overhauled README, added examples and hopefully made things clearer

[Hendrik-code]

No description provided.

[Copilot]

Pull request overview

This PR refreshes and expands the project’s Markdown documentation to make TPTBox easier to understand and adopt, adding more examples, screenshots, and a new contribution guide.

Changes:

• Reworked the top-level README.md structure (features, quick usage, module index, publications).
• Added/expanded per-subpackage READMEs with more detailed examples and visuals (core pillars, snapshot2D, mesh3D, stitching, segmentation, registration).
• Added a new CONTRIBUTING.md describing local setup and project style/check commands.

Reviewed changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 15 comments.

Show a summary per file

File	Description
README.md	Reorganized project landing page; added navigation, features list, module index, and publications list.
CONTRIBUTING.md	New contributor guide with setup, checks, and code style expectations.
TPTBox/core/README.md	Refocused “core” docs around NII/POI/BIDS and added NumPy utility examples.
TPTBox/core/README_NII.md	New NII-focused README with a quick usage snippet.
TPTBox/core/README_POI.md	New POI-focused README with screenshots and extended examples.
TPTBox/core/README_BIDS.md	New BIDS-focused README with dataset iteration and path-derivation examples.
TPTBox/spine/snapshot2D/README.md	Added screenshot and a more extensive snapshot example.
TPTBox/mesh3D/README.md	Added screenshot, installation section, and a more extensive parallel snapshot example.
TPTBox/stitching/README.md	Updated stitching usage example to use file lists and expanded parameters.
TPTBox/segmentation/README.md	Added a fuller VIBESeg script example and adjusted API documentation.
TPTBox/registration/README.md	Added an additional Point_Registration usage example.

Suppressed comments (2)

TPTBox/core/README.md:12

• The link target here is written as TPTBox/core/README_POI.md, but this README lives inside TPTBox/core/, so that relative link resolves to a non-existent nested path on GitHub. Use a local relative link instead.

### <a href=TPTBox/core/README_POI.md>POI: poi.py -- Points of Interests </a>

TPTBox/registration/README.md:63

• Spelling/grammar issues in these comments ("resampe", "an specific", "appling") and the NII.load call uses a positional boolean. Fixing this improves readability and makes the snippet clearer for users copying it.

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[robert-graf]

Missing one Read-Me for Visualization.

[robert-graf]

I do not like that all images disappear for the main Readme. Instead, we get a wall of text with citations.

I do not like that parts of the main Readme are links (big ugly links in addition)

[Hendrik-code]

I do not like that all images disappear for the main Readme. Instead, we get a wall of text with citations.

I do not like that parts of the main Readme are links (big ugly links in addition)

Hmm okay, how do you like it to be?
Because if all examples, documentation, and figures are in main README, it becomes unreadable and you cannot find anything anymore. That's why I split this up.
Regarding links being ugly, make it nicer :D