Filenames issue in Cellprofiler 3.0 on Windows



Hi there,

I just installed Cellprofiler 3.0 on Windows and it can’t open a tiff file that Cellprofiler 2 had no problem opening. Here’s the actual name of the file: “Project001.lif_d142aa Pa 6h PABPC-488-5_ch00.tif”. When I try to open it I get the following message: "Failed to open file, “Project001.lif_d142aa%20Pa%206h%20%20PABPC-488-5_ch00.tif”. It looks the spaces that version 3.0 doesn’t like. I did not try, but I am guessing that it won’t process such files if it can’t open. Any ideas?

Thanks, Jama.


It’s only an hypothesis… but you could try to change all the special characters in the name with always safe (_).


Great idea to at least try thAt, to help us diagnose! If that doesn’t work please upload the actual file.


If spaces are removed, then there is no problem. Btw, the file with a name containing spaces actually analyzed just fine, contrary to what I initially expected. But It can not be opened (viewed) from the “Images” window. So it seems like a bug in the display/open operation or the viewer.


Often name full of special characters are filtered out by antivirus and other security systems integrated in windows because are too similar to “codes” used to do sql injection and other informatics attacks. That’s why it’s always better to avoid use names with that meshup. Keep the name simple and add more data in the Tif itself or just keep the information in a .txt file associated to the images.


I understand keeping the name simple is a good idea generally. But the point here is that CP 2.0 did not have this problem. And when you deal with many users, old files and personal habits, etc., renaming isn’t a practical solution. So is it a bug that can be put in the queue to be fixed? There are of course work around this, but it was convenient to open loaded images from within CP because of rescaling, etc. As you all know a Windows viewer doesn’t show dim grayscale images well.


The team has opened a bug report for this. Hopefully if it’s straightforward it can be fixed soon!


Btw, because of the bug help files can not be accessed.


Can you elaborate on that last point?


Sure, here are my observations:

  • If I right click on a module and select “Help for module xx”, I don’t get any results.
  • If from the Welcome screen I click “In-App Help”, I get the error message shown in the First pic uploaded.
  • If, in the main window, I go to “Help >> Search help…” and search for something (let’s say morph) I get the error message shown in the uploaded Second pic.

Thanks, Jama.

First pic:

Second pic



I don’t think any of those bugs is directly related to the filename issue, but I’ve verified and will report all 3. Thanks so much for letting us know!