Mercurial > repos > imgteam > spot_detection_2d

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
author imgteam
date Wed, 25 Sep 2024 08:19:30 +0000
parents 14f9986800fa
children
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e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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1 <tool id="ip_spot_detection_2d" name="Perform 2-D spot detection" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description></description>
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3 <macros>
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4 <import>creators.xml</import>
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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5 <token name="@TOOL_VERSION@">0.1</token>
e8c9e104e109 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit f1b9207ec23c0af1681c929281bcbf1d0638368e
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6 <token name="@VERSION_SUFFIX@">0</token>
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7 </macros>
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8 <creator>
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9 <expand macro="creators/bmcv" />
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10 </creator>
4
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11 <edam_operations>
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12 <edam_operation>operation_3443</edam_operation>
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13 </edam_operations>
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14 <xrefs>
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15 <xref type="bio.tools">galaxy_image_analysis</xref>
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16 </xrefs>
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17 <requirements>
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18 <requirement type="package" version="0.2.0">giatools</requirement>
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19 <requirement type="package" version="1.26.4">numpy</requirement>
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20 <requirement type="package" version="1.2.4">pandas</requirement>
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21 <requirement type="package" version="0.21">scikit-image</requirement>
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22 <requirement type="package" version="2024.6.18">tifffile</requirement>
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23 </requirements>
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24 <command detect_errors="aggressive">
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25 <![CDATA[
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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26 python '$__tool_directory__/spot_detection_2d.py'
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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27 '$fn_in'
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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28 '$fn_out'
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29 '$frame_1st'
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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30 '$frame_end'
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31 '$filter_type'
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32 '$min_scale'
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33 '$max_scale'
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34 '$abs_threshold'
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35 '$rel_threshold'
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36 '$boundary'
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37 ]]>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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38 </command>
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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39 <inputs>
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40 <param name="fn_in" type="data" format="tiff" label="Intensity image or a stack of images" />
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41 <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
d78372040976 "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/spot_detection_2d/ commit 481cd51a76341c0ec3759f919454e95139f0cc4e"
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42 <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
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43 <param name="filter_type" type="select" label="Detection filter">
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44 <option value="LoG" selected="True">Laplacian of Gaussian</option>
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45 <option value="DoG">Difference of Gaussians</option>
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46 <option value="DoH">Determinant of Hessian</option>
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47 </param>
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48 <param name="min_scale" type="float" value="1.0" min="1.0" label="Minimum scale" />
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49 <param name="max_scale" type="float" value="2.0" min="1.0" label="Maximum scale" />
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50 <param name="abs_threshold" type="float" value=".25" min="0" label="Minimum filter response (absolute)" help="Filter responses below this threshold will be ignored. Only filter responses above this thresholding will be considered as blobs. This threshold is ignored if the relative threshold (below) corresponds to a higher response." />
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51 <param name="rel_threshold" type="float" value="0" min="0" max="1" label="Minimum filter response (relative)" help="Same as the absolute threshold (above), but as a fraction of the overall maximum filter response of an image. This threshold is ignored if it corresponds to a response below the absolute threshold." />
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52 <param name="boundary" type="integer" value="10" min="0" label="Image boundary" help="Width of image boundaries (in pixel) where spots will be ignored." />
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53 </inputs>
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54 <outputs>
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55 <data format="tabular" name="fn_out" />
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56 </outputs>
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57 <tests>
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58 <!-- Multi-frame input -->
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59 <test>
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60 <param name="fn_in" value="input1.tif"/>
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61 <param name="frame_1st" value="1"/>
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62 <param name="frame_end" value="0"/>
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63 <param name="filter_type" value="LoG"/>
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64 <param name="min_scale" value="1"/>
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65 <param name="max_scale" value="2"/>
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66 <param name="abs_threshold" value="0"/>
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67 <param name="rel_threshold" value="0.1"/>
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68 <param name="boundary" value="10"/>
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69 <output name="fn_out" value="output1.tsv" ftype="tabular" />
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70 </test>
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71 <!-- Single-frame input -->
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72 <test>
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73 <param name="fn_in" value="input2.tif"/>
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74 <param name="frame_1st" value="1"/>
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75 <param name="frame_end" value="0"/>
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76 <param name="filter_type" value="LoG"/>
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77 <param name="min_scale" value="1"/>
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78 <param name="max_scale" value="2"/>
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79 <param name="abs_threshold" value="0.04"/>
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80 <param name="rel_threshold" value="0"/>
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81 <param name="boundary" value="10"/>
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82 <output name="fn_out" value="output2.tsv" ftype="tabular" />
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83 </test>
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84 </tests>
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85 <help>
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86
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87 **Perform spot detection and measure the image intensities.**
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88
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89 This tool detects spots (blobs) and measures the image intensities in a single-channel 2-D image (or a stack of such images).
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90
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91 The tool produces a TSV file containing all detections, with the following columns:
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92
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93 - ``frame``: The frame of the image stack
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94 - ``pos_x``: The horizontal coordinate of the detection
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95 - ``pos_y``: The vertical coordinate of the detection
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96 - ``scale``: The scale at which the detection was found
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97 - ``radius``: The radius of the detected spot
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98 - ``intensity``: The mean intensity of the spot
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99
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100 </help>
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101 <citations>
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102 <citation type="doi">10.1097/j.pain.0000000000002642</citation>
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103 </citations>
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104 </tool>