Volumetric (three-dimensional) processing and analysis

I’ve been working on volumetric (three-dimensional) processing and analysis for a month or two and have reached a place where some features are sharable.

While a number of modules have been patched (and a few modules have been added) to the master branch and nightly builds, you’ll need to work from this branch:


to open your three-dimensional images.

A few notes:

  • Multi-page TIFFs are supported. While we don’t support other formats, we plan on supporting a few in the future. Alternatively, patches to support your preferred formats are encouraged!

  • It’s slow! Sometimes it’s frustratingly slow. This is due to a mixture of the complexity of the underlying algorithms, processor performance, and serial implementations. While parallel implementation work has started it’ll be a few months before this work is merged.

  • Support for multi-channel three-dimensional images is “iffy.” Support for time-lapse three-dimensional images is non-existent.

  • There’s no support for existing measurement modules. I plan on working on this over the next month or two.

Let me know what you think.

Thank @derek and his colleagues at the Allen Institute for their financial and technical support!


Nice! I’m very curious, thanks for the great work!

Exciting update!

Most 3D-related features that exist are now in the master branch. This means they will eventually be in the nightly builds, although those are a little funky right now.

1 Like

We’ve been working on updating existing measurement modules to measure three-dimensional features. You can follow this work in various branches. I expect it’ll be merged into master sometime next week.


Nightly builds are working now, so you can check out the new 3D features that are a work-in-progress by downloading the nightly build here: http://cellprofiler.org/releases/

Slight edit- the nightly build of CellProfiler for Mac has the 3D functionality, the Windows version doesn’t have it yet (but hopefully soon!). If you want to try the new 3D features on a Windows machine, you can still run CP from source as described above.