Contents

Apply registration

Contents

Apply registration¶

Applies registration to DAPI and barcodes

Invoke¶

Inside the folder with your input data, run:

pyhim -C register_global

registration

Inputs¶

Name shape	Quantity	Mandatory	Description
parameters.json	1	Yes	Parameter file.
register_global.ecsv	1	Yes	XY alignment resulting from the XY alignment produced while running `register_global`.

Outputs¶

Name shape	Quantity	Description
2D_registered.npy	2..n	2D registered images

Relevant options¶

Description¶

To run this function exclusively, run pyHiM using the -C register_global argument. It loads masks, RNA, and barcodes 2D projected images, and applies registrations to them. The resulting images are saved as npy arrays in the alignImages folder.