(quite slow) fast stack acquisition

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(quite slow) fast stack acquisition

Fernandez, Pablo

Dear all,


I have been using MM for a long time but only recently

it became important to acquire fast stacks, and I

cannot say I'm succeeding...


My setup is a spinning disc confocal (Yokogawa CSU-X)

plus Andor Neo camera and ASI MS-2000 stage, controlled

by MM 2.0 running on a TS150 (3.3 GHz, 8 GB RAM, windows Pro 10).

Following the instructions on "hardware-based synchronization",

I connected the fire signal from the camera to the TTL in port in the 

MS-2000 controller and enabled "use sequence" in MM.

This seems to work fine: the stage moves at the speed I

expect from the exposure time and I can get a single

stack without errors.


But here comes the funny thing: when I set multiple time points with

zero time interval I get the stacks separated by huge pauses of

several seconds. E.g., if I run 512x51 11-bit slices, 10 slices per stack,

100 ms exposure time, then each frame takes about 6 s. This seems

very slow to me.


The strange thing is that it is equally slow if I record 2 slices per stack.

And in live mode I can continuousy stream at a rate close to 10 Hz, so

it doesn't look like a limitation of the communication rate with the

devices.


Everything is similarly slow whether I save the data or not, and using MM 1.4.23

as well.


Has anyone achieved higher rates with a similar setup? Any pointers

whatsoever will be very appreciated.


Cheers,

Pablo





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Re: (quite slow) fast stack acquisition

Stuurman, Nico
Hi Pablo,

> My setup is a spinning disc confocal (Yokogawa CSU-X)
>
> plus Andor Neo camera and ASI MS-2000 stage, controlled
>
> by MM 2.0 running on a TS150 (3.3 GHz, 8 GB RAM, windows Pro 10).
>
> Following the instructions on "hardware-based synchronization",
>
> I connected the fire signal from the camera to the TTL in port in the
>
> MS-2000 controller and enabled "use sequence" in MM.
>
> This seems to work fine: the stage moves at the speed I
>
> expect from the exposure time and I can get a single
>
> stack without errors.
>
>
> But here comes the funny thing: when I set multiple time points with
>
> zero time interval I get the stacks separated by huge pauses of
>
> several seconds. E.g., if I run 512x51 11-bit slices, 10 slices per
> stack,
>
> 100 ms exposure time, then each frame takes about 6 s. This seems
>
> very slow to me.
>

This is caused by MM sending the sequence (again) to the controller. 
Since you have an ASI controller, you can try to circumvent this by
using the "Fast Sequence" property.  See:
https://micro-manager.org/wiki/ASIStage

Let us know if you get this to work faster!

Best,

Nico





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