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06-processed-data.yaml
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Data Type:
description: Specify if OME-TIFF provided is a segmentation mask or QC-checked image
type: string
significance: required
valid-values:
- mask
- image
Data File ID:
description: unique e.g., “self” HTAN ID for data file described by this metadata
type: string
significance: required
Filename:
description: name of data file as submitted to repository
type: filename
significance: required
File Format:
description: format of data file
type: string
significance: required
Parent Data File ID:
description: HTAN ID of Data File from which this Data File was derived
type: string
significance: recommended
Protocol ID(s):
description: unique identifier (e.g. protocols.io) -- may be a delimited list of
identifiers
type: doi
significance: required
Software and Version:
description: method(s) and parameters used for any quality control, transformation,
and visualization to create this image
type: doi
significance: required
Commit SHA:
description: Short SHA for software version (8 hexadecimal characters for github)
type: string
significance: required
Passed QC:
description: did all masks pass QC
type: boolean
significance:
required: Data type == ‘image’
Comment:
description: Free text field to use if necessary
type: string
significance: recommended
Object class:
description: Defines if the mask delineates nucleus, the cytoplasm, plasma membrane, the whole cell or other
type: string
significance:
required: Data type == 'mask'
valid-values:
- nuclei
- cytoplasm
- cell
- plasma membrane
- other
Object class Description:
description: Free text description of object class
type: string
significance:
required: Object class == 'other'
Minimum Intensity Display Range:
description: Lower-bound intensity value
type: integer
significance: recommended
Maximum Intensity Display Range:
description: Upper-bound intensity value
type: integer
significance: recommended
FOV_number:
description: Index of FOV (as it pertains to its place in the Experiment)
type: integer
valid-values:
min: 1.0
significance: recommended
FOV_SizeX:
description: FOV size in X-dimension (micron)
type: float
significance: recommended
FOV_SizeY:
description: FOV size in Y-dimension (micron)
type: float
significance: recommended
Pyramid:
description: whether or not image file contains a pyramid stack
type: boolean
significance: recommended
Z_stack:
description: whether or not image file contains a Z-stack
type: boolean
significance: recommended
T_series:
description: whether or not image file contains a time series
type: boolean
significance: recommended
PhysicalSizeX:
description: physical size of one pixel in x-dimension
type: float
significance: required
PhysicalSizeXUnit:
description: unit for PhysicalSizeX
type: string
significance: required
PhysicalSizeY:
description: physical size of one pixel in y-dimension
type: float
significance: required
PhysicalSizeYUnit:
description: unit for PhysicalSizeY
type: string
significance: required
PhysicalSizeZ:
description: physical size of one pixel in z-dimension
type: float
significance:
required: Z_stack == True
PhysicalSizeZUnit:
description: unit for PhysicalSizeZ
type: string
significance:
required: Z_stack == True
Type:
description: data type for each pixel value
type: string
significance: required