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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:26:16 +0000
parents d10a46ef77d3
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1:d10a46ef77d3 2:e438d87ef91a
1 <tool id="rfove" name="Perform segmentation using region-based fitting of overlapping ellipses" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 1 <tool id="rfove" name="Perform segmentation using region-based fitting of overlapping ellipses" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>with RFOVE</description> 2 <description>with RFOVE</description>
3 <macros> 3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
4 <token name="@TOOL_VERSION@">2023.11.12</token> 6 <token name="@TOOL_VERSION@">2023.11.12</token>
5 <token name="@VERSION_SUFFIX@">1</token> 7 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 8 </macros>
9 <creator>
10 <expand macro="creators/bmcv"/>
11 </creator>
7 <edam_operations> 12 <edam_operations>
8 <edam_operation>operation_3443</edam_operation> 13 <edam_operation>operation_3443</edam_operation>
9 </edam_operations> 14 </edam_operations>
10 <xrefs> 15 <xrefs>
11 <xref type="bio.tools">rfove</xref> 16 <xref type="bio.tools">rfove</xref>
25 30
26 output.tiff 31 output.tiff
27 ]]> 32 ]]>
28 </command> 33 </command>
29 <inputs> 34 <inputs>
30 <param name="dataset" type="data" format="tiff,png" label="Dataset" /> 35 <param name="dataset" type="data" format="tiff,png" label="Input image" />
31 <param name="area_ub" type="integer" label="Maximum ellipse area" min="5" value="250" /> 36 <param name="area_ub" type="integer" label="Maximum ellipse area" min="5" value="250" />
32 <param name="min_area_max_area_ratio_ub" type="float" min="0" max="1" value="0.1" label="Upper bound of the ratio: minimum area / maximum area" /> 37 <param name="min_area_max_area_ratio_ub" type="float" min="0" max="1" value="0.1" label="Upper bound of the ratio: minimum area / maximum area" />
33 38
34 <param name="overlap_ub" type="float" label="Maximum ellipse overlap" min="0" value="0.2" /> 39 <param name="overlap_ub" type="float" label="Maximum ellipse overlap" min="0" value="0.2" />
35 <param name="half_neighborhood_size" type="integer" label="Half neighborhood size" min="1" value="100" /> 40 <param name="half_neighborhood_size" type="integer" label="Half neighborhood size" min="1" value="100" />
38 <data format="tiff" name="masks" from_work_dir="output.tiff" label="${tool.name} on ${on_string}" /> 43 <data format="tiff" name="masks" from_work_dir="output.tiff" label="${tool.name} on ${on_string}" />
39 </outputs> 44 </outputs>
40 <tests> 45 <tests>
41 <test> 46 <test>
42 <param name="dataset" value="BBBC033_C2_z28.png" /> 47 <param name="dataset" value="BBBC033_C2_z28.png" />
43 <output name="masks" value="output.tiff" ftype="tiff" compare="sim_size" /> 48 <expand macro="tests/label_image_diff" name="masks" value="output.tiff" ftype="tiff"/>
44 </test> 49 </test>
45 </tests> 50 </tests>
46 <help> 51 <help>
47 RFOVE is completely unsupervised, operates without any assumption or prior knowledge on the object’s shape and extends and improves the Decremental Ellipse Fitting Algorithm (DEFA). Both RFOVE and DEFA solve the multi-ellipse fitting problem by performing model selection that is guided by the minimization of the Akaike Information Criterion on a suitably defined shape complexity measure. However, in contrast to DEFA, RFOVE minimizes an objective function that allows for ellipses with higher degree of overlap and, thus, achieves better ellipse-based shape approximation. 52
53 **Perform segmentation using shape decomposition based on elliptical models and expectation maximization.**
54
55 RFOVE is completely unsupervised, operates without any assumption or prior knowledge on the object's shape
56 and extends and improves the *Decremental Ellipse Fitting Algorithm* (DEFA). Both RFOVE and DEFA solve the
57 multi-ellipse fitting problem by performing model selection that is guided by the minimization of the
58 *Akaike Information Criterion* on a suitably defined shape complexity measure. However, in contrast to
59 DEFA, RFOVE minimizes an objective function that allows for ellipses with higher degree of overlap and,
60 thus, achieves better ellipse-based shape approximation.
61
48 </help> 62 </help>
49 <citations> 63 <citations>
50 <citation type="doi">10.1016/j.imavis.2019.09.001</citation> 64 <citation type="doi">10.1016/j.imavis.2019.09.001</citation>
51 </citations> 65 </citations>
52 </tool> 66 </tool>