Cell Profiler 3.1.9 Java Issues

Okay, if Java is there and pointed to correctly then there’s really no reason why this wouldn’t be working.

You might want to try the latest CellProfiler 4.0 prerelease, which is currently available on our GitHub.

I am having the same problem as originally described. I am using Windows10 and cannot get the program to open. I have confirmed everything in the troubleshooting sections. I have also done 2 “clean” installs after the first original install failed. Still just getting the flash of error message and then a blank black screen.

What am I missing?

Hi @m_bemrose,

Could you try launching CellProfiler from Command Prompt and copy the exact error message here? It’d also help to see your environment variables. Thanks

Thank you for taking the time to respond, @DStirling!

I am pretty much computer illiterate if the program isn’t running correctly. So, if you can walk me through how to launch from command prompt, I would gladly appreciate it. I can follow directions well, just can’t come up with the correct prompts on my own.

Here is a screen shot of the enivronmental variables. They appear to be correct per the “troubleshooting” section of CellProfiler.

Okay, try opening command prompt and type cd "C:\Program Files\CellProfiler". Hit ‘enter’.

Then type cellprofiler.exe and hit ‘enter’.

This should display the error message CellProfiler is producing.

@DStirling,

Ok, so if I just open Command Prompt, this is the first prompt:
C:\Users\mbemrose>

If I open Command Prompt as the Administrator, I see this:
C:\WINDOWS\system32>

In either case it won’t accept the prompt you suggested. If this is too much trouble, I completely understand.I know anyone with a shred of IT or CompSci knowledge is snickering at the pathetic nature of this thread right now…but this is just such a foreign area to me.

However, if you’re willing to work a bit with me, I’d like to try to figure this out.

What do you mean by “it won’t accept the prompt”?

I don’t know how to get to a blank line? I can’t just type it after the existing prompt… and if I add to the line in this way: C:\Users\mbemrose\Program Files\CellProfiler
it says that it doesn’t recognize “program”.

If I go into File Explorer to locate the program, this is the file path where I saved the program:
C:\Program Files\CellProfiler

I don’t understand how to type that into Command Prompt given the lines that the program opens with…

lost cause?

Entering cd into command prompt followed by a directory is used to switch the current directory.

Did you enter the entirety of cd "C:\Program Files\CellProfiler"?

Thank you for your continued patience.
Here’s what we have after finally excecuting your instructions correctly!

C:\Users\mbemrose>cd “C:\Program Files\CellProfiler”

C:\Program Files\CellProfiler>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 17, in
File “c:\python27\Lib\site-packages\PyInstaller\loader\pyimod03_importers.py”, line 395, in load_module
File “CellProfiler\cellprofiler\object.py”, line 3, in
File “c:\python27\Lib\site-packages\PyInstaller\loader\pyimod03_importers.py”, line 395, in load_module
File “site-packages\matplotlib_init_.py”, line 1162, in
File “site-packages\matplotlib_init_.py”, line 1006, in rc_params
File “site-packages\matplotlib_init_.py”, line 1133, in rc_params_from_file
File “site-packages\matplotlib_init_.py”, line 1049, in rc_params_in_file
File “contextlib.py”, line 17, in enter
File "site-packages\matplotlib_init
.py", line 1034, in _open_file_or_url
LookupError: unknown encoding: cp65001
[10324] Failed to execute script CellProfiler

Ok, here is what we have after I finally executed your (what should have been perfectly clear) instructions correctly:

C:\Users\mbemrose>cd “C:\Program Files\CellProfiler”

C:\Program Files\CellProfiler>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 17, in
File “c:\python27\Lib\site-packages\PyInstaller\loader\pyimod03_importers.py”, line 395, in load_module
File “CellProfiler\cellprofiler\object.py”, line 3, in
File “c:\python27\Lib\site-packages\PyInstaller\loader\pyimod03_importers.py”, line 395, in load_module
File “site-packages\matplotlib_init_.py”, line 1162, in
File “site-packages\matplotlib_init_.py”, line 1006, in rc_params
File “site-packages\matplotlib_init_.py”, line 1133, in rc_params_from_file
File “site-packages\matplotlib_init_.py”, line 1049, in rc_params_in_file
File “contextlib.py”, line 17, in enter
File "site-packages\matplotlib_init
.py", line 1034, in _open_file_or_url
LookupError: unknown encoding: cp65001
[10324] Failed to execute script CellProfiler

This is the latest error I’ve received as well.

Thanks, that’s super helpful!

Would you be able to try going back to the environment variables screen you found earlier, then add a new variable called “PYTHONIOENCODING” with the value set to “UTF-8”? Let me know if you still get the problem with this set.

Ok, I made that change - then repeated the command prompt from earlier.
Here is what happened (screen shot of both windows). It appears to be the same error?

Okay, if you restarted command prompt after adding the variable I’m not sure there’s much more we can do.

Could I suggest that you try the latest pre-release build for CellProfiler 4? It’s available here. We’ve done a lot of work to prevent this sort of issue from happening in the new version.

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Hey! I managed to install CellProfiler4 and it opened successfully!
Thank you so much for your patience & help @DStirling.

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Cell Profiler 4.0 works for my user as well, thank you @DStirling

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