SEM image analysis: DiameterJ with Auto thresholding - #1970
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bgruening
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Aug 28, 2026
bgruening
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Aug 28, 2026
| <token name="@TOOL_VERSION@">1-018</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">24.2</token> | ||
| <token name="@CONTAINER_VERSION@">0.2</token> |
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why is the container version not the same as the tool version?
bgruening
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Aug 28, 2026
| mkdir -p results && | ||
| export ANALYSIS_RESULTS_DIR='results' && | ||
| ln -s '$input_image' input.tif && | ||
| set -- --input input.tif --output results --segmentation '$segmentation.workflow' && |
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I don't understand why this set -- is needed.
bgruening
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Aug 28, 2026
bgruening
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Aug 28, 2026
| <option value="pixel_size">Specify pixel size directly</option> | ||
| </param> | ||
| <when value="hfw"> | ||
| <param name="hfw_um" type="float" value="27.04" label="Horizontal field width (µm)"> |
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is a min/max value useful here?
bgruening
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Aug 28, 2026
| </param> | ||
| <when value="auto-thresholding"/> | ||
| <when value="recursive-srm"> | ||
| <param name="srm_q" type="integer" value="100" min="1" label="Starting SRM granularity (q)"/> |
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use argument here and elsewhere?
bgruening
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Aug 28, 2026
| </param> | ||
| <when value="hfw"> | ||
| <param name="hfw_um" type="float" value="27.04" label="Horizontal field width (µm)"> | ||
| <validator type="expression" message="Horizontal field width must be greater than zero">value > 0</validator> |
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
SaimMomin12
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Aug 31, 2026
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LGTM. Some minor comments.
| <macros> | ||
| <token name="@TOOL_VERSION@">1-018</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> | ||
| <token name="@PROFILE@">24.2</token> |
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Suggested change
| <token name="@PROFILE@">24.2</token> | |
| <token name="@PROFILE@">25.0</token> |
| <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/"/> | ||
| </creator> | ||
| <requirements> | ||
| <container type="docker">quay.io/galaxy/sem-analysis-fiji-diameterj:@CONTAINER_VERSION@</container> |
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| <container type="docker">quay.io/galaxy/sem-analysis-fiji-diameterj:@CONTAINER_VERSION@</container> | |
| <container type="docker">quay.io/galaxy/sem-analysis-fiji-diameterj:@TOOL_VERSION@</container> |
Can we use TOOL_VERSION here? This removes redundancy of additional token
bgruening
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Aug 31, 2026
| @@ -0,0 +1,19 @@ | |||
| #!/usr/bin/env python3 | |||
| """Convert all DiameterJ radius-plot TIFFs in a result directory to PNG.""" | |||
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why is this actually needed? Is TIFF not useful?
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I agree. But not sure what our collaborators will require. We share them the tool and fix other feedbacks along with this.
bgruening
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Aug 31, 2026
bgruening
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Small things could be improved, like the arguments, but good to go from my side.
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This PR adds a SEM image analysis tool based on Fiji, DiameterJ with different Auto-thresholding methods
It supports three segmentation methods:
Discussion:
https://gitlab.cc-asp.fraunhofer.de/materialvital-digital/orga/-/work_items/97
@bgruening @paulzierep: we can share this tool with our collaborators and ask their feedback
Analysis image:
PVA-A_004.tif
Analysed by collaborators