcie2rgb</option> 55 <option value="rgb_from_hax">Recompose RGB from Hematoxylin + AEC</option>
45 <option value="hdx_from_rgb">hdx_from_rgb</option> 56 <option value="ahx_from_rgb">Deconvolve RGB into Alcian Blue + Hematoxylin</option>
46 <option value="xyz2luv">xyz2luv</option> 57 <option value="rgb_from_ahx">Recompose RGB from Alcian Blue + Hematoxylin</option>
47 <option value="rgb2lab">rgb2lab</option> 58 <option value="bro_from_rgb">Deconvolve RGB to AZAN</option>
48 <option value="hpx_from_rgb">hpx_from_rgb</option> 59 <option value="rgb_from_bro">Recompose RGB from AZAN</option>
49 <option value="rgb_from_fgx">rgb_from_fgx</option> 60 <option value="rbd_from_rgb">Deconvolve RGB into FastRed + FastBlue + DAB</option>
50 <option value="rgb_from_gdx">rgb_from_gdx</option> 61 <option value="rgb_from_rbd">Recompose RGB from FastRed + FastBlue + DAB</option>
51 <option value="lab2xyz">lab2xyz</option> 62 <option value="fgx_from_rgb">Deconvolve RGB into Feulgen + Light Green</option>
52 <option value="rgb_from_hpx">rgb_from_hpx</option> 63 <option value="rgb_from_fgx">Recompose RGB from Feulgen + Light Green</option>
53 <option value="lab2rgb">lab2rgb</option> 64 <option value="bex_from_rgb">Deconvolve RGB into Giemsa stain (Methyl Blue + Eosin)</option>
54 <option value="rgb2rgbcie">rgb2rgbcie</option> 65 <option value="rgb_from_bex">Recompose RGB from Giemsa stain (Methyl Blue + Eosin)</option>
55 <option value="bex_from_rgb">bex_from_rgb</option> 66 <option value="bpx_from_rgb">Deconvolve RGB into Methyl Blue + Ponceau Fuchsin</option>
56 <option value="xyz2lab">xyz2lab</option> 67 <option value="rgb_from_bpx">Recompose RGB from Methyl Blue + Ponceau Fuchsin</option>
57 <option value="rgb_from_bex">rgb_from_bex</option> 68 <option value="gdx_from_rgb">Deconvolve RGB into Methyl Green + DAB</option>
58 <option value="fgx_from_rgb">fgx_from_rgb</option> 69 <option value="rgb_from_gdx">Recompose RGB from Methyl Green + DAB</option>
59 <option value="rbd_from_rgb">rbd_from_rgb</option> 70
60 <option value="rgb2hed">rgb2hed</option> 71 <!-- Unsupervised machine learning-based operations -->
61 <option value="hed2rgb">hed2rgb</option> 72 <option value="ica">Project onto independent components (ICA)</option>
62 <option value="luv2rgb">luv2rgb</option> 73 <option value="pca">Project onto principal components (PCA)</option>
63 <option value="luv2xyz">luv2xyz</option> 74 <option value="nmf">Non-negative matrix factorization</option>
64 <option value="lch2lab">lch2lab</option> 75 <option value="fa">Factor analysis</option>
65 <option value="rgb2luv">rgb2luv</option> 76
66 <option value="ahx_from_rgb">ahx_from_rgb</option> 77 <!-- General color space conversion operations -->
67 <option value="rgb_from_hax">rgb_from_hax</option> 78 <option value="rgb2hsv" selected="True">Convert RGB to HSV</option>
68 <option value="hax_from_rgb">hax_from_rgb</option> 79 <option value="hsv2rgb">Convert HSV to RGB</option>
69 <option value="rgb_from_bpx">rgb_from_bpx</option> 80 <option value="rgb2xyz">Convert RGB to XYZ (CIE 1931)</option>
70 <option value="rgb2xyz">rgb2xyz</option> 81 <option value="xyz2rgb">Convert XYZ (CIE 1931) to RGB</option>
71 <option value="gdx_from_rgb">gdx_from_rgb</option> 82 <option value="rgb2luv">Convert RGB to CIE-LUV</option>
72 <option value="rgb_from_ahx">rgb_from_ahx</option> 83 <option value="luv2rgb">Convert CIE-LUV to RGB</option>
