Describe each tool better within the docs

[adamltyson]

Currently the page dedicated to each tool in the docs often doesn't describe what the tool actually does. Paragraph 1 should be a succint description of the tool, along with main advantages and disadvantages.

[sid-42-d]

Hi, @adamltyson

I have started exploring brainglobe-registration and would like to help with this documentation task. Over the last few days I set up the plugin in napari, installed the allen_mouse_25um atlas, and ran the sample 2D coronal mouse brain section through the default affine + bspline registration to see how the tool behaves and what files it produces.

Based on this first exploration, here is a draft of the short description + advantages/disadvantages that you requested for the docs page:

What brainglobe-registration does

brainglobe-registration is a napari plugin for interactively registering 2D or 3D microscopy images of the brain to BrainGlobe atlases using Elastix. It allows a user to choose an atlas and approximate slice, adjust the relative pose of image and atlas, run a configurable affine + non‑linear (bspline) registration pipeline, and visualise the aligned atlas boundaries and annotations directly on top of their data.

Main advantages

• Interactive, visual registration inside napari, which makes it easy to inspect alignment and manually refine slice selection and pose before and after optimisation

• Uses the BrainGlobe atlas ecosystem, so multiple species/atlas resolutions are supported and outputs can be reused in other BrainGlobe tools.

• Provides both forward and inverse transforms and derived images (e.g. registered atlas, boundaries, deformation fields), which are useful for downstream analysis.

Main disadvantages / current limitations

• Designed mainly for registering individual slices or small volumes rather than fully automated, large‑scale whole‑brain processing.

• Early‑stage interface (as noted in the README), so parameters and UI layout may change and some advanced features are still missing.

• Depends on napari and Elastix, so installation and performance can be more demanding than simpler, non‑GUI tools.

Would this style and level of detail fit what you have in mind for the first paragraph of each tool’s docs page? If yes, I can open a PR adding this text (or a refined version) to the brainglobe-registration docs, and then repeat the same pattern for other tools as I explore them.

[alessandrofelder]

Hi @sid-42-d - thanks for your interest in BrainGlobe.

I think this is best left for core developers (it's technically on my plate... but I am slow 🐌 😂 ) as it requires in-depth knowledge of the appropriate use cases for each tool.