MRXS Format ...

[Benjamin Gilbert]

On Wed, Jul 27, 2022 at 11:55 AM Derek Magee <D.R.Magee at leeds.ac.uk> wrote:
> 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).

Hi Derek,

OpenSlide does render the low-resolution tiles.  It's been a while
since I looked at that code, but as I recall, the tile top left corner
in the position file is accurate.  A couple possibilities that might
explain what you're seeing:

- At higher downsamples, the junk in the middle of the tiles may not
be visually apparent, but if you don't remove it, the tiles will have
larger dimensions than expected.
- Fluorescence slides, or newer MRXS files generally, may store
position information in a different format.

It may be helpful to run OpenSlide with OPENSLIDE_DEBUG=tiles to see
how OpenSlide places the tiles in a sample brightfield slide.

Best,
--Benjamin Gilbert