.mrxsmiraxOpenSlide will detect a file as MIRAX if:
.mrxs.Slidedat.ini exists in the directory.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.
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 two values which are usually zero, followed by an offset, length, and file number as in hierarchical records.
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. (In newer slides, the
SLIDE_ID and file number are encoded as UTF-16LE, so the second half of
each value is truncated away.) The remainder of the file contains packed
data referenced by the index 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.
In some such slides, the nonhierarchical record has a second data item
which points to a DEFLATE-compressed blob with four bytes of additional
metadata per camera position.
labelScanDataLayer_SlideBarcode” in Slidedat.ini (optional)macroScanDataLayer_SlideThumbnail” in Slidedat.ini (optional)thumbnailScanDataLayer_SlidePreview” in Slidedat.ini (optional)All key-value data stored in the Slidedat.ini file are encoded as
properties prefixed with “mirax.”.
openslide.mpp-xMICROMETER_PER_PIXEL_X from the Slidedat section
corresponding to level 0 (typically
mirax.LAYER_0_LEVEL_0_SECTION.MICROMETER_PER_PIXEL_X)openslide.mpp-yMICROMETER_PER_PIXEL_Y from the Slidedat section
corresponding to level 0 (typically
mirax.LAYER_0_LEVEL_0_SECTION.MICROMETER_PER_PIXEL_Y)openslide.objective-powermirax.GENERAL.OBJECTIVE_MAGNIFICATIONIntroduction 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”.
https://openslide.cs.cmu.edu/download/openslide-testdata/Mirax/