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src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json

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"Singleton time dimension"
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],
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"docs_info": "### Purpose\n- Removes a **singleton time (T) dimension** from an OME-Zarr image. \n- Creates a new OME-Zarr image with updated metadata and dimensions.\n- Optionally overwrites the input image if `overwrite_input` is set to True.\n\n### Outputs\n- A **new Zarr image** without the singleton T-dimension, stored with a configurable suffix. \n\n### Limitations\n- Only processes OME-Zarr images where the **T-axis is the first axis**. \n- Assumes the T-dimension is **singleton**; does not process non-singleton time axes. \n- Does not copy associated **label images** or **ROI tables** to the new Zarr structure. ",
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"type": "parallel",
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"executable_parallel": "drop_t_dimension.py",
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"meta_parallel": {
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"cpus_per_task": 2,
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"2D to 3D workflows"
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],
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"docs_info": "### Purpose\n- Converts a **2D segmentation** image into a **3D segmentation** by replicating the 2D segmentation across Z-slices. \n- Supports OME-Zarr datasets where **2D and 3D images** share the same base name but differ by suffixes. \n- Optionally copies associated ROI tables and adjusts them to align with the replicated Z-dimensions. \n\n### Outputs\n- A **3D segmentation label image** saved with a new name. \n- Updated **ROI tables** adjusted for Z-dimensions (optional). \n\n### Limitations\n- Only supports **same-base 2D and 3D Zarr names**; full flexibility in file names is not yet implemented. \n- Assumes **2D OME-Zarr images** and corresponding 3D images are stored in the same base folder and just differ with a suffix before the .zarr. \n",
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"type": "parallel",
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"executable_parallel": "convert_2D_segmentation_to_3D.py",
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"meta_parallel": {
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"cpus_per_task": 2,
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"Many files"
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],
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"docs_info": "### Purpose\n- Rechunks OME-Zarr to new chunking parameters: Changes whether the array is stored as many small files or few larger files.\n- Optionally applies the same rechunking to label images.\n\n### Outputs\n- A **new Zarr image** that is rechunked.\n",
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"type": "parallel",
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"executable_parallel": "rechunk_zarr.py",
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"meta_parallel": {
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"cpus_per_task": 1,

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