Parameter name	Default value	Function
ROIs	all	By default, a distance map for all ROIs that have been saved will be populated. You can choose to change this for a specific ROI (e.g. “A1”). If you choose to view multiple ROIs, make sure to not insert a space between each ROI (e.g. “A1,A2,A3”)
threshold	150	This will display the fraction of cells in which the pairwise interactions are within 150 nm
figHandle	200	‘200’ is the default figure handle of the distance map (see the bottom-right corner of Fig. 13c). Having figures with unique figure handles allows you to access a specific figure, such as saving a specific figure. To avoid clearing a previously generated distance map, change the figHandle number to one that has not been previously used (e.g. 307)
badHybes		After generating the distance map, you may notice that some barcodes have poor labeling (e.g. prominent stripes that are seen throughout the distance map). If so, enter the barcode number(s) that did not label well (e.g. 16,26,39). Additionally, if you have previously generated distance maps for the total population of cells after running ChrTracer3, you might already know which barcode(s) labeled poorly. Enter those barcode numbers here