CellProfiler 3.1.9 crashes while executing the 2D projection pipeline

I am trying to combine a Z stack(11) into one 2D projection. I have a total of 21,120 images. 11 images per set/group. so it leaves me with 1920 image sets. Thus in the end a total of 1920 2D projections should be created. However, CellProfiler stops in the middle of executing my pipeline after generating 190 2D projections. The pipeline is very simple, it just groups and creates a projection based on Average intensity. (Attached below for reference)

I thought there was something wrong with the 191 image set, so I ran the pipeline for just that image set and it worked fine. I can’t seem to figure out why it crashes.
Can someone please help me out. Thanks in advance2D_trial.cpproj (675.0 KB) !

Hi @Swati,

You could try using the “Load data” module. For the usage, check here.

The same has worked in earlier cases

If still not working, a screenshot of the error will be more helpful to check the problem.

Hope this helps.

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

Hi @lakshmi ,

Thank you for your reply.
creating CSV with name and location is just not feasible for 21,120 images so I would not be able to this every time I have a new dataset.
Also, no error shows up. CellProfiler just crashes and closes automatically.

Hi @Swati,

Which operating system are you using? It’s going to be difficult to figure out why the software is crashing without any error message. It may be worth trying to launch CellProfiler from the command line, which should then capture any such error.

I notice you have the “eyes” open - if you try closing them, does it keep it from crashing? It could be causing either a) CellProfiler to run out of window IDs and b) memory to accumulate, such that CellProfiler starts to crash unceremoniously.

Thank you for your replies.
@DStirling I’m using Windows 10.

@bcimini I ran it with the “eyes” off. I got an error prompt this time. (Screenshot Attached).
Please let me know your suggestions on how to resolve this

Hi @Swati,
@bcimini
O.K. One more thing which you could check is that if any of the image files are corrupted (may be check the file size). This was a bug sometime back I think, but not sure if it is fixed.

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

Did it crash out at the same time, or deeper in this time?

Hi,

@bcimini It crashed a little later.
@lakshmi okay I’ll try checking. Thanks