diff --git a/conf/modules.config b/conf/modules.config
index 1bcde4a..1022027 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -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",
diff --git a/nextflow.config b/nextflow.config
index 900c616..f6f81a2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -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'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 29145b0..e90350e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -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",
@@ -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"
                 },