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Fix no_interp parameter in Cellpose-SAM wrapper
Updated version suffix and modified interpolation parameter settings.
1 parent 887d878 commit 0112c53

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Lines changed: 9 additions & 2 deletions

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tools/cellpose_v4/cellpose.xml

Lines changed: 9 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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<description>with Cellpose-SAM</description>
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<macros>
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<token name="@TOOL_VERSION@">4.0.8</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<token name="@VERSION_SUFFIX@">1</token>
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</macros>
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<requirements>
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<requirement type="package" version="@TOOL_VERSION@">cellpose</requirement>
@@ -97,7 +97,7 @@
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<param name="diameter" type="float" optional="true" label="Cell or nuclei diameter in pixels" help="Use to resize cells to the training diameter. Leave blank for automated estimation."/>
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<param name="no_resample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables flows/cellprob resampling to original image size before computing masks."
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help="Using this flag will make more masks more jagged with larger diameter settings."/>
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<param name="no_interp" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Interpolate when running dynamics."/>
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<param name="no_interp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not interpolate when running dynamics."/>
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<param name="flow_threshold" type="float" min="0" value="0.4" label="Flow error threshold (all cells with errors below threshold are kept) (not used for 3D)"/>
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<param name="cellprob_threshold" type="float" value="0.0" label="Cell probability threshold (all pixels with prob above threshold kept for masks)"/>
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<param name="niter" type="integer" min="0" value="0" label="Number of iterations"
@@ -137,6 +137,9 @@
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<param name="save_tif" value="true"/>
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<output name="cp_tiff" file="image_cp_masks.tiff" compare="image_diff" metric="iou"/>
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<output name="cp_png" file="image_cp_masks.png" compare="image_diff" metric="iou"/>
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<section name="options">
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<param name="no_interp" value="true"/>
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</section>
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</test>
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<test expect_num_outputs="1">
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<param name="img_in" value="image3d.tiff"/>
@@ -159,6 +162,9 @@
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<param name="save_outlines" value="true" />
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<param name="use_gpu" value="true" />
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<param name="detailed_output" value="true" />
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<section name="options">
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<param name="no_interp" value="true"/>
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</section>
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<output name="cp_png" file="image_cp_masks.png" compare="image_diff" metric="iou"/>
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<output name="cp_flows" file="image_flows_cp_masks.tiff" compare="image_diff" />
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<output name="cp_flows_dp" file="image_dP_cp_masks.tiff" compare="image_diff" />
@@ -177,6 +183,7 @@
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<section name="options">
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<param name="no_norm" value="false" />
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<param name="no_resample" value="false" />
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<param name="no_interp" value="true"/>
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<param name="diameter" value="10" />
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<param name="flow_threshold" value="0.5" />
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<param name="cellprob_threshold" value="0.0" />

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