CellProfiler unable to start when TMP is pointing to D drive



Dear all,

We are using CellProfiler on our image processing virtual machines infrastructure. The VMs are running Windows 7 64Bit in a multi user setup with Active Directory. On some VMs we have a group policy which points TMP to D:\UserTemp to prevent the users filling up the C drive and also for storage space reasons.

Cell Profiler is installed to C:\Program Files\CellProfiler3.1.8.

If a user starts CellProfiler he gets the following error and the software does not open:
C:\Program Files\CellProfiler3.1.8>CellProfiler.exe
Traceback (most recent call last):
File “CellProfiler.py”, line 3, in
File “c:\python27\Lib\site-packages\PyInstaller\loader\pyimod03_importers.py”,
line 395, in load_module
File “CellProfiler\cellprofiler_main_.py”, line 16, in
File “c:\python27\Lib\site-packages\PyInstaller\loader\pyimod03_importers.py”,
line 395, in load_module
File “CellProfiler\cellprofiler\measurement.py”, line 15, in
File “c:\python27\Lib\site-packages\PyInstaller\loader\pyimod03_importers.py”,
line 395, in load_module
File “CellProfiler\cellprofiler\preferences.py”, line 25, in
File “c:\python27\Lib\site-packages\PyInstaller\loader\pyimod03_importers.py”,
line 395, in load_module
File “CellProfiler\cellprofiler\gui\help\content.py”, line 60, in
File “CellProfiler\cellprofiler\gui\help\content.py”, line 33, in image_resour
File “ntpath.py”, line 529, in relpath
ValueError: path is on drive D:, start on drive C:
[8452] Failed to execute script CellProfiler

I found the same issue in another topic but I couldn’t find a real fix, only workarounds:

So if i start CellProfiler after I change the TMP to C:\Temp (set TMP=C:\temp) in a command prompt. Cell Profiler has no problems to run.

In our environment it is not a solution to change the TMP back to C:\Temp since this is a different storage type with less space and we don’t want users to fill up the C drive. Is there another solution or a way to configure CellProfiler to use the C drive but not changing the TMP variable for the whole user session?

Thank you and best regards,



Unfortunately there isn’t a solution right now, but I’ll try to boost this issue higher up in our priority queue to take a look at! Thanks and sorry.


Same issue here - we have several workstations (10) with basic SSDs for startup but the calculations are being performed on dedicated PCIe NVME drives. All jobs fail due to lack of space on c - pointing the temp DIR to any other drives causes the software to crash on startup.