Autthresholding when importing Imaris file as Virtual Hyperstacks

[Jeff Hardin-2]

Hi all,
I am using the BioFormats importer in Fiji (most recently updated version). 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 effects 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 a is a large one (sorry, but is representative). You can download it here (640 Mb, sorry):

http://worms.zoology.wisc.edu /drop/IJM_archive.zip

Might someone from the BioFormats team take a look?

Thanks!
Jeff
******
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Integrative Biology
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: [phone]
fax: [phone]
email: [hidden email]
web page: http://worms.zoology.wisc.edu


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