Grouping per well triplicates



My images filenames contain a well ID (e.g. A1, A2, A3, etc…). I would like to group the images per well triplicates: group #1 would images A1 + images A2 + images A3. Is there a way to do that?
Many thanks.


Not natively, but you can take advantage of CP’s metadata extraction tools to do it. If you’re already extracting well metadata from the file name, you can feed in a CSV that links “Well” to “Triplicate” - see this recent post for an example of what such a CSV might look like. Then just import the CSV in the Metadata module and group however you’d like.



Could I use a regular expressions rules that enable me to group wells A1,2,3?


Not that I could think of, though certainly if someone has an idea please jump in; the creation of the grouping CSV should take only a very few minutes though, so personally that’s how I’d do it. Up to you, of course.


happy to try the grouping in csv, still need to understand a bit more what to do…



  1. Turn on Metadata extraction in CP, if you haven’t already.
  2. Turn on the ‘Extract metadata from file name’ settings and set up a regular expression for extracting the Well information from your file names. If you need help with this, I’d read the CP help on it or search the forum for other examples; I also like this online tool as a way to test out different regular expressions to make sure they work.
  3. Make a CSV (in Excel or some other program like that) matching the well information to the triplicate information- it’ll look a bit like this:
Well     Triplicate
A01      1
A02      1
A03      1
A04      2
  1. Click “Add another extraction method” in the Metadata module and hit “Import from file”, then load your CSV.
  2. When it asks you how to associate the file with your images, tell it the “Well” metatdata you extracted from the file name should be the same as the “Well” metadata in the CSV.

Load images problem with loading .lif database

Great, many thanks.
However, I’m getting an error, step 5 does not seem to work. The regular expression seems ok, I can extract the Well info. but I can’t make “triplicate” appears anywhere. I’ve attached my pipeline, if you have time, could I ask you to have a look?

Many thanks.

test2.cppipe (13.4 KB)Book1.csv (689 Bytes)


Can you upload your CSV as well?


Hi, yes, just realised I forgot the csv file.

Many thanks


Can you maybe provide a link to a sample image or two as well? It seems like you’re trying to edit your previous post to include them but they seem to be stuck at the ‘Uploading’ stage. A google drive/dropbox/ etc link might work better.


Yes, I was trying indeed.

now, on google drive:



Two things-

  1. Your regular expression does not seem to work on the images you shared; make sure that you’re getting metadata extraction from that expression alone.
  2. I’m not sure exactly how you created the CSV, but even once I got 1) working there was something weird with the CSV; I literally just re-saved it in Excel and now CP works fine with it- test1.csv (686 Bytes)


many thanks, it works now. Even though I did not upload the exact images for this exact pipeline (sorry), with your csv file, it works, that’s great. I don’t understand why my csv file does not work, in excel, both yours and mine look exactly the same. Anyway, it works now, many thanks.



Now that I can group my images per well triplicates, can I, when exporting the data, have in the data export csv file the results of the measure modules and the group number for each IDed object?


If you’re asking what I think you’re asking, yes you can have the Group ID in the object CSVs- there’s an option in ExportToSpreadsheet to ‘Add image metadata columns to your object data file’, set that to yes and then all of the metadata (including your Triplicate values) will be on the object spreadsheets. If that’s NOT what you were asking, can you please clarify?


yes, thanks, that’s what I was looking for. Many thanks.