# Confocal imaging alignment
**URL:** https://discourse.itk.org/t/confocal-imaging-alignment/5252
**Category:** Beginner Questions
**Created:** [August 9, 2022, 8:41am UTC](https://discourse.itk.org/t/confocal-imaging-alignment/5252 "2022-08-09T08:41:00Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@mixail\_orfanakis](https://discourse.itk.org/u/mixail_orfanakis)
#### Post date: [August 9, 2022, 8:41am UTC](https://discourse.itk.org/t/confocal-imaging-alignment/5252/1 "2022-08-09T08:41:00Z")
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!
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### Author:  [@zivy](https://discourse.itk.org/u/zivy)
#### Post date: [August 10, 2022, 2:10am UTC](https://discourse.itk.org/t/confocal-imaging-alignment/5252/2 "2022-08-10T02:10:36Z")
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](https://github.com/niaid/imaris_extensions/issues) to ask for help with those programs. This forum is dedicated to the ITK/SimpleITK toolkits.