Thanks @matt.mccormick, I would go for your last suggestion.
Fixing it will be way better of course, but maybe it’s not even a bug but a failure in converting the image from the microscopy format to tiff.
The bioformat reader is reading the image as a 4D:
In itk: Dimensions: ( 64 64 1 16 ).
In OME Metadata (from imageJ bioformats plugins):
<Pixels BigEndian="true" DimensionOrder="XYCZT" ID="Pixels:0" Interleaved="false" SignificantBits="16"
SizeC="1" SizeT="16" SizeX="64" SizeY="64" SizeZ="1" TimeIncrement="1.0" TimeIncrementUnit="s" Type="uint16">
So maybe it is just a metadata conversion error…