Cellprofiler metadata issue

Hi everyone,
I’m a new user of Cellprofiler, using a mac (10.15.1) and I have installed both Java (1.8) and Cellprofiler (3.1.9).
I’m trying to extract metadata from a .czi using the method to “Extract from image file headers”, followed by “Update Metadata” (which takes 5 minutes before the program can respond) before pressing “Update” at the table below, and it only finds one image, but there are over 60.
Unfortunately, I cannot progress to “NamesAndTypes” because the program says “no image sets are available”.
Any ideas how to progress or solve this issue?

Hi @jstunden,

From what you describe it sounds like you’re approaching this correctly, so there may be an issue with the file. If you’re able to send a copy of the file we might be able to provide some further assistance. If not, would you be able to describe what contents you’re expecting to be inside (stacks, time series, etc)?


Hi @DStirling
Thank you for the reply.
The file was generate using Zen Blue, with images from a Celldiscoverer7. The .czi should have images of the orthogonal projection (max), from 5 z-stacks, across 3 channels.
I’m not sure if there is a plug-in or something similar that I must install before it works?

Hi @jstunden,

I understand that your single image file in .czi has 3 channels with Z-stack of 5 planes. Or does your image have Max projection for all the 3 channels? But you had mentioned about 60 images. Do you mean a folder with .czi files?
Other option you could try is split the channel and try with the single image. Nevertheless, you can give further details as mentiioned above to help you better.

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