My complaint about a problem opening large fused multichannel images seems to have hit a nerve. The CZI images open fine in Zen, but Zen will not export them as TIF. Our correspondence with Zeiss regarding this matter dates to at least
early 2018. There have been new releases of Zen Blue 2.6 since we reported the issue. BioFormats, which is a fantastic resource that we rely on heavily, does not open this particular version of CZI. We uploaded example files to BioFormats in mid-2018 and
as of version 6.0.2, they do not open properly. This includes CZI saved with Zen 2.5 without pyramid and files saved with Zen 2.6 with pyramid. I have not pursued this because, although it was a high priority back in 2018, it no longer is a priority for
But I think the responses here require further discussion.
Most biologists need solutions that are simple. This means turnkey solutions in the software package they know. The power of ImageJ is that is does everything in in one place. The power of the Fiji version is that it is supposed to have
additional features automatically available. To do a simple task, opening a file, having to hunt down a Python wrapper for someone’s custom code on Github is not a solution; it is more of a problem. Another open source library is not a solution for biologists.
A seamless transparent method for opening images is the necessary solution.
Also, this statement is incorrect: “above the limitations or issues are not caused by the CZI but are rather are fundamental limit.”
If Zeiss made fixing this problem a priority, then Zen 2.6 would successfully export the fused stitched images as TIF. They could even add a modicum of metadata, such as spatial scale. There is nothing “fundamental” that cannot be fixed
here. We last spoke to Zeiss about this last month. As we pay Zeiss a lot of money for service contracts and new instruments, they really have a responsibility to 1.) fix this problem of exporting files and 2.) make CZI available so that the data are useable
in other programs.