Philips format

Format
single-file pyramidal tiled TIFF or BigTIFF with non-standard metadata
File extensions
.tiff
OpenSlide vendor backend
philips

Detection

Philips TIFF files are stored in single-file TIFF or BigTIFF format. OpenSlide will detect a file as Philips if:

  1. The file is TIFF.
  2. The TIFF Software tag starts with Philips.
  3. The ImageDescription tag contains valid XML.
  4. The root element of the XML is DataObject and has an ObjectType attribute with a value of DPUfsImport.

To open BigTIFF files, OpenSlide must be built with libtiff 4 or above.

File Organization

Philips TIFF is an export format. The native Philips format, iSyntax, is a custom multi-file format not currently supported by OpenSlide.

The ImageDescription tag of the first TIFF directory contains an XML document with a hierarchical structure containing key-value pairs. The keys are based on DICOM tags.

The level dimensions given in the TIFF ImageWidth and ImageLength fields, and also in the ImageDescription XML, are merely the TIFF tile size multiplied by the number of tiles in each dimension. Thus, they include the size of the padding in the right-most column and bottom-most row of tiles. Each level typically uses the same tile size but requires a different amount of padding, so the aspect ratios of the levels are inconsistent and the level dimensions are not proportional to the level downsamples. Correct downsamples can be calculated from the levels’ pixel spacings in the XML metadata.

Slides with multiple regions of interest are structured as a single image pyramid enclosing all regions. Slides may omit pixel data for TIFF tiles not in an ROI; this is represented as a TileOffset of 0 and a TileByteCount of 0. When such tiles are downsampled into a tile that does contain pixel data, their contents are rendered as white pixels.

Label and macro images are stored as Base64-encoded JPEGs in the ImageDescription XML. Some slides also store these images as stripped TIFF directories whose ImageDescriptions start with Label and Macro, respectively.

Relevant TIFF tags

Tag Description
ImageDescription Stores an XML document containing various metadata and associated image data
Software Starts with Philips

Associated Images

label
the TIFF directory with an ImageDescription starting with Label, or the image data in the DPScannedImage with a PIM_DP_IMAGE_TYPE of LABELIMAGE
macro
the TIFF directory with an ImageDescription starting with Macro, or the image data in the DPScannedImage with a PIM_DP_IMAGE_TYPE of MACROIMAGE

Known Properties

All key-value data encoded in the DPUfsImport object, in the first DPScannedImage object with a PIM_DP_IMAGE_TYPE of WSI, and in that object’s PixelDataRepresentation objects is represented as properties prefixed with “philips.”.

openslide.mpp-x
calculated as 1000 * philips.DICOM_PIXEL_SPACING[1]
openslide.mpp-y
calculated as 1000 * philips.DICOM_PIXEL_SPACING[0]

Test Data

No public data available. Contact the mailing list if you have some.