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The `run_pipeline` and `run_pipeline_save` functions have been removed to simplify the pipeline execution flow. The main entry point is now `run_pipeline_and_post`, which has been updated for clarity by renaming the `out_dir` parameter to `output_path`. Additional dead code and comments have also been removed across several modules.
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Nahual is a companion tool that allows us to deploy a multitude of models for segmentation (e.g., cellpose), tracking (e.g., trackastra) or featurization (e.g., Dinov2) in an independent Python environment or server altogether. I have integrated its functionality for multiple reasons:
There is a bit of an overhead of moving data around, but at least for pipelines running within the same server it is not an issue (it may become if we start calling servers with low transfer speeds).