brainglobe / brainglobe-registration

Registration to BrainGlobe atlases in napari using Elastix

BrainGlobe

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brainglobe-registration's Issues

[BUG] Changing atlas selection doesn't replace annotations layer

Describe the bug
When changing the selected atlas using the UI, the reference image of the old atlas is replaced with the new one, however the annotations layer of the old atlas remains.

To Reproduce
Have at least two atlases, open the plugin and select the first atlas, then change the selection to the other atlas.

Expected behaviour
Both the reference and atlas image of the old atlas are replaced with the new one

[Feature] Filter the moving and fixed image prior to registration

brainreg preprocesses the images prior to registration by filtering. We should replicate this functionality.

This will need a toggle in the UI, maybe a checkbox right above the Run button labelled Filter Images.

[BUG] Crash on opening latest plugin version

Describe the bug
On opening Napari, and selecting Plugins > BrainGlobe Registration, it crashes with Process finished with exit code -1073741819 (0xC0000005)

To Reproduce
I have a local development environment setup like so:

conda create -n brainglobe-dev -c conda-forge python=3.10 napari
conda activate brainglobe-dev
pip install -e .[dev]
pip install lxml_html_clean

Then I open Napari, and select Plugins > BrainGlobe Registration.

Computer used (please complete the following information):

• OS: Windows
• Version: Windows 11, version 23H2

Communicate napari layer deletions appropriately to the plugin

Currently, if a user deletes the atlas or moving image layer the plugin goes into undefined behaviour and will probably throw index out of bounds errors.

Need to make sure that layer deletions are communicated appropriately and the plugin can handle restarting the entire workflow without having to restart the plugin.

BrainGlobe general-purpose registration tool

This issue is to start listing features and plans for a general purpose BrainGlobe registration tool. We can discuss here, and then priorities features, turning these into issues and milestones.

Scientific requirements

• Registration of any brain subvolume, including:
  • 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)

Tech requirements

• Python-based (compatibility with BrainGlobe & other bioimage analysis tools)
• Includes a napari plugin for pre-processing and compatibility with BrainGlobe ecosystem
• Registration using elastix (likely itk-elastix) due to community support and existing parameter sets
• Includes default preprocessing options (e.g. using scikit-image)
• Registers to any BrainGlobe atlas
• Compatible with downstream BrainGlobe tools (brainreg-segment, cellfinder etc)
• Compatible with other napari plugins
• Can be automated

Potential steps

• Flexible interface to allow:
  • Data preprocessing
  • Appropriate atlas cropping
  • Running registration
  • Saving results

Mockup

cc @alessandrofelder @raacampbell @viktorpm

Mark the advanced settings menu as optional

The Advanced Setting part should be somehow marked as different to the others, because the current UI might imply that it's a mandatory rather than optional step on the way to clicking the "Run" button?

Originally posted by @alessandrofelder in #25 (review)

[BUG] Plugin crash when no brainglobe atlases available

Describe the bug
Napari plugin crashes if there are no Brainglobe atlases available

To Reproduce
Open the plugin in a fresh install with no Brainglobe atlases available.

Expected behaviour
Plugin should open successfully and prompt user to download an atlas

Computer used (please complete the following information):

• OS: Linux
• Version Ubuntu 20.04.6
• Hardware specs i9-13900K, 32GB RAM, RTX 4080

Integrate better with elastix napari plugin

https://github.com/SuperElastix/elastix_napari

Don't want to reproduce functionality of this plugin, and we want to better integrate with the napari plugin ecosystem

Create high level tests for plugin

Maybe think about adding high-level tests checking things like "does the napari plugin have the expected number of widgets with the expected/type name"? (in a separate PR)

Originally posted by @alessandrofelder in #25 (review)

Support different image resolutions

I may be wrong, but this plugin seems like it relies on the input data being the same resolution as the atlas.

Update to Python 3.12

Add tests

Store sample data on GIN and fetch with pooch

This plugin may end up with a lot of test/sample data, and it would be good to host it outside of git, before the repo size inflates.

Rename tool

The name should better describe what it does. Could be something as similar as brainglobe-registration

Standardise package structure and tooling with other BG repos

The tooling is different to other tools we use, and is missing some elements (like a [dev] extra). The package structure and tooling can just be taken from our cookiecutter and looking at other repos.