Leica format

Format

single-file pyramidal tiled BigTIFF with non-standard metadata

File extensions

.scn

OpenSlide vendor backend

leica

Detection

Leica slides are stored in single-file BigTIFF format. OpenSlide will detect a file as Leica if:

1. The file is TIFF.
2. The initial image is tiled.
3. The ImageDescription tag contains valid XML in either of these namespaces:
   • http://www.leica-microsystems.com/scn/2010/03/10
   • http://www.leica-microsystems.com/scn/2010/10/01

Relevant TIFF tags

Tag	Description
ImageDescription	Stores an XML document containing various metadata

File Organization

The ImageDescription tag of the first TIFF directory contains an XML document that defines the structure of the slide.

Leica slides are structured as a collection of images, each of which has multiple dimensions (pyramid levels). The collection has a size, and images have a size and position, measured in nanometers. Each dimension has a size in pixels, an optional focal plane number, and a TIFF directory containing the image data. Fluorescence images have different dimensions (and thus different TIFF directories) for each channel. OpenSlide currently rejects fluorescence images and ignores focal planes other than plane 0.

Brightfield slides have at least two images: a low-resolution macro image and one or more main images corresponding to regions of the macro image. The macro image has a position of (0, 0) and a size matching the size of the collection. Fluorescence slides can have two macro images: one brightfield and one fluorescence.

The slide provides enough information to composite the various images, including the macro image, into a single pyramid. However, there are some complications:

• The resolution of the macro image is generally not related to the resolution of the main images by a power of two.
• Downsampled dimensions are generally downsampled from the next larger dimension by a factor of 4, but main images can be scanned with distinct objectives that may differ by only a factor of 2.

Thus, in general, the images in a collection cannot be rendered into a unified pyramid without scaling the original pixel data. OpenSlide does not attempt to do this. Instead, OpenSlide omits the macro image from the pyramid and refuses to open slides whose main images have inconsistent resolutions.

Associated Images

macro

the highest-resolution dimension of the macro image

Known Properties

leica.aperture

the numericalAperture of the main image

leica.barcode

the barcode text. (For slides in the 2010/10/01 namespace, OpenSlide 3.4.0 and earlier report this property as a Base64-encoded string; OpenSlide 3.4.1 and later report it in plain text. For slides in the 2010/03/10 namespace, OpenSlide reports the barcode as it is stored in the XML, since we do not know whether those barcodes are Base64-encoded. If you have a 2010/03/10 slide with a bar code, please comment in this bug or contact the OpenSlide mailing list.)

leica.creation-date

the creationDate of the main image

leica.device-model

the device model of the main image

leica.device-version

the device version of the main image

leica.illumination-source

the illuminationSource of the main image

leica.objective

the objective of the main image

openslide.mpp-x

calculated as 10000/tiff.XResolution, if tiff.ResolutionUnit is centimeter

openslide.mpp-y

calculated as 10000/tiff.YResolution, if tiff.ResolutionUnit is centimeter

openslide.objective-power

normalized leica.objective

Test Data

https://openslide.cs.cmu.edu/download/openslide-testdata/Leica/