our facility users record H&E tile scans on a Leica system, generating .xlef and .lof files. They stitch the files using LASX, creating a merged image within the same Leica file (project).
Following Opening .lof Leica files it is best to open the .xlef/.lof files with LASX and resave them.
Following BioFormats - Lifext: pyramid support for Leica LIF file : status? .lifext files containing pyramids and are read easily.
I encounter the following problems when handling the stitched file (~3GB). Resaving the stitched file as .lif or exporting as .tif creates a file with unexpected behavior:
- in QuPath: QuPath works best with pyramidial files; when clicking yes or no: Java.lang.NullPointerException
- in Fiji: open the file as a 3-channel (R, G, B in separate channels) that look normal. When switching to composite view the image as attached becomes visible.
- In LASX I cannot choose to generate a .lifext file. Some of the users’ tile scans come with a lifext file (maybe dependent on the size of the lif-file?). I can handle the lifext-file without problems in both Fiji and QuPath.
How do I obtain a (pyramid) file that I can handle properly with Fiji/QuPath?