Tissuefax files

I have an issue with images created with the TissueFax slide scanner from TissueGnostics. They did not make their file format bioformats compatible. The overview scans are saved as a folder with images, a folder with DAT files and a Cache folder. A project wrapper opens the hole imaging project. Somehow their software uses this to read it as a pyramidal file format. The exported overview tifs are too big to handle comfortably and Qupath does not read this format . Is there any way to make Qupath handle this type of files?

I’m afraid I don’t know anything about this format at all. The best way to add support for it in QuPath is through Bio-Formats - but considering the challenge of handling proprietary formats and OME’s position on this is really may be best to ask the vendor to consider adopting an open format such as OME-TIFF.

Perhaps someone from the OME team could be more helpful than me.

If you can get them to export at all, and QuPath can read them, even poorly, you might want to consider converting them into pyramidal ome-tiff files through QuPath. It likely won’t be a quick process, but it might make them easier to work with. You can find the option in the File menu under Export region->OME-TIFF. It only exists in, I think, M4 and above, and M5 should have improved support once it is out.

But the best option will be to get the company to support BioFormats or otherwise open source their file format.

thanks for the replies. will have a look into both suggestions!

Tissuegnostics have promised to have this solved with the next update. promised for beginning 2020!

thanks for helping with this!

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