what's their directory pathname on lines 24 and 29.

Hello,

Thank you for asking this question. The directory pathname, or directory, is your computers pathway that is associated with a specific folder or file. In this case, the Pathname is associated with the 'pixel_classifiers' folder. This folder should contain the Fibrosis.json and Macrophages.json file. Please see below a schematic outlining the steps to get the pathname. An example of a directory pathname would be:

'/home/user/documents/New Folder/classifiers/pixel_classifiers/Fibrosis.json'

Note: This pathname should be entered into the appropriate line within the intensity script. The lines where you should put your pathname should start with 'Def file' and 'new File'.

Note 2: Step C in the protocol outlines the steps to generate the appropriate folders and where to place specific files. Each .GROOVY script is well annotated, and can be helpful when read.

Please do not hesitate to reach out to me with any additional questions or concerns - I am happy to help: Dominick.hellen@emory.edu

Best,

Dominick