# 2D histological image registration, human prefrontal brain

**URL:** <https://community.brain-map.org/t/2d-histological-image-registration-human-prefrontal-brain/879>\
**Category:** Technical\
**Tags:** atlas-human-brain-adult\
**Created:** [January 5, 2021, 12:30pm UTC](https://community.brain-map.org/t/2d-histological-image-registration-human-prefrontal-brain/879 "2021-01-05T12:30:10Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![pjanjic](https://avatars.discourse-cdn.com/v4/letter/p/8dc957/32.png) [@pjanjic](https://community.brain-map.org/u/pjanjic)\
**Post date:** [January 5, 2021, 12:30pm UTC](https://community.brain-map.org/t/2d-histological-image-registration-human-prefrontal-brain/879/1 "2021-01-05T12:30:11Z")

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Hi,  
Which tool & atlas combination tested on BICCN human brain atlases would support 2d registration of fluorescent image stacks of 30micron samples from thick prefrontal coronal slices of human brain? The purpose is to obtain comparable XY orientation of the samples from different brains.

As a missing spatial coordinate we have the position of the thick slice/side of the sample along the rostral-caudal axis to eventually select range of slices (if we refer to the Allen’s interactive 2d atlas).

Thanks,  
Predrag Janjic

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**Author:** ![lydian](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/lydian/32/174_2.png) [@lydian](https://community.brain-map.org/u/lydian)\
**Post date:** [March 8, 2021, 8:54pm UTC](https://community.brain-map.org/t/2d-histological-image-registration-human-prefrontal-brain/879/2 "2021-03-08T20:54:44Z")

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Hi Predrag,

Re: atlases

Beyond the 2D Allen Human Reference Atlas, here are some other atlas resources you could take a look at

- 3D Allen Human Reference Atlas annotation on MNI space  
[Allen Human Reference Atlas - 3D, 2020 (new!)](https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405)

- The Big Brain project  
[https://bigbrainproject.org/](https://bigbrainproject.org/) with integration of layers and cytoarchitectonic maps

- The Human Connectome Project has multi-modal cortical parcellation  
[A multi-modal parcellation of human cerebral cortex](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990127/)

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**Author:** ![mkunst23](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/mkunst23/32/320_2.png) [@mkunst23](https://community.brain-map.org/u/mkunst23)\
**Post date:** [March 8, 2021, 10:08pm UTC](https://community.brain-map.org/t/2d-histological-image-registration-human-prefrontal-brain/879/3 "2021-03-08T22:08:26Z")

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Hi Predrag,

there are currently multiple options available to register 2D sections onto a 3D atlas. You can find a brief discussion and further links here:

> **[Development of Python-based 2D section -\> 3D atlas registration tool](https://forum.image.sc/t/development-of-python-based-2d-section-3d-atlas-registration-tool/39719)**
>
> Hi all, During the development of cellfinder and amap, I have been asked many times about registration of 2D tissue sections to a 3D anatomical atlas, and there appears to be demand for a new Python-based tool to do this. To be clear, there are...

I also suggest checking out the slicereg project which aims at providing a python module to make exactly this problem easier.

> **[brainglobe/slicereg](https://github.com/brainglobe/slicereg)**
>
> A 2D-3D histological brain slice registration application for mouse brains.