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  Indian J Med Microbiol
 

Figure 2: Encoding of whole slide imaging information in DICOM data set. (a) Schematic of multiresolution whole slide image pyramid. The pyramid base level represents the original image that was acquired by the microscope/slide scanning system. Higher pyramid level images (=lower power) are derived through successive downsampling. The frame of reference for images is the slide coordinate system in millimeter units, where the origin is defined as the lower left corner of the upright standing slide. (b) Total pixel matrix. An image is defined as a continuous, rectangular area of pixels. Shown is the image at ×10 resolution. Note that it is rotated 90° (counterclockwise) relative to the slide coordinate system. (c) Tiled image grid. The pixel matrix may be tiled into smaller rectangular, equally sized regions. Tiles are organized such that the first dimension spans the matrix rows and the second dimension the matrix columns, respectively. (d) Image pyramid encoded as series of VL Whole Slide Microscopy Image instances. Each image instance (=pyramid layer =downsampled magnification) is encoded as a separate DICOM data set. (e) DICOM data set of a multiframe image instance with encapsulated Pixel Data element. Each tile is compressed and encoded as a separate Frame item. Frames are implicitly numbered, based on the order of encoding. The dimensional organization of frames in the real world is described by the dimension index sequence attribute (green), which contains a dimension index pointer and a functional group pointer attribute for each dimension. The values of these attributes point to other attributes in the per-frame functional groups sequence attribute (yellow), which encode the actual values for each frame. The frame content sequence attribute hereby describes the relative position of each frame in the tiled image grid whereas the plane position (slide) sequence attribute describes the absolute position of each frame in the slide coordinate system as well as the total pixel matrix. The byte offset to individual frame items in the pixel data element (grey box labeled 1-6) is specified by the basic offset table item (purple), which is itself part of (the first item of) the encapsulated pixel data element

Figure 2: Encoding of whole slide imaging information in DICOM data set. (a) Schematic of multiresolution whole slide image pyramid. The pyramid base level represents the original image that was acquired by the microscope/slide scanning system. Higher pyramid level images (=lower power) are derived through successive downsampling. The frame of reference for images is the slide coordinate system in millimeter units, where the origin is defined as the lower left corner of the upright standing slide. (b) Total pixel matrix. An image is defined as a continuous, rectangular area of pixels. Shown is the image at ×10 resolution. Note that it is rotated 90° (counterclockwise) relative to the slide coordinate system. (c) Tiled image grid. The pixel matrix may be tiled into smaller rectangular, equally sized regions. Tiles are organized such that the first dimension spans the matrix rows and the second dimension the matrix columns, respectively. (d) Image pyramid encoded as series of VL Whole Slide Microscopy Image instances. Each image instance (=pyramid layer =downsampled magnification) is encoded as a separate DICOM data set. (e) DICOM data set of a multiframe image instance with encapsulated Pixel Data element. Each tile is compressed and encoded as a separate Frame item. Frames are implicitly numbered, based on the order of encoding. The dimensional organization of frames in the real world is described by the dimension index sequence attribute (green), which contains a dimension index pointer and a functional group pointer attribute for each dimension. The values of these attributes point to other attributes in the per-frame functional groups sequence attribute (yellow), which encode the actual values for each frame. The frame content sequence attribute hereby describes the relative position of each frame in the tiled image grid whereas the plane position (slide) sequence attribute describes the absolute position of each frame in the slide coordinate system as well as the total pixel matrix. The byte offset to individual frame items in the pixel data element (grey box labeled 1-6) is specified by the basic offset table item (purple), which is itself part of (the first item of) the encapsulated pixel data element