. Author manuscript; available in PMC: 2021 Oct 19.

Published in final edited form as: Nat Protoc. 2021 Feb 22;16(3):1647–1713. doi: 10.1038/s41596-020-00478-x

Table 7 |.

Loading parameters for RNA data in BuildMosaicsGUI

Parameter name	Default value	Function
chnTableFile		Enter the path to your experiment layout file here (e.g. E:\20l7-11-30_WT_10-12hrs_(HoxRNA)_(BXC3kb)\RNA\RNAtable.xlsx)
analysisFolder	.\Analysis\	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’
dataType	all	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 RNA mosaic, do not change the default setting. ‘All’ is necessary for loading RNA data as it will take the fiducial information for drift correction and the readout data to display RNA information. Depending on how many RNAs you labeled and the number of FOVs recorded, this step will take a while
hybNumber	inf	Do not change the default ‘inf’ as this will use fiducial data from all RNA readouts for drift correction
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]”)