[OpenSPIM] how many slices per second by the system

[胡衍]

Hello, Robert,

Thank you very much for your explanation.

I got to know from the Picard Industries, the following information:
The 4D-Stage can not move 10 times in one second.
The USB communications takes about 100 ms to tell the 4D-Stage to move.
Then the 4D-Stage begins to move for the number of steps you wish to move.
This takes time along with detecting when the move is completed (more USB
communications).
It looks like the 4D-Stage can do about 3-4 moves per second, not 10.
You may be able to optimize this by reducing the amount of USB
communications.

I thought the system could take 3 or 4 slices per second, but after reading the paper by Pete,
I found that he took 1.35 or 1.7 slices per second from the data in the paper.
So I am confused about the movement.

Anyone knows how to improve the speed?

I am looking forward for your reply.

Sincerely,
Yan


----- 原始邮件 -----
发件人: "Robert Hauschild" <robert.hauschild at ist.ac.at>
收件人: openspim at openspim.org
发送时间: 星期四, 2016年 6 月 02日 下午 3:11:14
主题: Re: [OpenSPIM] how many slices per second by the system

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
>
> _______________________________________________
> OpenSPIM mailing list
> 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


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