diff --git a/_includes/links.md b/_includes/links.md index 368fdce..7adb9d8 100644 --- a/_includes/links.md +++ b/_includes/links.md @@ -32,6 +32,7 @@ [format-dicom]: /formats/dicom/ [format-generic-tiff]: /formats/generic-tiff/ [format-hamamatsu]: /formats/hamamatsu/ +[format-huron]: /formats/huron/ [format-leica]: /formats/leica/ [format-mirax]: /formats/mirax/ [format-philips]: /formats/philips/ diff --git a/formats/huron/index.md b/formats/huron/index.md new file mode 100644 index 0000000..5a89bac --- /dev/null +++ b/formats/huron/index.md @@ -0,0 +1,83 @@ +--- +title: Huron format +permalink: /formats/huron/ +--- + +{% include links.md %} + +Format +: single-file pyramidal tiled TIFF with non-standard metadata + +File extensions +: `.tif` + +OpenSlide vendor backend +: `huron` + + +## Detection + +Huron slides are stored in single-file TIFF format. OpenSlide will detect a +file as Huron if: + + 1. The file is TIFF. + 2. The initial image is tiled. + 3. The `ImageMake` tag starts with `Huron`. + + +## Relevant TIFF tags + +Tag | Description | +--------------------|--------------------------------| +`ImageDescription`|Stores some important key-value pairs, see below| +`ImageMake`|Starts with `Huron`| +`NewSubfileType`|1 for the label associated image, 9 for the macro associated image| +`XResolution`, `YResolution`, `ResolutionUnit`|The pixel size in pyramid level 0| + + +## Extra data stored in `ImageDescription` + +The `ImageDescription` tag of the first TIFF directory contains +newline-delimited key-value pairs. A key-value pair is equals-delimited +with extra padding spaces. These key-values are stored as properties +starting with "`huron.`". Currently, OpenSlide does not use any of the +information present in these key-value fields. + + +## TIFF Image Directory Organization + +The directory organization follows the same pattern as the +[Aperio format][format-aperio]. + + +## Associated Images + +There are up to three stripped images: a thumbnail image, which is +always the second image in the file; and label and macro images at the +end of the file, with subfile types 1 and 9 respectively. + +`label` +: optional, non-tiled image with subfile type 1 + +`macro` +: optional, non-tiled image with subfile type 9 + +`thumbnail` +: the second image in the file + + +## Known Properties + +All key-value data encoded in the `ImageDescription` TIFF field is +represented as properties prefixed with "`huron.`". + +`openslide.mpp-x` +: normalized TIFF resolution + +`openslide.mpp-y` +: normalized TIFF resolution + + +## Test Data + + diff --git a/formats/index.md b/formats/index.md index 76c3741..5c9c53a 100644 --- a/formats/index.md +++ b/formats/index.md @@ -55,6 +55,20 @@ More info : [Hamamatsu format][format-hamamatsu] +## Huron + +Single-file pyramidal tiled TIFF with non-standard metadata. + +File extensions +: `.tif` + +OpenSlide vendor backend +: `huron` + +More info +: [Huron format][format-huron] + + ## Leica Single-file pyramidal tiled BigTIFF with non-standard metadata. diff --git a/index.md b/index.md index c1d6809..e696327 100644 --- a/index.md +++ b/index.md @@ -46,6 +46,7 @@ The library can read virtual slides in the following formats: * [Aperio (.svs, .tif)][format-aperio] * [DICOM (.dcm)][format-dicom] * [Hamamatsu (.vms, .vmu, .ndpi)][format-hamamatsu] + * [Huron (.tif)][format-huron] * [Leica (.scn)][format-leica] * [MIRAX (.mrxs)][format-mirax] * [Philips (.tiff)][format-philips]