Nd2 z-stack metadata import: series = 0?



I would like to use CellProfiler to measure cell area, cell shape, and cell volume from z-stacks that are saved as .nd2 files.
I loaded my images by dragging and dropping them into the images module. Then when I use the “protocol” described in the manual (http://cellprofiler.org/manuals/current/) to extract the metadata from these images most things look good. I only wondered if it is alright that the Series column only gives zeros (see printscreen below) I would expect that every file would become a new serie.

When I continue following the manual to the NamesAndTypes module problems arise when selecting Metadata as ‘image set matching method’. I get this error:

Can someone help me solve this problem?

Thanks in advance.
Kind Regards, Hanneke


Each file is its own series, but you can see it’s populating it as 156 frames with 3 channels and 52 Z planes for your first movie and 47 Z planes for the second(Size C and Size Z).

Your NamesAndTypes issue is due to the fact that you’re doing this in CellProfiler 2.2, which doesn’t support 3D images (you could analyze this planewise, of course, by adding “Z” under “File location” to your NamesAndTypes matching setup).

Our CellProfiler 3.0 3D release will hopefully be coming soon- in the meantime you can install from source if you want to try it, but note that a lot of documentation etc is still missing; we do have a tutorial for finding cells in 3D here.

Good luck!


Thanks for your answer bcimini. I will try the source code!