Export DAPI channel of a mrxs

I tried to export the DAPI channel of a certain level of a mrxs image with QuPath to do image registration.
There are 5 channels in this mrxs image. I didn’t know where to find them and how to only export the Dapi channel in Qupath. Besides, I can not properly open it in the Qupath. It lacks some key data like pyramid. But it works fine with 3DHISTECH Case Viewer, which can not do the export sadly.

I also tried openslide.read_region to get the level of the mrxs image. But the return image was wired. It has large white space. No matter which level I try to read, it only returns the image with the smallest level and a large white area.

5 channels showed in 3DHISTECH CASE VIEWER

the image information in QuPath

Unfortunately .mrxs is a very unfriendly format for open source software. There is some more information (and potential workarounds) at https://qupath.readthedocs.io/en/latest/docs/intro/formats.html#mrxs-3d-histech


It is included in the link Pete mentioned but I would also recommend trying the Glencoe Software workflow for converting to OME-TIFF: https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html


Thank you! It worked. I converted my mrxs into OME-TIFF. But I still have several questions.
1: I checked converted OME-TIFF with opensilde. There is only one level in it. But the Qupath showed the pyraimd is 1 2 4 8 16 32. I used --resolutions 6 trying to only export the level 6 with the size of level 6. But it seems that it still has the size of the largest level(84234 124079). I opened it in Qupath. Its resolution was right. How to extract certain level of a converted OME-TIFF?
2: There are 5 channels in my MRXS, how to just extract one channel with openslide or QuPath?

Did the original mrxs file have 6 resolutions or were you trying to create them via downsampling during the conversion?

Im afraid the bioformats2raw tool at the moment doesn’t enable you to select only a single a resolution when converting mrxs files. If you really wanted to remove the extra resolutions you could perform a separate conversion on the OME-TIFF afterwards using the standard Bio-Formats command line tools (https://www.openmicroscopy.org/bio-formats/downloads/), with the command bfconvert -series 5 /path/to/input.ome.tiff output-sixth-series.ome.tiff.

Thank you. I got what I wanted with 3Dhistech slide converter. Not open source but at least I got something to use.