Image_registration_2 macro

Relevant to Figure 2; Extended Data Figure 5, 6

This ImageJ macro follows on from Image_registration_1 and applies the transformation to the other channels of the IMHC image.

Close any open images and open the 2P z-projected image and the IMHC image.

Parameters to change:

• date: date of the 2P imaging in the form YYYYMMDD (important that it matches the Transformation file)
• stainReg: the name of the antibody and fluorophore of the registration channel
• stain1/stain2/stain3: antibody and fluorophore for the other channels (not registration channel)
• stain1ch/stain2ch/stain3ch: matching channels for stain1/stain2/stain3 antibodies
• pixels_permicron: set to the scaling used (match the confocal image)

Output:

• Reg_source images for each channel: the remaining IMHC image channels registered to 2P image. These are saved individually.
• Final_reg image: all IMHC channels registered to the 2P image.