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2 | 2 | <description>with Cellpose-SAM</description> |
3 | 3 | <macros> |
4 | 4 | <token name="@TOOL_VERSION@">4.0.8</token> |
5 | | - <token name="@VERSION_SUFFIX@">0</token> |
| 5 | + <token name="@VERSION_SUFFIX@">1</token> |
6 | 6 | </macros> |
7 | 7 | <requirements> |
8 | 8 | <requirement type="package" version="@TOOL_VERSION@">cellpose</requirement> |
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97 | 97 | <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."/> |
98 | 98 | <param name="no_resample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables flows/cellprob resampling to original image size before computing masks." |
99 | 99 | help="Using this flag will make more masks more jagged with larger diameter settings."/> |
100 | | - <param name="no_interp" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Interpolate when running dynamics."/> |
| 100 | + <param name="no_interp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not interpolate when running dynamics."/> |
101 | 101 | <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)"/> |
102 | 102 | <param name="cellprob_threshold" type="float" value="0.0" label="Cell probability threshold (all pixels with prob above threshold kept for masks)"/> |
103 | 103 | <param name="niter" type="integer" min="0" value="0" label="Number of iterations" |
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137 | 137 | <param name="save_tif" value="true"/> |
138 | 138 | <output name="cp_tiff" file="image_cp_masks.tiff" compare="image_diff" metric="iou"/> |
139 | 139 | <output name="cp_png" file="image_cp_masks.png" compare="image_diff" metric="iou"/> |
| 140 | + <section name="options"> |
| 141 | + <param name="no_interp" value="true"/> |
| 142 | + </section> |
140 | 143 | </test> |
141 | 144 | <test expect_num_outputs="1"> |
142 | 145 | <param name="img_in" value="image3d.tiff"/> |
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159 | 162 | <param name="save_outlines" value="true" /> |
160 | 163 | <param name="use_gpu" value="true" /> |
161 | 164 | <param name="detailed_output" value="true" /> |
| 165 | + <section name="options"> |
| 166 | + <param name="no_interp" value="true"/> |
| 167 | + </section> |
162 | 168 | <output name="cp_png" file="image_cp_masks.png" compare="image_diff" metric="iou"/> |
163 | 169 | <output name="cp_flows" file="image_flows_cp_masks.tiff" compare="image_diff" /> |
164 | 170 | <output name="cp_flows_dp" file="image_dP_cp_masks.tiff" compare="image_diff" /> |
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177 | 183 | <section name="options"> |
178 | 184 | <param name="no_norm" value="false" /> |
179 | 185 | <param name="no_resample" value="false" /> |
| 186 | + <param name="no_interp" value="true"/> |
180 | 187 | <param name="diameter" value="10" /> |
181 | 188 | <param name="flow_threshold" value="0.5" /> |
182 | 189 | <param name="cellprob_threshold" value="0.0" /> |
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