Incorrect 12/16 bit intensity scaling in .czi file?

Not sure I have this right, but I’d appreciate any thoughts. I have .czi files exported from Zeiss ZEN Blue software. I’m pretty sure they are 12 bit. When I load them in CP, I get very very low intensity values, which I think are almost certainly from using 16-bit scaling on 12-bit data. When I display image scaling for the raw image in the ‘View’ panel in test mode, it reports 65535.

I thought the thing to do for this was to specify a max intensity of 4095 in the NamesAndTypes module. Instead, I need to put 0.0625 in this box to get original scaling back. This suggests that maybe scaling to 16 bit depth was performed before NamesAndTypes gets to it?

I’m using CP 2.2.0 on MacOS 10.10.5, latest JDK. Also seen with the latest CP 3.0 nightly version.

An example czi file can be found here:


Hi there,
I load your provided image into Fiji and it contain 3 series: first series 12-bit, second and third are 16-bit.
So you may need to first clarify which series to use to proceed…

Whoa, I did not know it was possible to have bit depth differ within the same image file!