Matching an individual metadata.txt file to an individual image.tif file




New to cell profiler here. I use micromanager to acquire my time series of images at different positions. Therefore, I have a folder with for example 10 .tif files representing the 10 different positions on the slide, each a time series. Also in that folder, I will have 10 .txt metadata files corresponding to each time series. I am currently struggling to match the metadata to the correct tif file, is this possible? Any suggestions?

Many thanks,



Can you try Metadata module, and set:
Extract metadata = Yes
Metadata extraction method = Import from file
Then "Match file and image metadata " accordingly

Can you try and see if that helps?



Hi, thanks for the reply.

I’ve tried the match file and image meta data but I can’t seem to get it to work.
First of all, I don’t have a single metadata file, but one for each series so I can’t choose a metadata location. Secondly, in the drop down menu for CSV metadata, the only option is none.

I’ve attached some images to help.



(May sound very laborious, but let’s try this experiment)

  • At “Extract metadata from”, set it to "Images matching a rule"
    Then follow the name of each image file >> assign a name to it.
  • At “Metadata file location” of each of these images, put the metadata text file accordingly

Click “Add another extraction method” at the bottom of the window and repeat this process to another pair of files (1 image + 1 metadata text)

Let’s see if you can now assign each image one different metadata file.

Good luck.


It’s a good point, there may not be a way for CellProfiler to consume multiple data files beyond what Minh just described. I wonder if it might be possible for you to concatenate the contents of the metadata files into a single file (using something outside of CellProfiler) to solve this workflow problem? Would the resulting file be able to provide metadata to match to each image?

I’ve not looked into detail at the goal here so consider this a random idea thrown out there, not a recommendation!



I have tried this but now get an error when I try and update. Do you think the .txt file which micromanager generates is incompatible with cell profiler?




The Metadata module is designed to import CSVs, not text files; you’re not the first person who has asked about this though, please see this thread for some solutions as to how to convert these files for use in CP.