Setup

Images

1. Add TIFF / TIF images

   [Formatting should be such as HL60_full_1_DAPI2-T2]

   • Requires extracting separate image channels from ZEN Blue

Metadata

^(?P<Cell>.*)_(?P<Type>.*)_(?P<Number>[0-9]{1,2})(_(?P<Channel>.*))?(?=.tif$)

• Cell, Type and Channel can be any length of characters
• Number is 1 or 2 numbers
• Channel is Optional (denoted by the ?)
• (?=.tif$) gets rid of the tif
• https://regex101.com/

Names and Types

• Select “Assign images matching rules”.
• Make a new rule [Metadata][Does][Have Stain matching][DAPI2-T2] and name it DAPI.
• Click the “Add” button to define another image with a rule.
• Make a new rule [Metadata][Does][Have Stain matching][FITC-T1] and name it  $\beta$-catenin.
• Click the “Add” button to define another image with a rule.
• Make a new rule [Metadata][Does][Have Stain matching][phase] and name it OrigPhase.
• In the “Image set matching method” setting, select “Metadata”.
• Click the “Update” button below the divider to view the resulting table and confirm that the proper files are listed and matched across the channels. The corresponding well and frame for each channel should now be matched to each other.