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Confocal image stacks were processed using Leica AS AF v2.3.5 (Leica Microsystems).
The MRI stacks were processed with a custom toolbox, implemented using open source software.
Image stacks were processed with an ImageJ macro (Text S1).
The resulting image stacks were processed using "National Institutes of Health" Image software™.
Confocal stacks were processed for maximum intensity projections with Leica LCS software and movies were assembled using ImageJ (MacBiophotonics).
Image stacks were processed using ImageJ.
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The input stacks are processed in a 1-1 pairing.
Figures from the Z-stack were processed in Adobe Photoshop 6.0 (Adobe Systems,San Jose, CA, USA).
For confocal images, channels were scanned sequentially, and confocal z-stacks were processed using FIJI.
Maximum intensity projections of confocal z-stacks were processed by using ImageJ software (NIH).
A2P-stacks were processed using IMARIS software (Bitplane, Zurich, Switzerland) for three-dimensional analysis of mucosal morphology.
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