Mercurial > repos > imgteam > color_deconvolution

annotate color_deconvolution.xml @ 2:387414aa6496 draft default tip

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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 18:12:13 +0000
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2
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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1 <tool id="ip_color_deconvolution" name="Perform color deconvolution or transformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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2 <description></description>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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3 <macros>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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4 <import>creators.xml</import>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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5 <import>tests.xml</import>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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6 <token name="@TOOL_VERSION@">0.9</token>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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7 <token name="@VERSION_SUFFIX@">0</token>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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8 </macros>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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9 <creator>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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10 <expand macro="creators/bmcv"/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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11 </creator>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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12 <edam_operations>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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13 <edam_operation>operation_3443</edam_operation>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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14 </edam_operations>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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15 <xrefs>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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16 <xref type="bio.tools">galaxy_image_analysis</xref>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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17 </xrefs>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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18 <requirements>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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19 <requirement type="package" version="0.24.0">scikit-image</requirement>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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20 <requirement type="package" version="11.0.0">pillow</requirement>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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21 <requirement type="package" version="1.5.2">scikit-learn</requirement>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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22 <requirement type="package" version="2.1.2">numpy</requirement>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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23 <requirement type="package" version="2024.9.20">tifffile</requirement>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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24 <requirement type="package" version="0.3.1">giatools</requirement>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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25 </requirements>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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26 <command detect_errors="aggressive">
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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27 <![CDATA[
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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28
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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29 python '$__tool_directory__/color_deconvolution.py'
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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30
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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31 '$input'
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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32 '$output'
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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33 '$convtype'
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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34
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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35 #if str($isolate_channel) != '':
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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36 --isolate_channel '${isolate_channel}'
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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37 #end if
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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38
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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39 ]]>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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40 </command>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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41 <inputs>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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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."/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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43 <param name="convtype" type="select" label="Transformation type">
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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44
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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45 <!-- Color deconvolution and recomposition operations -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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46 <option value="he_from_rgb">Deconvolve RGB into H&#38;E (Hematoxylin + Eosin)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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47 <option value="rgb_from_he">Recompose RGB from H&#38;E (Hematoxylin + Eosin)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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48 <option value="hdx_from_rgb">Deconvolve RGB into Hematoxylin + DAB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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49 <option value="rgb_from_hdx">Recompose RGB from Hematoxylin + DAB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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50 <option value="rgb2hed">Deconvolve RGB into Hematoxylin + Eosin + DAB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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51 <option value="hed2rgb">Recompose RGB from Hematoxylin + Eosin + DAB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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52 <option value="hpx_from_rgb">Deconvolve RGB into Hematoxylin + PAS</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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53 <option value="rgb_from_hpx">Recompose RGB from Hematoxylin + PAS</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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54 <option value="hax_from_rgb">Deconvolve RGB into Hematoxylin + AEC</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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55 <option value="rgb_from_hax">Recompose RGB from Hematoxylin + AEC</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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56 <option value="ahx_from_rgb">Deconvolve RGB into Alcian Blue + Hematoxylin</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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57 <option value="rgb_from_ahx">Recompose RGB from Alcian Blue + Hematoxylin</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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58 <option value="bro_from_rgb">Deconvolve RGB to AZAN</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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59 <option value="rgb_from_bro">Recompose RGB from AZAN</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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60 <option value="rbd_from_rgb">Deconvolve RGB into FastRed + FastBlue + DAB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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61 <option value="rgb_from_rbd">Recompose RGB from FastRed + FastBlue + DAB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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62 <option value="fgx_from_rgb">Deconvolve RGB into Feulgen + Light Green</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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63 <option value="rgb_from_fgx">Recompose RGB from Feulgen + Light Green</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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64 <option value="bex_from_rgb">Deconvolve RGB into Giemsa stain (Methyl Blue + Eosin)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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65 <option value="rgb_from_bex">Recompose RGB from Giemsa stain (Methyl Blue + Eosin)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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66 <option value="bpx_from_rgb">Deconvolve RGB into Methyl Blue + Ponceau Fuchsin</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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67 <option value="rgb_from_bpx">Recompose RGB from Methyl Blue + Ponceau Fuchsin</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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68 <option value="gdx_from_rgb">Deconvolve RGB into Methyl Green + DAB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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69 <option value="rgb_from_gdx">Recompose RGB from Methyl Green + DAB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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70
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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71 <!-- Unsupervised machine learning-based operations -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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72 <option value="ica">Project onto independent components (ICA)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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73 <option value="pca">Project onto principal components (PCA)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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74 <option value="nmf">Non-negative matrix factorization</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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75 <option value="fa">Factor analysis</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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76
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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77 <!-- General color space conversion operations -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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78 <option value="rgb2hsv" selected="True">Convert RGB to HSV</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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79 <option value="hsv2rgb">Convert HSV to RGB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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80 <option value="rgb2xyz">Convert RGB to XYZ (CIE 1931)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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81 <option value="xyz2rgb">Convert XYZ (CIE 1931) to RGB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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diff changeset
82 <option value="rgb2luv">Convert RGB to CIE-LUV</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
parents:
diff changeset
83 <option value="luv2rgb">Convert CIE-LUV to RGB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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diff changeset
84 <option value="xyz2luv">Convert XYZ (CIE 1931) to CIE-LUV</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
parents:
diff changeset
85 <option value="luv2xyz">Convert CIE-LUV to XYZ (CIE 1931)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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86 <option value="rgb2lab">Convert RGB to CIE-LAB (illuminant D65, aperture angle 2&#xb0;)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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diff changeset
87 <option value="lab2rgb">Convert CIE-LAB (illuminant D65, aperture angle 2&#xb0;) to RGB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
parents:
diff changeset
88 <option value="lab2xyz">Convert CIE-LAB (illuminant D65, aperture angle 2&#xb0;) to XYZ (CIE 1931)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
parents:
diff changeset
89 <option value="xyz2lab">Convert XYZ (CIE 1931) to CIE-LAB (illuminant D65, aperture angle 2&#xb0;)</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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diff changeset
90 <option value="lch2lab">Convert CIE-LCh to CIE-LAB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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diff changeset
91 <option value="lab2lch">Convert CIE-LAB to CIE-LCh</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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92 <option value="rgb2rgbcie">Convert RGB to RGB-CIE</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
