MIRAX format

Format
multi-file with very complicated proprietary metadata and indexes
File extensions
.mrxs
OpenSlide vendor backend
mirax

Detection

OpenSlide will detect a file as MIRAX if:

  1. The file is not a TIFF.
  2. The filename ends with .mrxs.
  3. A directory exists in the same location as the file, with the same name as the file minus the extension.
  4. A file named Slidedat.ini exists in the directory.

Overview

MIRAX can store slides in JPEG, PNG, or BMP formats. Because JPEG does not allow for large images, and JPEG and PNG provide very poor support for random-access decoding of part of an image, multiple images are needed to encode a slide. To avoid having many individual files, MIRAX packs these images into a small number of data files. The index file provides offsets into the data files for each required piece of data.

The camera on MIRAX scanners takes overlapping photos and records the position of each one. Each photo is then split into multiple images which do not overlap. Overlaps only occur between images that come from different photos.

To generate level n + 1, each image from level n is downsampled by 2 and then concatenated into a new image, 4 old images per new image (2 x 2). This process is repeated for each level, irrespective of image overlaps. Therefore, at sufficiently high levels, a single image can contain one or more embedded overlaps of non-integral width.

Index File

The index file starts with a five-character ASCII version string, followed by the SLIDE_ID from the slidedat file. The rest of the file consists of 32-bit little-endian integers (unaligned), which can be data values or pointers to byte offsets within the index file.

The first two integers point to offset tables for the hierarchical and nonhierarchical roots, respectively. These tables contain one record for each VAL in the HIERARCHICAL slidedat section. For example, the record for NONHIER_1_VAL_2 would be stored at nonhier_root + 4 * (NONHIER_0_COUNT + 2).

Each record is a pointer to a linked list of data pages. The first two values in a data page are the number of data items in the page and a pointer to the next page. The first page always has 0 data items, and the last page has a 0 next pointer.

There is one hierarchical record for each zoom level. The record contains data items consisting of an image index, offset and length within a file, and a file number. The file number can be converted to a data file name via the DATAFILE slidedat section. The image index is equal to image_y * GENERAL.IMAGENUMBER_X + image_x. Image coordinates which are not multiples of the zoom level’s downsample factor are omitted.

Nonhierarchical records refer to associated images and additional metadata. Nonhierarchical data items consist of three zero values followed by an offset, length, and file number as in hierarchical records.

Data Files

A data file begins with a header containing a five-character ASCII version string, the SLIDE_ID from the slidedat file, the file number encoded into three ASCII characters, and 256 bytes of padding. The remainder of the file contains packed data referenced by the index file.

Slide Position File

The slide position file is referenced by the VIMSLIDE_POSITION_BUFFER.default nonhierarchical section. It contains one entry for each camera position (not each image position) in row-major order. Each entry is nine bytes: a flag byte, the X pixel coordinate of the photo (4 bytes, little-endian, may be negative), and the Y coordinate (4 bytes, little-endian, may be negative). In slides with CURRENT_SLIDE_VERSION ≥ 1.9, the flag byte is 1 if the slide file contains images for this camera position, 0 otherwise. In older slides, the flag byte is always 0.

In slides with CURRENT_SLIDE_VERSION ≥ 2.2, the slide position file is compressed with DEFLATE and referenced by the StitchingIntensityLayer.StitchingIntensityLevel nonhierarchical section.

Associated Images

thumbnail
the image named “ScanDataLayer_SlidePreview” in Slidedat.ini (optional)
label
the image named “ScanDataLayer_SlideBarcode” in Slidedat.ini (optional)
macro
the image named “ScanDataLayer_SlideThumbnail” in Slidedat.ini (optional)

Known Properties

All key-value data stored in the Slidedat.ini file are encoded as properties prefixed with “mirax.”.

openslide.mpp-x
normalized MICROMETER_PER_PIXEL_X from the Slidedat section corresponding to level 0 (typically mirax.LAYER_0_LEVEL_0_SECTION.MICROMETER_PER_PIXEL_X)
openslide.mpp-y
normalized MICROMETER_PER_PIXEL_Y from the Slidedat section corresponding to level 0 (typically mirax.LAYER_0_LEVEL_0_SECTION.MICROMETER_PER_PIXEL_Y)
openslide.objective-power
normalized mirax.GENERAL.OBJECTIVE_MAGNIFICATION

See Also

Introduction to MIRAX/MRXS. Note that our terminology has changed since that document was written; where it says “tile”, substitute “image”, and where it says “subtile”, substitute “tile”.

Test Data

http://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/