Confocal imaging alignment

Hallo everyone,

I am trying to align different images obtained either from confocal microscopy or from vectra polaris. I am using the Simple ITK imaris python extension, but since I do not have any idea of how the algorithm is working I can not do troubleshooting. Especially, with confocal obtained 3D images the algorithm sometimes is working and sometimes is not, but I can not find a specific pattern to address why this is happening. Do you have any recommendations, tips, in order to improve the process?

Thank you in advance!

1 Like

Hello @mixail_orfanakis,

If the registration of confocal 3D images fails when using the default settings in that program:

  1. Change the defaults, under the advanced registration settings: uncheck the “FFT based initialization” and check the “2D affine”.
  2. If the fixed image is the first in the iterative bleaching/staining cycles, change it to one of the other images (the first doesn’t undergo bleaching).

For further discussion please use the imaris extension’s GitHub issue tracker to ask for help with those programs. This forum is dedicated to the ITK/SimpleITK toolkits.