Fix #468: Implemented search space restrictions in all dimensions (z, y, x) for cell detection

[0Anshu1]

Description

What is this PR

• Bug fix
• Addition of a new feature
• Other

Why is this PR needed?

• Allows users to restrict the search space in all dimensions using coordinates like (:, 100:400, 200:500) for (z, y, x).
• The implementation maintains compatibility with both napari plugin data and dask-loaded data, ensuring proper handling of boundary conditions and coordinate transformations.

What does this PR do?

• Adds a new feature to run cell detection on a subvolume of an image and not just select z by :-
  1.) Adding new parameters to DetectionSettings class:
  - start_y, end_y: for restricting the y-dimension search space.
  - start_x, end_x: for restricting the x-dimension search space.
  - added roi_shape property to calculate the shape of the region of interest.
  - updated the main detection function in detect.py.

2.) modified DetectionSettings initialization to include these parameters.

References

• [Feature] Run cell detection on subvolume of an image and not just select z planes #468
• [Feature] Run cell detection on subvolume of an image and not just select z planes #468 #491
• Added detect subvolume crop support #494

How has this PR been tested?

• Verified functionality with:

  • Full volume detection (no restrictions)
  • Partial volume detection in all dimensions
  • Edge cases (coordinates at/outside volume boundaries)

• Tested with both:

  • Napari plugin interface
  • Direct dask array input

Is this a breaking change?

• No

Does this PR require an update to the documentation?

• No

Checklist:

• The code has been tested locally
• Tests have been added to cover all new functionality (unit & integration)
• The documentation has been updated to reflect any changes
• The code has been formatted with pre-commit

[0Anshu1]

the unwanted (as far as the changes in this PR are concerned)train_yaml.py file was pushed by mistake...deleted that one from this PR.

[0Anshu1]

Will raise a new PR shortly by fixing the conflicts and by adding tests also for covering the new functionality that I have added i.e. for region of interest. Closing this PR.

[adamltyson]

Would you mind keeping everything in a single PR? Opening and closing multiple PRs makes it hard for the core developers to keep track of everything. Thanks!