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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/rfove/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:22:59 +0000
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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>
3 <macros>
4 <import>creators.xml</import>
5 <import>tests.xml</import>
6 <token name="@TOOL_VERSION@">2023.11.12</token>
7 <token name="@VERSION_SUFFIX@">2</token>
8 </macros>
9 <creator>
10 <expand macro="creators/bmcv"/>
11 </creator>
12 <edam_operations>
13 <edam_operation>operation_3443</edam_operation>
14 </edam_operations>
15 <xrefs>
16 <xref type="bio.tools">rfove</xref>
17 </xrefs>
18 <requirements>
19 <container type="docker">docker.io/kostrykin/rfove:@TOOL_VERSION@</container>
20 </requirements>
21 <command detect_errors="aggressive">
22 <![CDATA[
23 #set $neighborhood_size = "%d" % ($half_neighborhood_size.value * 2 + 1)
24 /rfove
25 ${area_ub}
26 ${min_area_max_area_ratio_ub}
27 ${overlap_ub}
28 ${neighborhood_size}
29 '${dataset}'
30
31 output.tiff
32 ]]>
33 </command>
34 <inputs>
35 <param name="dataset" type="data" format="tiff,png" label="Input image" />
36 <param name="area_ub" type="integer" label="Maximum ellipse area" min="5" value="250" />
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" />
38
39 <param name="overlap_ub" type="float" label="Maximum ellipse overlap" min="0" value="0.2" />
40 <param name="half_neighborhood_size" type="integer" label="Half neighborhood size" min="1" value="100" />
41 </inputs>
42 <outputs>
43 <data format="tiff" name="masks" from_work_dir="output.tiff" label="${tool.name} on ${on_string}" />
44 </outputs>
45 <tests>
46 <test>
47 <param name="dataset" value="BBBC033_C2_z28.png" />
48 <expand macro="tests/label_image_diff" name="masks" value="output.tiff" ftype="tiff"/>
49 </test>
50 </tests>
51 <help>
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
62 </help>
63 <citations>
64 <citation type="doi">10.1016/j.imavis.2019.09.001</citation>
65 </citations>
66 </tool>