Here, you want to select a method that will accurately identify the protein of interest as foreground. We chose to discard small and large objects, which tend to be spurious, and discard those objects at the border because we will be making area-based measurements.', '', 'The chosen thresholding method can greatly affect segmentation. IdentifyPrimaryObjects: for the min/max size we expect the objects to be. Select where to measure correlation:Across entire imageĬalculate correlation and slope metrics?:YesĬalculate the Rank Weighted Colocalization coefficients?:YesĬalculate the Manders coefficients using Costes auto threshold?:Yes Set threshold as percentage of maximum intensity for the images:15.0 MeasureColocalization:|batch_state:array(, dtype=uint8)|enabled:True|wants_pause:False] Select the alignment method:Mutual Information Set output image values greater than 1 equal to 1?:YesĪlign:|batch_state:array(, dtype=uint8)|enabled:True|wants_pause:False] Set output image values less than 0 equal to 0?:Yes Select the illumination function:IllumStain2 Select how the illumination function is applied:Divide Select the illumination function:IllumStain1 Method to calculate smoothing filter size:AutomaticĪutomatically calculate spline parameters?:YesĬorrectIlluminationApply:|batch_state:array(, dtype=uint8)|enabled:True|wants_pause:False] Select how the illumination function is calculated:Regularĭilate objects in the final averaged image?:NoĬalculate function for each image individually, or based on all images?:Each Groups:|batch_state:array(, dtype=uint8)|enabled:True|wants_pause:False]ĬorrectIlluminationCalculate:|batch_state:array(, dtype=uint8)|enabled:True|wants_pause:False] Select the rule criteria:and (file does contain "N_G") Select the rule criteria:and (file does contain "N_R") NamesAndTypes:|batch_state:array(, dtype=uint8)|enabled:True|wants_pause:False] Select the filtering criteria:and (file does contain "") Regular expression to extract from file name:^(?P.*)_(?P)$ Metadata extraction method:Extract from file/folder names Metadata:|batch_state:array(, dtype=uint8)|enabled:True|wants_pause:False] Select the rule criteria:and (extension does isimage) (directory doesnot containregexp "\\.") to distinguish between colocalized objects with children (child count of 1 or. Images:|batch_state:array(, dtype=uint8)|enabled:True|wants_pause:False] Contribute to CellProfiler/examples development by creating an account on.
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