Table 6 |.

Loading parameters for DNA data in BuildMosaicsGUI

Parameter name	Default value	Change	Function value to
chnTableFile			Enter the path to your experiment layout file here (e.g. E:\2017-11-30_WT_10-12hrs_(HoxRNA)_(BXC3kb)\DNA\ExperimentLayout.xlsx)
analysisFolder	.\Analysis\		Default value “.\Analysis\” is recommended. Saved alignment results and mosaics will be placed in the Analysis folder. “.\” notation saves data in whichever folder the chnTableFile is located, inside the newly created folder ‘Analysis’. There should already be an ‘Analysis’ folder created if ChrTracer3 ran before this step. No changes need to be made here
dataType	all	fiducial	This specifies which data to create max projections of, fiducial, readout data, or all. The default is ‘all’, which corresponds to both the fiducial and readout channel. For creating a DNA/ORCA mosaic, type in 'fiducial' since you will only need to know the nanoscale positions of fiducial spots and do not need to create a mosaic for individual DNA readouts. If ChrTracer3 was already used in this dataset, it would have already created max-projections and this step will go by quickly as BuildMosaicsGUI will only need to load already created max projected fiducial data
hybNumber	inf	1	To create a DNA mosaic, only the fiducial data from readout 1 is needed. Thus, change the default ‘inf’ to ‘1’ to specify to use data only from readout 1
fov	inf		The default is ‘inf’ to process data from all FOVs in the folder. This default value is recommended to use. It is optional to select a subset of FOVs (e.g. “[2:10,15:35]”)