CLIJJx 3D Object Counter GPU Compatibility?

Hello,
I am attempting to run the CLIJX 3D Object Counter for GPU on a computer with an RTX 2080, but I keep getting a couple of different error messages after the user input screen.
When I attempted to run object counter on a thresholded 3d stack, I got this error message with no additional windows popping up:

When I attempted to run object counter on the nonthresholded 3d stack, I got the following error, but the program still managed to generate the objects map:

And this is what the user input GUI looks like:

This seems to be due to GPU compatibility, since I tested the script on a computer with a Radeon RX 5700XT without any issues.

I have included the sample 3d stacks that I was using.

Thanks

1 Like

Dear @SpencerLab,

happy to take care of your issue. Would you mind sharing the used data again? The links were apparently lost.

Thanks!

Cheers,
Robert

It looks like I cannot upload the files to the forum. Here is a box link:
https://ucmerced.box.com/s/wyjn42ojk8yawjdpdf386lt4mlyxf2uf

Thanks

1 Like

Hey @SpencerLab,

thanks for the data! I can reproduce the issue. The underlying reason is that the binary image contains 191915 objects, which is overwhelming for further analysis in the GPU. I will make sure that a better error message comes up or something prevents that from happening again. In the meantime: Try bluring the image before thresholding to get rid of single pixels being misinterpreted as objects or apply binary filters such as opening before sending the image to the 3D objects counter. I have an online tutorial explaining a bit different strategies for optimizing thresholding operations.

Let me know if this helps!

Cheers,
Robert

1 Like

Dear Robert,
Is their a reason why this issue is specific to the RTX 2080? Because I was able to run the 3D object counter script on the same data set on a Raedon RX 5700 XT without any issues. The two GPU have similar specs, although I’ve found the RX 5700 XT to perform CLIJ operations slower.

Thanks

Edit: I’ve done some testing and I was able to apply the object counter after applying a blur. However, I also found that if I try and run the any CLIJ operation after the Object Counter fails to run, then the Dedicated GPU Memory becomes full and I get the following error message:

After this, I need to restart Fiji, otherwise I can no longer run any CLIJ operations. With the RX 5700 XT, I do not have the same issue.

Edit2: I was able to get the object counter to work normally after I applied a blur and threshold to the 3D stack.

1 Like

I assume you have recent drivers installed, e.g. downloaded from the vendors website?

Could you do me favor and run this little script and copy &paste its output here in the forum? (please copy the text; no screenshot this time :wink: ) This would allow me to see the specs of the systems.

run("CLIJ2 Macro Extensions", "cl_device=");
Ext.CLIJ2_clInfo();

Thanks!

Cheers,
Robert

1 Like

Dear Robert,
The drivers on both computers are up to date. Here is the output for the 2080:
2080Log.txt (1.7 KB)

Here is the output from the 5700:
5700Log.txt (1.9 KB)

Thanks