DICOM WG 26 WSI Annotation
Please fill out the below questions to the best of your ability
Software viewer name/Vendor name
What is the annotation file format? Which formats are accepted - local database only (can't be exported or re-imported) - serialized to: - text file (describe) - CSV file (describe columns and values) - tab delimited text file (describe columns and values) - XML file (identify or specify schema) - JSON file (identify, e.g., GeoJSON, or describe) - binary file of some type (describe) - other described file format (e.g., well known text (WKT) (specify) - other (specify)
Your answer
Coordinate origin (0,0) what is the coordinate system origin (e.g., TLHC of TLHC pixel of tile) i.e. middle of image, or top left/slide label left)
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3D (x,y,z) volumetric or multi-slice (z stack)
ID# = Tool (if applicable)
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Hierarchy Tree
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Does the annotation assert classes (i.e. Cellular structures (nuclear, cytoplasmic, membranous))
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Is there an ontology that is used for classes/for annotation variables
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Graphical annotation type support
The below questions relate to annotation types and their representations, please add possible variables, their data representation, and coordinate based systems, if applicable
Is the software able to annotate , which of the below if any are available: single points (pointer, pins, tip of arrow, cross-hair center)
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free-hand- irregularly shaped lines around objects ("contours")/open-closed?
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are contours interpolated (e.g., spline)
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geometric shapes (rectangles/squares, ellipses./circles, ...)
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Ruler
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Ruler
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set of pixels (e.g., paintbrush)
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How does the file handle Boolean sets of related shapes (e.g., union, intersection) Holes/nested representations
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Is sub-pixel resolution supported
Are units pixels, microns, nm, or other
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What layer is the coordinate system relative to (e.g., base layer)
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"Label map (image where pixel value is category) - is the resolution that of the base layer or other? - is every tile stored or just those with categorized pixels"
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"Bit plane (mask, image where 1 or 0 pixel value is selected or not) - is the resolution that of the base layer or other? - is every tile stored or just those with categorized pixels"
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Does the annotation include 4D data? - e.g., concept of time? sequence?
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Graphical annotation metadata, what meta (semantic) data is supported - quantitative measurements of size, intensity, other? - ordinal scores? - categorical observations? - plain text observations? - pre-defined or user-configurable name-value pairs? - what pre-defined data field/element/variable names are used? - for each, what pre-defined text or coded values are used? - is any standard lexicon used (e.g., SNOMED CT)? - identification or label of the annotation (e.g., for tracking)? - record of provenance? - creator? - creation date/time? - changes (what, by whom, when)? Please list/include all
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How are the attributes presented (appearance) attributes recorded? - color? - transparency? - line thickness? - fill? - font? - location of non-semantic graphics (e.g., tail of arrow, text bounding box) ?
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Are entire other than pixel or region level annotations supported? - case? - slide? - channel of image? - other (specify)?
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Can annotations reference/describe other annotations?
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Annotation index/indices characteristics also serialized? - is an index of the annotations location stored? - is an index of any annotation metadata stored?
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Is an information object required?
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Is the format Case-sensitive?
Please provide a list of all attributes and corresponding description (i.e. example of single attributge: Rectangle <x1, y1> Position of the top left corner of the rectangle <x2, y2> Position of the diagonally opposite corner)
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Please include any other data that you feel has not been addressed in your specific annotation file
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