fix: index shift correction for blob detection in 2d tiles

[shachafl]

This closes #2075 & #1870

There might be another solution to this as I couldn't figure why when running blob detection with is_volume=False and with a reference image gives a 4d result (z, y, x, sigma) vs. without a reference image which gives a 3d output (y, x, sigma).

[berl]

so the reference_image handles things a bit differently, first runningskimage spotfinding function on the whole stack, or at least that's my read of this after a squeeze which may be leading to the weird behavior here.

somewhat orthogonally, the is_volume parameter is supposed to change the behavior of the spotfinding from per z plane (is_volume=False) to finding 3D blobs (is_volume=True). This was intended to be used for different kinds of data (sparse sampling in z vs dense sampling) but should be able to work both ways on a given input stack. the underlying skimage functions don't know anything about this (they just return 3d information on a 3d image stack or 2d on a 2d stack).
not sure if this helps clarify anything @shachafl, but getting rid of the is_volume condition should be done carefully to maintain this functionality

[Copilot]

Pull Request Overview

This PR fixes an index shift issue in blob detection for 2D tiles by correcting how array dimensions are interpreted and indexed. The change addresses a discrepancy where blob detection results have different dimensionality (3D vs 4D) depending on whether a reference image is used.

• Replaces is_volume flag check with dynamic shape inspection of fitted_blobs_array
• Corrects 2D indexing to use (y_inds, x_inds) instead of incorrectly including z_inds for 2D data

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[Copilot]

The condition checks only for shapes with 3 or 4 columns, but doesn't handle other potential array shapes. If fitted_blobs_array.shape[1] is neither 3 nor 4, the code will silently skip both branches, leaving intensities, z_inds, y_inds, x_inds, and radius undefined, which will cause errors in subsequent code. Add an else clause to raise an informative error for unexpected array shapes.

[shachafl]

closing this here, as a more comprehensive fix is done in #2154.
The new fix maintains the ability to process a 3d image as a set of 2d tiles instead.