Fetching .MRXS data via QuPath fails

[nmduonggg]

Hi guys,

I successfully start the MONAI label server for my pathology tasks, using QuPath. However, when I use file ".mrxs" to place in datasets folder, QuPath cannot fetch the WSI image. It works fine with the sample WSI image with format of ".svs". It seems that MONAI fails to support ".mrxs" format, which is supported by OpenSlide ??

Does anyone have suggestion on this ? Thanks guys

[diazandr3s]

Hi @nmduonggg,

Thanks for sharing this.
Here are the supported file formats:

MONAILabel/monailabel/config.py

Lines 72 to 81 in 4736d5f

	MONAI_LABEL_DATASTORE_FILE_EXT: List[str] = [
	"*.nii.gz",
	"*.nii",
	"*.nrrd",
	"*.jpg",
	"*.png",
	"*.tif",
	"*.svs",
	"*.xml",
	]

Do you know if there is an open-sourced ".mrxs" reader? Otherwise, is there an easy way to convert images from ".mrxs" to ".svs" format?

Hope this helps,