From 512bd5ca148d6ead633a0c3b1d8bde48aef954a7 Mon Sep 17 00:00:00 2001 From: Beth Cimini Date: Wed, 11 Sep 2024 09:13:31 +0200 Subject: [PATCH] Settings cleanup --- active_plugins/enforceobjectsonetoone.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/active_plugins/enforceobjectsonetoone.py b/active_plugins/enforceobjectsonetoone.py index aaaf64b..cbc3d42 100644 --- a/active_plugins/enforceobjectsonetoone.py +++ b/active_plugins/enforceobjectsonetoone.py @@ -81,13 +81,12 @@ def create_settings(self): Pre-primary objects are the objects that will be considered the Primary objects after one-to-one relationship is forced. In CellProfiler, we typically define an object as - *Primary* when it can be found in an object without needing the assistance of another - cellular feature. Nuclei are a common example of primary objects. + *Primary* when it can be found in an image directly, rather than being built by relationship to another object. + Nuclei are a common example of primary objects. - Unlike our typical definition of Primary object, in this module, the Pre-primary object may have been identified - using any other module (e.g. IdentifyPrimaryObjects, IdentifySecondaryObjects) or plugin (e.g. RunCellpose, RunStardist). - The Pre-primary objects will act as the seed objects and the Pre-secondary objects will be - filtered to a one-to-one-relationship. + In this module, the Pre-primary object may have been identified using any other module (e.g. IdentifyPrimaryObjects, + IdentifySecondaryObjects) or plugin (e.g. RunCellpose, RunStardist). + The Pre-primary objects and the Pre-secondary objects will be filtered to a one-to-one-relationship. """ self.y_name = LabelSubscriber( @@ -98,13 +97,13 @@ def create_settings(self): Pre-secondary objects are the objects that will be considered the Secondary objects after one-to-one relationship is forced. In CellProfiler, we typically define an object as - *Secondary* when it can be found in an image by using another cellular feature as a reference for guiding detection. + *Secondary* when it can be found in an image by expansion from a smaller, already-defined primary object as + a reference for guiding detection. Cell bodies are a common example of secondary objects identified using Nuclei as primary objects. Unlike our typical definition of Secondary object, in this module, the Pre-secondary object may have been identified using any other module (e.g. IdentifyPrimaryObjects, IdentifySecondaryObjects) or plugin (e.g. RunCellpose, RunStardist). - The Pre-primary objects will act as the seed objects and the Pre-secondary objects will be - filtered to a one-to-one-relationship. + The Pre-primary objects and the Pre-secondary objects will be filtered to a one-to-one-relationship. """, ) @@ -129,7 +128,8 @@ def create_settings(self): self.image_name = ImageSubscriber( "Select the image for visualization", - "None", + can_be_blank=True, + blank_text="None", doc="""\ Select an image to see enforced objects superimposed on in the module display.""", )