[OpenSPIM] how many slices per second by the system

[Robert Hauschild]

Hi Yan,

I  get about 1.5 slices /second with the openspim plugin. There is a lot 
of overhead in the communication with the hardware (e.g. everything 
(laser power, x,y,z etc.) is set and queried even if the only parameter 
that changes is the z position.
I never was able to quite figure out why it is so slow.
Here is a profile output I posted to the list some time ago:

> My setup is Orca R2, Coherent Cube, Picard stage.
> I tested a couple of things and it it still unclear to me where the 
> time is wasted.
>
> I attached the core log of a 10 frame long time series (100ms 
> exposure) recorded to memory with X/Y/Z Stage/Theta all unchecked and  
> without "Update Live preview".
>
> I tried two configurations:
> 1. Orca  + Cube + Picard
> 2. Orca  + Picard
>
> "1" took 7.6 s of which ("1"- "2") = 1.4 s are communication with 
> laser, which, while way too much, is not the source of the problem.
>
> Profiler("performAcquisition")[4 children]: 7.6113s
> 0.0017%:    Profiler("Output")[0 children]: 0.0001s
> 0.0000%:    Profiler("Acquisition")[0 children]: 0.0000s
> 24.0133%:    Profiler("Movement")[0 children]: 1.8277s
> 0.0013%:    Profiler("Setup")[0 children]: 0.0001s
>
> So most of the time the system is doing something that the Profiler is 
> not recording.

Best,

Robert


On 02.06.2016 05:08, 胡衍 wrote:
> Hello, everyone,
>
> This is Yan.
> Is there anyone who could tell me how many slices the system would take with the Picard Industries stage, and Andor camera?
>
> I am estimating the cost time for a tissue sample with 1*1*1 mm3.
>
> I am looking forward for your reply.
>
> Sincerely,
> Yan
>
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> OpenSPIM at openspim.org
> http://openspim.org/mailman/listinfo/openspim


-- 

Robert Hauschild
staff scientist

Institute of Science and Technology Austria (IST Austria)
Am Campus 1
A – 3400 Klosterneuburg
Phone: +43 (0)2243 - 9000 - 1047
Email:   robert.hauschild at ist.ac.at