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  • Jan 17 13:57
    tinevez closed #207
  • Jan 17 13:57
    tinevez commented #207
  • Jan 15 16:50
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  • Jan 15 10:07

    tinevez on TrackMate-7.5.1

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    tinevez on master

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  • Jan 10 16:57

    tinevez on master

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  • Jan 10 10:35
    tinevez closed #206
Marco Fidaleo
@marco.fidaleo_gitlab
Hello! I have some ApoTome images. Do you know if there is an available plugin to open them?
10 replies
Jean-Yves Tinevez
@tinevez
Hello folks.
I have found a way to run the Cellpose TrackMate detector in a multithreaded fashion:
It is not a true "Cellpose multithreaded":
If I have 100 time-points and 10 cores, I create 10 tasks, and each task launches its own Cellpose.
So you get 10 Cellpose that runs at the same time on your computer:
Screen Shot 2021-12-18 at 18.01.06.png
After that we sweep the results folder and rebuild a proper result image.
It works great on my Mac and is mainly useful here, because there is no GPU support for Mac.
But I was wondering and asking to you oh GPU-guru: What would happen if I do the same with GPU support? Will the 10 instances of Cellpose asking for GPU at the same time clash in each other and explode?
Jean-Yves Tinevez
@tinevez
Ok I moved to another Windows computer with a NVIDIA GeForce RTX 2080 SUPER, 8GB of RAM. And tested this.
It's.....not such a great idea to launch many python processes that access the GPU concurrently.
The python processes launch properly, and after some kind of warming up phase, the GPU RAM and usage ramp up to 100%.
image.png
Then for a few frames, the processes run normally, but after a while the Java UI started blinking and freezing.
Until my PC completely froze and I had to restart it.
I guess multiprocessing with a single GPU requires more care than I used.
Jean-Yves Tinevez
@tinevez
Hello folks.
Is there a library shipped within Fiji that offers a Swing range slider (a slider with two controls)?
Swingx has one but it does not seem to be functional (it does not pain).
JIDE too, but is not in Fiji.
4 replies
Suzann Barnasconi
@SBarnasconi_twitter
Hello everyone, I get an Macro error with: 'the plugin directory is not writable, so the file containing the vector list would not be copied into the plugin directory'. Someone who know how I can solve this?
Nicolas Chiaruttini
@NicoKiaru
Hello @SBarnasconi_twitter the best is to post your issue on forum.image.sc and to provide enough details so that we can reproduce your issue (image, macro code, update sites enabled if any)...
Also tell your OS, it could be that Fiji was not properly installed if it is on a Mac OS
Curtis Rueden
@ctrueden
@SBarnasconi_twitter You are not the only one having similar problems (though the "vector list" error specifically is new to me). It becomes harder and harder to install Fiji on macOS with each OS upgrade. Of course I want to fix it by changing how we build the Fiji bundles on macOS; it's just a matter of time. In the meantime, check out this forum post for a possible solution.
Jean-Yves Tinevez
@tinevez
Hi all.
I would like report a weird and maybe cool finding about running Cellpose from Fiji, and TrackMate in particular.
The way we run Cellpose from TrackMate is to create a sub-process that runs Cellpose with command-line arguments that point to a folder where TrackMate has exported individual time-points.
But nothing prevents us from splitting the let's say 100 time-points in 8 folders, and run 8 independent Cellpose processes.
That would be some kind of multithreading in Java that becomes multiprocessing...
I tried and I thought that it would be a means to accelerate Cellpose when no GPU is available. For cases when we are forced to use the CPU.
I implemented this in TrackMate and runs some metrics. Here are a summary of the results.
On a PC with Windows, forcing Cellpose to run with the CPU: There is no benefit from splitting the load between 1,2, 10 or 20 processes. It seems like 1 Cellpose process can already use ALL the cores by itself and running several Cellposes processes concurrently does not lead to shorter processing time.
I was about to give up but then I tried on my Mac.
And there there is a clear benefit.
for a source image 1024x502 over 92 timepoints, 3 channels.
Jean-Yves Tinevez
@tinevez
  • 1 thread -> 24.4 min
  • 8 thread -> 4.1 min
(there is not a x8 speedup factor, which is to be expected)
It's cool no? In particular noting the fact that there will never be GPU support on Mac amenable to our end-users and that Macs are still strong in biology labs.
Jan Eglinger
@imagejan
Interesting, thanks for sharing, @tinevez! I think this would merit a forum topic, instead of getting lost in the chat history here :slight_smile:
In general, instead of having a mac-specific “workaround” for multithreading, I think cellpose should be improved to work similarly efficient on a Mac as on a CPU-forced Windows. What do you think?
Jean-Yves Tinevez
@tinevez
Hehe :)
I think that this is the desirable path to have a better Cellpose for all of us.
But the 2nd path is one we have agency over.
Curtis Rueden
@ctrueden
Maybe a compromise would be to add a configuration option for number of processes to spawn, and try to set it to a reasonable default based on the platform OS and number of CPUs? That way, anyone can override it to be whatever they want, in case things change in the future, or they just want to play around.
Jean-Yves Tinevez
@tinevez
It's done already. TrackMate abides to the number of threads set in the ImageJ preference menu item.
And I trigger multithreading only on Mac:
Curtis Rueden
@ctrueden
Cool.
Jean-Yves Tinevez
@tinevez
.. re-reading myself I realize the doc string is not super clear nor proper english....
Jean-Yves Tinevez
@tinevez
If you are interested in testing it, I uploaded a tentative jar to an update site.
I am currently working on the doc in a branch of our wiki. The doc already contains installation information:
Nicolas Chiaruttini
@NicoKiaru
@tinevez awesome! I've got no time to test yet, but just to let you know, your link returns a 404 error
Jean-Yves Tinevez
@tinevez
Thanks! I just merged it and it is now on the main site:
https://imagej.net/plugins/trackmate/trackmate-cellpose
and now it links to the tutorial dataset.