# 3D image registration of microscopy image

**URL:** <https://discourse.slicer.org/t/3d-image-registration-of-microscopy-image/33604>\
**Category:** Feature requests\
**Tags:** microscopy\
**Created:** [January 3, 2024, 3:31pm UTC](https://discourse.slicer.org/t/3d-image-registration-of-microscopy-image/33604 "2024-01-03T15:31:18Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![ylcnkzy](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ylcnkzy/32/12189_2.png) [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Post date:** [January 3, 2024, 3:31pm UTC](https://discourse.slicer.org/t/3d-image-registration-of-microscopy-image/33604/1 "2024-01-03T15:31:19Z")

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Hi Everyone,

I have 2 different microscopy images in 3D tiff format. Now, both images cover similar areas and structures (image below).

 ![Picture1_mutual areas](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/4/0/4006a4c81534acd5a666488f7179e1dba2747181.jpeg)

I plan to align and register them, and create a deformation vector field) for them.

I am unsure which settings to go with.

The original tiff files are [here](https://drive.google.com/drive/folders/1f0wMa1CdFjkTpYRSjk2RivEr6JgGQUz0?usp=sharing).

it would be great to hear about the ideas and tools to perform that.

Best

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<div class="post-metadata">

**Author:** ![ylcnkzy](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ylcnkzy/32/12189_2.png) [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Post date:** [January 10, 2024, 12:16pm UTC](https://discourse.slicer.org/t/3d-image-registration-of-microscopy-image/33604/2 "2024-01-10T12:16:34Z")

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The data is now public.

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<div class="post-metadata">

**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [January 10, 2024, 3:16pm UTC](https://discourse.slicer.org/t/3d-image-registration-of-microscopy-image/33604/3 "2024-01-10T15:16:24Z")

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Have you looked at tools that are designed specifically to work with microscopy images?

Here’s a quick find that might be relevant from ImageJ documentation: [Registration](https://imagej.net/imaging/registration).