Add normalization settings to RunCellpose

* updated runcellpose.py

* update runcellpose

Author: ShataDg

active_plugins/runcellpose.py

@@ -83,9 +83,11 @@
 
 """
 
+"Select Cellpose Docker Image"
 CELLPOSE_DOCKER_NO_PRETRAINED = "cellprofiler/runcellpose_no_pretrained:0.1"
 CELLPOSE_DOCKER_IMAGE_WITH_PRETRAINED = "cellprofiler/runcellpose_with_pretrained:0.1"
 
+"Detection mode"
 MODEL_NAMES = ['cyto','nuclei','tissuenet','livecell', 'cyto2', 'general',
                 'CP', 'CPx', 'TN1', 'TN2', 'TN3', 'LC1', 'LC2', 'LC3', 'LC4', 'custom']
 
@@ -95,7 +97,7 @@ class RunCellpose(ImageSegmentation):
 
     module_name = "RunCellpose"
 
-    variable_revision_number = 4
+    variable_revision_number = 5
 
     doi = {
         "Please cite the following when using RunCellPose:": "https://doi.org/10.1038/s41592-020-01018-x",
@@ -105,6 +107,16 @@ class RunCellpose(ImageSegmentation):
     def create_settings(self):
         super(RunCellpose, self).create_settings()
 
+        self.rescale = Binary(
+            text="Rescale images before running Cellpose",
+            value=True,
+            doc="""\
+Reminds the user that the  normalization step will be performed to ensure suimilar segmentation behaviour inthe RunCellpose
+modul and the Cellpose app.
+"""
+        )
+
+
         self.docker_or_python = Choice(
             text="Run CellPose in docker or local python environment",
             choices=["Docker", "Python"],
@@ -340,6 +352,7 @@ def set_directory_fn(path):
     def settings(self):
         return [
             self.x_name,
+            self.rescale,
             self.docker_or_python,
             self.docker_image,
             self.expected_diameter,
@@ -365,7 +378,8 @@ def settings(self):
         ]
 
     def visible_settings(self):
-        vis_settings = [self.docker_or_python]
+        vis_settings = [self.rescale, self.docker_or_python]
+
 
         if self.docker_or_python.value == "Docker":
             vis_settings += [self.docker_image]
@@ -440,6 +454,13 @@ def run(self, workspace):
         x = images.get_image(x_name)
         dimensions = x.dimensions
         x_data = x.pixel_data
+
+        if self.rescale.value:
+            rescale_x = x_data.copy()
+            x01 = numpy.percentile(rescale_x, 1)
+            x99 = numpy.percentile(rescale_x, 99)
+            x_data = numpy.clip((rescale_x - x01) / (x99 - x01), a_min=0, a_max=1)
+
         anisotropy = 0.0
         if self.do_3D.value:
             anisotropy = x.spacing[0] / x.spacing[1]
@@ -699,4 +720,9 @@ def upgrade_settings(self, setting_values, variable_revision_number, module_name
         if variable_revision_number == 3:
             setting_values = [setting_values[0]] + ["Python",CELLPOSE_DOCKER_IMAGE_WITH_PRETRAINED] + setting_values[1:]
             variable_revision_number = 4
+        if variable_revision_number == 4:
+            setting_values = [setting_values[0]] + ['No'] + [setting_values[1:]]
+            variable_revision_number = 5
         return setting_values, variable_revision_number
+    
+