Problem extracting metadata from CZI files

Hi folks,

I recently ran into lots of trouble extracting metadata from CZI files. I have multiple images created on the same date, by the same system. CellProfiler seems to be unable to extract the metadata from most of them, although when analyzing them using Fiji, all the metadata seems to be available.

Attached to this post you will find a screenshot from Fiji (showing the metadata), one from the Images module and one from the Metadata module as well as an archive containing the two files used to demonstrate the issue.

I am using CellProfiler 3.1.8 on Windows 10.

Any ideas?

Marc (17.4 MB)

Hi Marc

It actually works for me. Can you try hitting the Update button in the top left corner of the table (next to Path / URL)?
It is new to me that CellProfiler can actually handle metadata extraction from .czi files well. I split them into individual files and name them (with a macro in Zen) with the info I need, which I then extract with a regular expression from the file name in CellProfiler.


Hi @ImNotGoodSry,

Welcome to the forum.

I use CellProfiler a lot with proprietary file formats. You have to click both the update buttons in the order in the image below - the “Update Metadata” one first and the “Update” one second.


If you click the 2nd update button before the 1st then it’s all screwed up and you have remove your filepaths in the images module and re-add them to try again. I’m guessing what you did was this correctly for the first image then added the second image and just clicked the second update button.

I did it the way I described with your two images and it read them fine.

Good luck!


Hi Laura, hi Esben,

thank you very much for your replies! Clicking the update buttons in the right order does not solve the issue.

However, I noticed the following, which might be some kind of a bug:

The metadata is only recognised if all the images are in the same folder. Please see the two screenshots attached to my post. Also it seems that I have to - first - only add one singe image file, then - secondly - let CellProfiler do its metadata update thingy and then thereafter add the second file. I hope you understand what I mean.


Hi @ImNotGoodSry,

What version of CellProfiler are you using and what are you running it on?

I can’t replicate this behaviour on CellProfiler 3.1.8 on Windows 7 but I have a vague memory of seeing this problem before on my home computer which is a Mac. I will test this later.

Hi Laura,

both of my machines are Windows 10 Home (64-Bit) and I am running Version 3.1.8 on them. The issue is the same on both of them.