CellProfiler - New User Issues

New CellProfiler user here. Have downloaded Java 8 and CellProfiler on Windows 10 and when I run the application, all I get is a black screen. Any advice?

Hi @MAC,

Just to be sure, you already tried the solution proposed here

where did you install CellProfiler? In the default “Program Files” folder. I experienced some error like this on some machine (could be due to win10 “protection” settings or antivirus, don’t really know I have to admit…)

Can you try yo uninstall and install at the root, ie C:\CellProfiler\ ?

Best,

Romain

Hi @MAC,

Did you try reinstalling? It might worth to have look here as well.

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

Join us at, https://www.slas2020.org

Hi @MAC,

If you’re using Windows we’ve also started collecting and writing up solutions to this issue here.

Hope that helps!

1 Like

Thank you for your suggestions but nothing has worked. I have uninstalled and reinstalled both CellProfiler and Java. The environment variable and windows language setting are compatible. Is there a possibility that the program is not running because I have downloaded the Java Version 8 Update 231?

Hi Romain,

After reinstalling at the root as you suggested (C:\CellProfiler), I was finally able to get an error message instead of a blank screen.

Which suggests to me that CP is unable to communicate with Java. So I checked to see if I could located CP_JAVA_HOME and it was found at C:\Program Files (x86)\CellProfiler so I changed it to C:\CellProfiler and got myself back to the blank screen.

In case this was a firewall issue with my University’s computer, I also tried installing on my personal laptop which was also unsuccessful. So at least I know that the problem isn’t the device! Do you have any other suggestions?

Thanks
Marcia

Hi @MAC,

You should set CP_JAVA_HOME to C:\CellProfiler\java

Best,

Romain

Hi Romain,

Thanks, I tried that also:
image

And I think that java is installed correctly:
image

But now I am back to a blank screen when I try to run Cell Profiler:
image

Thanks
Marcia

Hi Marcia,

Did you check your Windows language settings, as mentioned on the page I liked to previously?

In theory, since CellProfiler contains it’s own Java environment, you shouldn’t need to install an independent Java environment unless you’re trying to build from source.

Hello,

Yes, I did check to ensure the Windows language settings was correct. It doesn’t seem to matter what advice I follow, CP is not functional on either of my PCs. There has got to be something that I am missing?

Thanks
Marcia

It’s odd that you’d have the same issue on multiple machines. Which version of CellProfiler are you trying to install?

I downloaded CellProfilerStable 3.1.9 for Windows (https://cellprofiler.org/releases/) and Java Version 8 Update 231 (https://www.java.com/en/download/)

Hi @MAC,

In your language settings, did you disable Unicode UTF? Could you please share the screen shot of your language settings & the path where you have installed CP?

Did you try the earlier version I mean 3.1.8??

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

Read more on our site.
Yokogawa CV8000 - The Ultimate in Confocal HCS
https://www.wakoautomation.com/products/yokogawa-high-content-imaging

Join us at, https://www.slas2020.org

The environmental variables show that CR_JAVA_HOME is C:\CellProfiler\java:

  The region settings show the system locale as English (United States) and the Use Unicode UTF-8 is disabled:

image

 Java is installed:

image

I have uninstalled the program (from C:\Program Files(x86)\CellProfiler and re-installed at the root C:\CellProfiler

I also just tried downloading and installing CellProfiler version 3.1.5
image

and now the program won’t even run, I get a fatal error instead:

image

Hi @MAC,

Thanks for providing that. The java version bundled with CellProfiler should be fine, so you shouldn’t need to install java independently at all. One thing I do notice is that your temporary directory system variables are set to /adm.marciach/, but in cmd you’re within /marciach/. Do both of these folders exist? The current Windows build of CellProfiler unpacks itself to the temporary directory when running, so it’s possible that something might be going wrong here. I’m also not sure if having ‘.’ in the directory could also cause such a conflict.