index.qmd

---
title: brainglobe-registration
subtitle: A registration napari plugin for BrainGlobe
author: Igor Tatarnikov
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## Contents

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* Motivation for brainglobe-registration
* Current state of the project
* Future plans
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## Motivation

![](img/Accurate_determination_of_marker_location_Fig1.png){fig-align="center"}

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Tyson, A. L.*, Vélez-Fort, M.*, Rousseau, C. V.*, Cossell, L., Tsitoura, C., Obenhaus, H. A., Claudi, F., Lenzi, S. C., Branco, T., Margrie, T. W. (2022) “Accurate determination of marker location within whole-brain microscopy images” Scientific Reports, 12, 867, [doi.org/10.1038/s41598-021-04676-9](https://doi.org/10.1038/s41598-021-04676-9)
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## Motivation

![](img/2D_Example1.png){.absolute left=0 right=0 bottom=0 top=0 style="margin: auto auto;"}

## Motivation

![](img/2D_Example2.png){.absolute width="65%" left=0 right=0 bottom=0 top=0 style="margin: auto auto;"}

## Motivation

![](img/2D_Example3.png){.absolute left=0 right=0 bottom=0 top=0 style="margin: auto auto;"}

## Scientific Requirements

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* Register:
    * 2D sections (any orientation, inc some damage)
    * Whole brains
    * Thick sections (e.g. from tissue clearing, acute recordings)
    * Small blocks (e.g. from tissue clearing or expansion microscopy)
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## Tech Requirements

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* Python-based (compatibility with BrainGlobe)
* Includes a napari plugin for pre-processing and compatibility with BrainGlobe ecosystem
* Registration using itk-elastix due to community support and existing parameter sets
* Includes default preprocessing options
* Registers to any BrainGlobe atlas
* Compatible with downstream BrainGlobe tools
* Compatible with other napari plugins
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## Mockup

![](img/BrainGlobe_Registration_MockUp.png)

## Current state of the project

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* Demo Time!
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## Future plans

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* Data preprocessing
* Registering damaged 2D slices
* Optimising registration parameters to provide a good default
* Creating a pipeline to take images from the SlideScanner and register them to an atlas
* Registering arbitrary 3D volumes
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