73 <option value="lab2lch">lab2lch</option> 84 <option value="xyz2luv">Convert XYZ (CIE 1931) to CIE-LUV</option>
74 <option value="rgb_from_hed">rgb_from_hed</option> 85 <option value="luv2xyz">Convert CIE-LUV to XYZ (CIE 1931)</option>
75 <option value="bro_from_rgb">bro_from_rgb</option> 86 <option value="rgb2lab">Convert RGB to CIE-LAB (illuminant D65, aperture angle 2&#xb0;)</option>
76 <option value="hsv2rgb">hsv2rgb</option> 87 <option value="lab2rgb">Convert CIE-LAB (illuminant D65, aperture angle 2&#xb0;) to RGB</option>
88 <option value="lab2xyz">Convert CIE-LAB (illuminant D65, aperture angle 2&#xb0;) to XYZ (CIE 1931)</option>
89 <option value="xyz2lab">Convert XYZ (CIE 1931) to CIE-LAB (illuminant D65, aperture angle 2&#xb0;)</option>
90 <option value="lch2lab">Convert CIE-LCh to CIE-LAB</option>
91 <option value="lab2lch">Convert CIE-LAB to CIE-LCh</option>
92 <option value="rgb2rgbcie">Convert RGB to RGB-CIE</option>
93 <option value="rgbcie2rgb">Convert RGB-CIE to RGB</option>
94
77 </param> 95 </param>
96 <param name="isolate_channel" type="integer" optional="true" value="" label="Isolate channel" help="Must be empty or the number of a channel (1 to 3). If used, all other channels are set to zero before performing the chosen transformation." />
78 </inputs> 97 </inputs>
79 <outputs> 98 <outputs>
80 <data format="tiff" name="output"/> 99 <data format="tiff" name="output"/>
81 </outputs> 100 </outputs>
82 <tests> 101 <tests>
83 <test> 102
103 <!-- Tests with compatible input files -->
104
105 <test>
106 <!-- Test PNG input and standard color transformation -->
84 <param name="input" value="galaxyIcon_noText.png" /> 107 <param name="input" value="galaxyIcon_noText.png" />
85 <param name="convtype" value="rgb2hsv" /> 108 <param name="convtype" value="rgb2hsv" />
86 <expand macro="tests/intensity_image_diff" name="output" value="galaxyIcon_noText.tiff" ftype="tiff"/> 109 <expand macro="tests/intensity_image_diff" name="output" value="galaxyIcon_noText.tiff" ftype="tiff"/>
87 </test> 110 </test>
111 <test>
112 <!-- Test deconvolution using scikit-image (H&E + DAB) -->
113 <param name="input" value="he1.tiff" />
114 <param name="convtype" value="rgb2hed" />
115 <expand macro="tests/intensity_image_diff" name="output" value="he1_deconv_hed.tiff" ftype="tiff"/>
116 </test>
117 <test>
118 <!-- Test full recomposition -->
119 <param name="input" value="he1_deconv_hed.tiff" />
120 <param name="convtype" value="hed2rgb" />
121 <expand macro="tests/intensity_image_diff" name="output" value="he1_deconv_hed_recomposed.tiff" ftype="tiff"/>
122 </test>
123 <test>
124 <!-- Test recomposition with isolated channel -->
125 <param name="input" value="he1_deconv_hed.tiff" />
126 <param name="convtype" value="hed2rgb" />
127 <param name="isolate_channel" value="1" />
128 <expand macro="tests/intensity_image_diff" name="output" value="he1_deconv_hed_recomposed1.tiff" ftype="tiff"/>
129 </test>
130 <test>
131 <!-- Test deconvolution using custom stain matrix -->
132 <param name="input" value="he1.tiff" />
133 <param name="convtype" value="he_from_rgb" />
134 <expand macro="tests/intensity_image_diff" name="output" value="he1_deconv_he.tiff" ftype="tiff"/>
135 </test>
136 <test>
137 <!-- Test deconvolution using scikit-image (Hematoxylin + DAB) -->