imgteam
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diff changeset
93 <option value="rgbcie2rgb">Convert RGB-CIE to RGB</option>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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94
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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95 </param>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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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." />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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97 </inputs>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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98 <outputs>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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99 <data format="tiff" name="output"/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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100 </outputs>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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101 <tests>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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102
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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103 <!-- Tests with compatible input files -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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104
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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105 <test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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106 <!-- Test PNG input and standard color transformation -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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107 <param name="input" value="galaxyIcon_noText.png" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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108 <param name="convtype" value="rgb2hsv" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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109 <expand macro="tests/intensity_image_diff" name="output" value="galaxyIcon_noText.tiff" ftype="tiff"/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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110 </test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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111 <test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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112 <!-- Test deconvolution using scikit-image (H&E + DAB) -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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113 <param name="input" value="he1.tiff" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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114 <param name="convtype" value="rgb2hed" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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115 <expand macro="tests/intensity_image_diff" name="output" value="he1_deconv_hed.tiff" ftype="tiff"/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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116 </test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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117 <test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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118 <!-- Test full recomposition -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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119 <param name="input" value="he1_deconv_hed.tiff" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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120 <param name="convtype" value="hed2rgb" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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121 <expand macro="tests/intensity_image_diff" name="output" value="he1_deconv_hed_recomposed.tiff" ftype="tiff"/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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122 </test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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123 <test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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124 <!-- Test recomposition with isolated channel -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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125 <param name="input" value="he1_deconv_hed.tiff" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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126 <param name="convtype" value="hed2rgb" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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127 <param name="isolate_channel" value="1" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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128 <expand macro="tests/intensity_image_diff" name="output" value="he1_deconv_hed_recomposed1.tiff" ftype="tiff"/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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129 </test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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130 <test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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131 <!-- Test deconvolution using custom stain matrix -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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132 <param name="input" value="he1.tiff" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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133 <param name="convtype" value="he_from_rgb" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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134 <expand macro="tests/intensity_image_diff" name="output" value="he1_deconv_he.tiff" ftype="tiff"/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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135 </test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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136 <test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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137 <!-- Test deconvolution using scikit-image (Hematoxylin + DAB) -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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138 <param name="input" value="hdab1.tiff" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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139 <param name="convtype" value="hdx_from_rgb" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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140 <expand macro="tests/intensity_image_diff" name="output" value="hdab1_deconv_hdab.tiff" ftype="tiff"/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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141 </test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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142 <test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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143 <!-- Test with image that has 3 axes but in unusual order (and 3 channels) -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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144 <param name="input" value="he1_axes_cyx.tiff" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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145 <param name="convtype" value="rgb2hsv" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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146 <expand macro="tests/intensity_image_diff" name="output" value="he1_hsv.tiff" ftype="tiff"/>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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147 </test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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148
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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149 <!-- Tests with incompatible input files (should fail) -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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150
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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151 <test expect_failure="true">
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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152 <!-- Test with image that only has 2 axes instead of required 3 -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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153 <param name="input" value="im_axes_yx.tif" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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154 <param name="convtype" value="rgb2hsv" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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155 </test>
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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156 <test expect_failure="true">
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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157 <!-- Test with image that has 3 axes but YXZ instead of YXC (and 3 slices) -->
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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158 <param name="input" value="he1_axes_yxz.tiff" />
387414aa6496 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/color_deconvolution/ commit f546b3cd5cbd3a8613cd517975c7ad1d1f83514e
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159 <param name="convtype" value="rgb2hsv" />
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160 </test>
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161
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162 </tests>
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163 <help><![CDATA[
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164
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165 **This tool converts the color space of an image.**
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166
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167 Several color deconvolution techniques are also supported.
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168
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169 Color Deconvolution Example
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170 ===========================
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171
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172 In this example, we are going to perform color deconvolution of the following RGB image:
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173
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174 .. image:: he.png
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175 :width: 434px
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176 :scale: 50%
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177
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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:
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179
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180 .. image:: he_deconv.png
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181 :width: 1305px
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182 :scale: 50%
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183
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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.
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185
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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:
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187
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188 * **Input image:** The result of the color deconvolution (image shown in the figure above)
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189 * **Transformation type:** Recompose RGB from H&E (Hematoxylin + Eosin)
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190
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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:
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192
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193 .. image:: he_recomposed.png
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194 :width: 1305px
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195 :scale: 50%
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196
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197 ]]></help>
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198 <citations>
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199 <citation type="doi">10.7717/peerj.453</citation>
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200 <citation type="bibtex">@inproceedings{sklearn_api,
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201 author = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and
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202 Fabian Pedregosa and Andreas Mueller and Olivier Grisel and
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203 Vlad Niculae and Peter Prettenhofer and Alexandre Gramfort
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204 and Jaques Grobler and Robert Layton and Jake VanderPlas and
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205 Arnaud Joly and Brian Holt and Ga{\"{e}}l Varoquaux},
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206 title = {{API} design for machine learning software: experiences from the scikit-learn project},
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207 booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
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208 year = {2013},
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209 pages = {108--122},
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210 }</citation>
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211 </citations>
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212 </tool>