Extracting position file from new MIRAX format
jminnie at live.com
Sun Jul 29 23:46:25 EDT 2012
I have slowly been getting as educated as possible on the inner workings of
the MIRAX format. I am looking into bug #92 on the openslide bug tracker,
which deals with improper slide positioning of new MIRAX data. Thanks to the
very detailed description by Benjamin regarding the MIRAX format, I have
been able to understand that I will need as much help as I can get to get a
more detailed understanding of the format and its intricacies.
Fundamentally, as Benjamin has also enlightened me, is that in the new MIRAX
data (v2.2) the slide position data is not in the expected location and/or
format. There is a new NON_HIERARCHICAL section called
"StitchingIntensityLayer" instead of the previous "VIMSLIDE_POSITION_BUFFER"
that supposedly contains the slide position data that we are after. What is
now required is to parse this new "StitchingIntensityLayer" NON_HIER
The openslide package already contains a python script for the purpose of
parsing mirax data. It is called "parse-mirax.py". However, my understanding
of the script seems to indicate that it really just dumps the contents of
the MIRAX data based on the already-understood layout of the MIRAX index
file contents. In this case where we have new data that is not yet
understood, the MIRAX python parser is not going to be immediately useful
until the bits-and-bytes of the new "StitchingIntensityLayer" section is
Does this sound reasonable?
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