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{ | ||
"title": "CellvoyagerToOmeZarrInit", | ||
"type": "object", | ||
"properties": { | ||
"zarr_urls": { | ||
"title": "Zarr Urls", | ||
"type": "array", | ||
"items": { | ||
"type": "string" | ||
}, | ||
"description": "List of paths or urls to the individual OME-Zarr image to be processed. Not used by the converter task. (standard argument for Fractal tasks, managed by Fractal server)." | ||
}, | ||
"zarr_dir": { | ||
"title": "Zarr Dir", | ||
"type": "string", | ||
"description": "path of the directory where the new OME-Zarrs will be created. (standard argument for Fractal tasks, managed by Fractal server)." | ||
}, | ||
"image_dirs": { | ||
"title": "Image Dirs", | ||
"type": "array", | ||
"items": { | ||
"type": "string" | ||
}, | ||
"description": "list of paths to the folders that contains the Cellvoyager image files. Each entry is a path to a folder that contains the image files themselves for a multiwell plate and the MeasurementData & MeasurementDetail metadata files." | ||
}, | ||
"allowed_channels": { | ||
"title": "Allowed Channels", | ||
"type": "array", | ||
"items": { | ||
"$ref": "#/definitions/OmeroChannel" | ||
}, | ||
"description": "A list of `OmeroChannel` s, where each channel must include the `wavelength_id` attribute and where the `wavelength_id` values must be unique across the list." | ||
}, | ||
"image_glob_patterns": { | ||
"title": "Image Glob Patterns", | ||
"type": "array", | ||
"items": { | ||
"type": "string" | ||
}, | ||
"description": "If specified, only parse images with filenames that match with all these patterns. Patterns must be defined as in https://docs.python.org/3/library/fnmatch.html, Example: `image_glob_pattern=[\"*_B03_*\"]` => only process well B03 `image_glob_pattern=[\"*_C09_*\", \"*F016*\", \"*Z[0-5][0-9]C*\"]` => only process well C09, field of view 16 and Z planes 0-59." | ||
}, | ||
"num_levels": { | ||
"title": "Num Levels", | ||
"default": 5, | ||
"type": "integer", | ||
"description": "Number of resolution-pyramid levels. If set to `5`, there will be the full-resolution level and 4 levels of downsampled images." | ||
}, | ||
"coarsening_xy": { | ||
"title": "Coarsening Xy", | ||
"default": 2, | ||
"type": "integer", | ||
"description": "Linear coarsening factor between subsequent levels. If set to `2`, level 1 is 2x downsampled, level 2 is 4x downsampled etc." | ||
}, | ||
"image_extension": { | ||
"title": "Image Extension", | ||
"default": "tif", | ||
"type": "string", | ||
"description": "Filename extension of images (e.g. `\"tif\"` or `\"png\"`)" | ||
}, | ||
"metadata_table_file": { | ||
"title": "Metadata Table File", | ||
"type": "string", | ||
"description": "If `None`, parse Yokogawa metadata from mrf/mlf files in the input_path folder; else, the full path to a csv file containing the parsed metadata table." | ||
}, | ||
"overwrite": { | ||
"title": "Overwrite", | ||
"default": false, | ||
"type": "boolean", | ||
"description": "If `True`, overwrite the task output." | ||
} | ||
}, | ||
"required": [ | ||
"zarr_urls", | ||
"zarr_dir", | ||
"image_dirs", | ||
"allowed_channels" | ||
], | ||
"additionalProperties": false, | ||
"definitions": { | ||
"Window": { | ||
"title": "Window", | ||
"description": "Custom class for Omero-channel window, based on OME-NGFF v0.4.", | ||
"type": "object", | ||
"properties": { | ||
"min": { | ||
"title": "Min", | ||
"type": "integer", | ||
"description": "Do not change. It will be set to `0` by default." | ||
}, | ||
"max": { | ||
"title": "Max", | ||
"type": "integer", | ||
"description": "Do not change. It will be set according to bit-depth of the images by default (e.g. 65535 for 16 bit images)." | ||
}, | ||
"start": { | ||
"title": "Start", | ||
"type": "integer", | ||
"description": "Lower-bound rescaling value for visualization." | ||
}, | ||
"end": { | ||
"title": "End", | ||
"type": "integer", | ||
"description": "Upper-bound rescaling value for visualization." | ||
} | ||
}, | ||
"required": [ | ||
"start", | ||
"end" | ||
] | ||
}, | ||
"OmeroChannel": { | ||
"title": "OmeroChannel", | ||
"description": "Custom class for Omero channels, based on OME-NGFF v0.4.", | ||
"type": "object", | ||
"properties": { | ||
"wavelength_id": { | ||
"title": "Wavelength Id", | ||
"type": "string", | ||
"description": "Unique ID for the channel wavelength, e.g. `A01_C01`." | ||
}, | ||
"index": { | ||
"title": "Index", | ||
"type": "integer", | ||
"description": "Do not change. For internal use only." | ||
}, | ||
"label": { | ||
"title": "Label", | ||
"type": "string", | ||
"description": "Name of the channel." | ||
}, | ||
"window": { | ||
"$ref": "#/definitions/Window", | ||
"title": "Window", | ||
"description": "Optional `Window` object to set default display settings for napari." | ||
}, | ||
"color": { | ||
"title": "Color", | ||
"type": "string", | ||
"description": "Optional hex colormap to display the channel in napari (it must be of length 6, e.g. `00FFFF`)." | ||
}, | ||
"active": { | ||
"title": "Active", | ||
"default": true, | ||
"type": "boolean", | ||
"description": "Should this channel be shown in the viewer?" | ||
}, | ||
"coefficient": { | ||
"title": "Coefficient", | ||
"default": 1, | ||
"type": "integer", | ||
"description": "Do not change. Omero-channel attribute." | ||
}, | ||
"inverted": { | ||
"title": "Inverted", | ||
"default": false, | ||
"type": "boolean", | ||
"description": "Do not change. Omero-channel attribute." | ||
} | ||
}, | ||
"required": [ | ||
"wavelength_id" | ||
] | ||
} | ||
} | ||
} |