Add Huron format

_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/

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
+
+<https://openslide.cs.cmu.edu/download/openslide-testdata/Huron/>

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.

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]