I am using the BioFormats importer in Fiji (most recently updated version as of Oct 31, 2020). It provides options for import of the various sized 4/5d datasets in the .IMS file s (in my case from Andor’s Fusion software), and I can easily import the highest resolution version (thanks!). However, there seems to be some autothresholding/contrast enhancement applied to the individual images in the dataset, but only when the Virtual Stack option is selected. If I read into RAM it works correctly without this occurring. Since the Virtual Stack feature is important for speed and the only way to go for large dataset that exceed RAM, this is an import current limitation.
I cannot replicate this effect when I select Auto threshold on import using a RAM-based stack. I notice that when selecting the Virtual Stack option the Auto threshold option is disabled.
I have a sample dataset, but all I have is a large one (sorry, but is representative). You can download it here (640 Mb, sorry):
Might someone from the BioFormats team take a look?