138 <param name="input" value="hdab1.tiff" />
139 <param name="convtype" value="hdx_from_rgb" />
140 <expand macro="tests/intensity_image_diff" name="output" value="hdab1_deconv_hdab.tiff" ftype="tiff"/>
141 </test>
142 <test>
143 <!-- Test with image that has 3 axes but in unusual order (and 3 channels) -->
144 <param name="input" value="he1_axes_cyx.tiff" />
145 <param name="convtype" value="rgb2hsv" />
146 <expand macro="tests/intensity_image_diff" name="output" value="he1_hsv.tiff" ftype="tiff"/>
147 </test>
148
149 <!-- Tests with incompatible input files (should fail) -->
150
151 <test expect_failure="true">
152 <!-- Test with image that only has 2 axes instead of required 3 -->
153 <param name="input" value="im_axes_yx.tif" />
154 <param name="convtype" value="rgb2hsv" />
155 </test>
156 <test expect_failure="true">
157 <!-- Test with image that has 3 axes but YXZ instead of YXC (and 3 slices) -->
158 <param name="input" value="he1_axes_yxz.tiff" />
159 <param name="convtype" value="rgb2hsv" />
160 </test>
161
88 </tests> 162 </tests>
89 <help> 163 <help><![CDATA[
90 164
91 **What it does** 165 **This tool converts the color space of an image.**
92 166
93 This tools performs several color deconvolution techniques. 167 Several color deconvolution techniques are also supported.
94 168
95 </help> 169 Color Deconvolution Example
170 ===========================
171
172 In this example, we are going to perform color deconvolution of the following RGB image:
173
174 .. image:: he.png
175 :width: 434px
176 :scale: 50%
177
178 Using the option "Deconvolve RGB into H&E (Hematoxylin + Eosin)" for the **Transformation type** performs color deconvolution and yields a new image with three chnnales:
179
180 .. image:: he_deconv.png
181 :width: 1305px
182 :scale: 50%
183
184 The channels of the deconvolved image are the Hematoxylin intensities (Channel 1), the Eosin intensities (Channel 2), and the residuals (Channel 3). White image regions correspond to high intensities and black image regions correspond to low intensities.
185
186 For visual inspection of the color deconvolution results, it may be useful to recompose separate RGB images for the Hematoxylin, Eosin, and residual channels. To create such images, this tool must be run once for each channel of the deconvolved image (i.e. three times), using the following options:
187
188 * **Input image:** The result of the color deconvolution (image shown in the figure above)
189 * **Transformation type:** Recompose RGB from H&E (Hematoxylin + Eosin)
190
191 The **Isolate channel** field must be set to 1, 2, and 3 during the three runs, respectively. This will yield the following recomposed RGB images for better visualization of the color deconvolution results:
192
193 .. image:: he_recomposed.png
194 :width: 1305px
195 :scale: 50%
196
197 ]]></help>
96 <citations> 198 <citations>
97 <citation type="doi">10.7717/peerj.453</citation> 199 <citation type="doi">10.7717/peerj.453</citation>
98 <citation type="bibtex">@inproceedings{sklearn_api, 200 <citation type="bibtex">@inproceedings{sklearn_api,
99 author = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and 201 author = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and
100 Fabian Pedregosa and Andreas Mueller and Olivier Grisel and 202 Fabian Pedregosa and Andreas Mueller and Olivier Grisel and