Missing Images again


I still have problems with the module ‘LoadImages’. I have a file structure like this:


  • — Barcode1

    • — Well A1

      • — Ch1.tif
      • — Ch2.tif
    • — Well A2

      • — Ch1.tif
      • — Ch2.tif
    • — and so on

  • — Barcode2

I extract metadata from the path (experiment, barcode, well) and from the image (channel).
I don’t do any grouping by metadata. It fails to load the images by telling me that in the last image folder (Barcode-N, Well-M) the second image file is missing. But that’s not true. If I exclude this folder with the subfolder selection, I get the same error with the second last image pair. Any idea, what I could do?


Hi July,

I wanted to request a few things to diagnose this problem:

  • Could you upload the pipeline that’s causing the problem?
  • What is the full path and filename of the file that is says is missing?
  • Also, I assume that CP is showing a window reporting the missing files? If so, could you take a screenshot of that window, focusing on the image that it says is missing?


Hi Mark,

I’ve attached the screenshot as well as the pipeline for you. Looking closer at the error message shows me, that it’s not the last pair of files which causes the problem. Somewhen in the beginning there is the case that there is only one of both images present and from this point the files are not assigned correctly (e.g. channel 1 image from Well A03 gets channel 2 image from Well A04, channel 1 image from Well A04 gets channel 2 image from Well A05, and so on).
The module works if I remove the folder where only one of both images is present.

LoadImages.cp (2.42 KB)

Hi Antje,

The proper output should (will?) occur if you:

  • Check the “Check images…” box

  • Check the “Group images…” box

  • Make sure nothing is selected in the “Specify metadata…” box. On a PC, you can use Control-click to unselect an item if one is selected already.

I believe this should give you the conflict box again, but this time with the correct missing files specified. I don’t think this is way the “Check images…” box should work (it shouldn’t need the “Group metadata…” box to be checked), so we’ll fix that.

That said, this box is meant as a warning that something is wrong. The pipeline will not run correctly unless the offending images are replaced/fixed. We intend to have CellProfiler compensate for this issue by using blank image instead of the missing one, or otherwise skip the cycle, but we have not implemented it yet.