Community collective: viewing z-stacks in 3D

Posted by , on 14 June 2023

Have you ever sat at your computer and wondered if you have the best representation of your imaging data? Would another software give you better (or different) results? Joy Franco (@engineering_joy) asked the science community on Twitter for their software recommendations for viewing confocal Z-stacks in 3D. Joy’s top request was being able to finely position the viewing angle to create a rendered image of their data. Dive into the full thread to see all the recommendations.

Top of the pile in terms of mentions was Imaris, which is available as free to download software called Imaris Viewer – the full version is available as part of various software packages. There were also plenty of likes for open-source/free software including ChimeraX, Agave, FPBioimage, ClearVolume, napari and many others. Have you tried any of these software, or do have any top tips? Comment below or drop us an email at

We asked Joy for a some more information about her request and the viewer that she is currently using, this is what she said, “The biggest issue I ran into when trying to use ImageJ was that even with a fairly powerful laptop the rendering was slow and clunky. I started looking into a few other options but was turned off by the amount of effort it took to get the viewers up and running. When I found Imaris Viewer, free and available for Macs, it was a clear winner. It is so easy to use and had so many nice features; I love that it lets you change the look up tables for the channels and take snapshots. The rendering is also very efficient, and it has minimal sluggishness when it comes to manipulating the viewing angle. The only downside is you have to create an .ims file, which can eat up hard drive space. I haven’t had a chance to play around with many of the wonderful suggestions from the community but hope to do so in the future.”

If you have requested (or seen) any community advice that you would like to see be given a permanent, searchable home on FocalPlane, contact us at or on our social media pages. And if you are not on social media but would like to solicit community advice, then drop us and email and we’ll ask on your behalf.

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Categories: Discussions, Education

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