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Add cellpose parameter cellprob_threshold to the pipeline. Issue #92 #109

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Merged
merged 3 commits into from
Mar 24, 2025
Merged

Add cellpose parameter cellprob_threshold to the pipeline. Issue #92 #109

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d33d298
Merge pull request #105 from nf-core/dev
FloWuenne Mar 6, 2025
3d11386
Add cellpose cellprob_threshold parameter #92
felixS27 Mar 24, 2025
3b6b1cd
Build nextflow_schema
felixS27 Mar 24, 2025
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15 changes: 8 additions & 7 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -207,13 +207,14 @@ process {
ext.args = [ "",
"--channel_axis 0",
"--no_npy",
params.cellpose_save_flows ? "--save_flows" : "",
params.cellpose_diameter ? "--diameter ${params.cellpose_diameter}" : "",
params.cellpose_chan ? "--chan ${params.cellpose_chan}" : "",
params.cellpose_chan2 ? "--chan2 ${params.cellpose_chan2}" : "",
params.cellpose_custom_model ? "" : params.cellpose_pretrained_model ? "--pretrained_model ${params.cellpose_pretrained_model}" : "",
params.cellpose_flow_threshold ? "--flow_threshold ${params.cellpose_flow_threshold}" : "",
params.cellpose_edge_exclude ? "--exclude_on_edges" : ""
params.cellpose_save_flows ? "--save_flows" : "",
params.cellpose_diameter ? "--diameter ${params.cellpose_diameter}" : "",
params.cellpose_chan ? "--chan ${params.cellpose_chan}" : "",
params.cellpose_chan2 ? "--chan2 ${params.cellpose_chan2}" : "",
params.cellpose_custom_model ? "" : params.cellpose_pretrained_model ? "--pretrained_model ${params.cellpose_pretrained_model}" : "",
params.cellpose_flow_threshold ? "--flow_threshold ${params.cellpose_flow_threshold}" : "",
params.cellpose_edge_exclude ? "--exclude_on_edges" : "",
params.cellpose_cellprob_threshold ? "--cellprob_threshold ${params.cellpose_cellprob_threshold}": ""
].join(" ").trim()
publishDir = [
path: "${params.outdir}/segmentation/cellpose",
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17 changes: 9 additions & 8 deletions nextflow.config
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Expand Up @@ -17,14 +17,15 @@ params {
segmentation_min_area = null
segmentation_max_area = null
// cellpose
cellpose_save_flows = false
cellpose_diameter = 30
cellpose_chan = 0
cellpose_chan2 = null
cellpose_pretrained_model = 'cyto'
cellpose_custom_model = null
cellpose_flow_threshold = 0.4
cellpose_edge_exclude = true
cellpose_save_flows = false
cellpose_diameter = 30
cellpose_chan = 0
cellpose_chan2 = null
cellpose_pretrained_model = 'cyto'
cellpose_custom_model = null
cellpose_flow_threshold = 0.4
cellpose_edge_exclude = true
cellpose_cellprob_threshold = 0
// mesmer
mesmer_image_mpp = 0.138
mesmer_compartment = 'whole-cell'
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11 changes: 8 additions & 3 deletions nextflow_schema.json
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Expand Up @@ -70,8 +70,13 @@
"cellpose_save_flows": {
"type": "boolean",
"description": "Should flow fields from Cellpose be saved?",
"fa_icon": "fas fa-arrows-alt",
"hidden": true
"fa_icon": "fas fa-arrows-alt"
},
"cellpose_cellprob_threshold": {
"type": "integer",
"default": 0,
"fa_icon": "fas fa-border-style",
"description": "Cell probability threshold for Cellpose"
},
"mesmer_image_mpp": {
"type": "number",
Expand Down Expand Up @@ -164,7 +169,7 @@
},
"clahe_kernel": {
"type": "number",
"default": 25.0,
"default": 25,
"description": "Kernel size to be used by CLAHE.",
"fa_icon": "far fa-object-group"
},
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