fix: inference and analysis workflow bugs

[jtschwar]

Summary

Fixes several bugs in the inference and analysis workflows surfaced during user testing.

• inference_core.py: Fixed incorrect dimension check - the condition image.ndim == 2 was guarding a 3D slice [:,:,0], causing a crash on 2D images. Now correctly checks if the output is 3D before slicing.
• run_tomogram_segment.py: Fixed parameter name mismatch - run_ids was passed where the function expected run_id.
• results.py: Fixed a crash in save_slab_seg when a run string contains more than one - (e.g. TS_001-0-1). The split is now handled safely, joining any extra segments back into the session ID.
• run_analysis.py: Added -o/--output option to the coordinates, statistics, and slurm commands to allow users to specify the output CSV path (previously hardcoded as {organelle_name}_statistics.csv). Also added no_args_is_help=True to the coordinates and statistics commands.

Acknowledgements

Thanks to @KatrinaABlack and @jowagner91 for identifying these bugs and providing recommendations for the fixes.