MRXS Format ...

[Derek Magee]

Hi,

I've been working on reading Fluorescence MRXS files for a project (they are near identical to brightfield ones, just with extra RGB tiles for extra channels despite what the rant on the open microscopy page says) using openslide's excellent resources (MIRAX format (openslide.org)<https://openslide.org/formats/mirax/>, Introduction to MIRAX/MRXS (cmu.edu)<https://lists.andrew.cmu.edu/pipermail/openslide-users/2012-July/000373.html>). I was wondering if anyone could explain to me the last bit I've not quite understood, which is the low resolution levels where multiple scanner images are combined into a single tile. These appear to have an index that when used to look up the location in the position file puts the composite tile in more-or-less the right place, but not exactly. The error seems slightly different for each tile, but there seems to be a systematic shift in both horizontal and vertical position as well as a random one. The introduction to MRXS says:

In order to render this tile, we have to separately extract the
pixels corresponding to each camera position -- many of which are
fractional pixels due to repeated downsampling -- and render them in
their correct positions at sub-pixel resolution.

However, in the file I have the tiles at this resolution seem to be coherent (i.e. no junk in the middle). However, the index isn't quite right. I'm  not exactly sure how to "render them in their correct positions" as I'd assume the index would be correct at least for the top left part of the tile.

I note Openslide renders the first 3 channels of these type of slides "correctly" (in location anyway) as RGB, ignoring the subsequent channels. What I'm not sure is whether Openslide renders the low resolution composite tiles, or ignores them (which is what I'm doing for now, but it makes rendering at low resolution a bit slow).

Any pointers appreciated!

Thanks

Derek
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