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"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)."
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},
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"zarr_dir": {
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"title": "Zarr Dir",
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"type": "string",
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"description": "path of the directory where the new OME-Zarrs will be created. (standard argument for Fractal tasks, managed by Fractal server)."
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},
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"image_dirs": {
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"title": "Image Dirs",
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"type": "array",
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"items": {
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"type": "string"
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},
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"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."
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},
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"allowed_channels": {
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"title": "Allowed Channels",
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"type": "array",
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"items": {
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"$ref": "#/definitions/OmeroChannel"
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},
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"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."
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},
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"image_glob_patterns": {
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"title": "Image Glob Patterns",
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"type": "array",
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"items": {
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"type": "string"
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},
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"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."
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},
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"num_levels": {
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"title": "Num Levels",
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"default": 5,
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"type": "integer",
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"description": "Number of resolution-pyramid levels. If set to `5`, there will be the full-resolution level and 4 levels of downsampled images."
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},
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"coarsening_xy": {
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"title": "Coarsening Xy",
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"default": 2,
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"type": "integer",
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"description": "Linear coarsening factor between subsequent levels. If set to `2`, level 1 is 2x downsampled, level 2 is 4x downsampled etc."
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},
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"image_extension": {
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"title": "Image Extension",
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"default": "tif",
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"type": "string",
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"description": "Filename extension of images (e.g. `\"tif\"` or `\"png\"`)"
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},
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"metadata_table_file": {
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"title": "Metadata Table File",
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"type": "string",
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"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."
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},
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"overwrite": {
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"title": "Overwrite",
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"default": false,
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"type": "boolean",
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"description": "If `True`, overwrite the task output."
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}
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},
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"required": [
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"zarr_urls",
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"zarr_dir",
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"image_dirs",
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"allowed_channels"
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],
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"additionalProperties": false,
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"definitions": {
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"Window": {
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"title": "Window",
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"description": "Custom class for Omero-channel window, based on OME-NGFF v0.4.",
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"type": "object",
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"properties": {
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"min": {
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"title": "Min",
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"type": "integer",
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"description": "Do not change. It will be set to `0` by default."
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},
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"max": {
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"title": "Max",
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"type": "integer",
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"description": "Do not change. It will be set according to bit-depth of the images by default (e.g. 65535 for 16 bit images)."
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},
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"start": {
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"title": "Start",
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"type": "integer",
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"description": "Lower-bound rescaling value for visualization."
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},
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"end": {
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"title": "End",
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"type": "integer",
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"description": "Upper-bound rescaling value for visualization."
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}
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},
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"required": [
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"start",
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"end"
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]
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},
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"OmeroChannel": {
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"title": "OmeroChannel",
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"description": "Custom class for Omero channels, based on OME-NGFF v0.4.",
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"type": "object",
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"properties": {
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"wavelength_id": {
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"title": "Wavelength Id",
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"type": "string",
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"description": "Unique ID for the channel wavelength, e.g. `A01_C01`."
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},
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"index": {
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"title": "Index",
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"type": "integer",
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"description": "Do not change. For internal use only."
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},
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"label": {
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"title": "Label",
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"type": "string",
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"description": "Name of the channel."
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},
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"window": {
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"$ref": "#/definitions/Window",
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"title": "Window",
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"description": "Optional `Window` object to set default display settings for napari."
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},
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"color": {
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"title": "Color",
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"type": "string",
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"description": "Optional hex colormap to display the channel in napari (it must be of length 6, e.g. `00FFFF`)."
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},
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"active": {
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"title": "Active",
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"default": true,
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"type": "boolean",
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"description": "Should this channel be shown in the viewer?"
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},
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"coefficient": {
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"title": "Coefficient",
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"default": 1,
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"type": "integer",
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"description": "Do not change. Omero-channel attribute."
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},
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"inverted": {
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"title": "Inverted",
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"default": false,
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"type": "boolean",
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"description": "Do not change. Omero-channel attribute."
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