timelapse interval

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timelapse interval

Shunsuke Miyamoto
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Re: timelapse interval

Mark Tsuchida-2
Hi Shunsuke,

On Thu, Jun 25, 2015 at 1:58 AM, Shunsuke Miyamoto <[hidden email]> wrote:

> I am trying to carry out a bit complicated time-lapse for a long period.
> eg) Record for 10 sec in 20ms interval, wait 50 sec. This sequence is
> reiterated in 6000 times. In this setting, I will film for 6000 min (=100
> hr= 5 days!). I have already bought a huge hard disk, but I can't make the
> time-lapse setting in micromanager.
>
> I have tried to set this sequence through "advanced of multi-dimension
> acquisition", the setting was very time-consuming.
>
>
> Does anyone know about a simple way for the setting using existing tabs in
> micromanager or any useful macro?

This kind of acquisition currently requires the use of a script. There
are two possible ways to do it: write a script that performs all the
steps, or write a script that start MDA every 60 seconds and use MDA
settings with timepoints only (500 frames and zero interval). If you
take the latter approach, you will get separate files for each
iteration (i.e. 6000 separate datasets), which is probably easier to
handle anyway.

Also, to get an exact 20 ms interval (if that is important for your
experiment), you will need to adjust your camera settings (exposure,
and any settings that affect the read out time). The interval setting
in the MDA window will not allow you to accurately record at
sub-second intervals, so you should set it to zero to enable fast
sequence acquisition (timed by the camera, rather than the computer).
I would recommend starting by making sure you can get a single
10-second sequence to run as desired.

Let us know if you'd like an example script to use at a starting point
- it should be pretty quick for us to write.

Best,
Mark

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Re: timelapse interval

hunwalla
In reply to this post by Shunsuke Miyamoto
Hi Mark,
I read your post. I am also trying to do something similar. I have to take time lapse videos. Essentially 2 sec recordings at 250 frames-per-second followed by a 30 second delay and then repeat. This is done for a total of 15 minutes. Can you suggest how I can go about it?
Thanks
Hoshang
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Re: timelapse interval

Shunsuke Miyamoto
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Re: timelapse interval

Chris Weisiger
Hi Shunsuke,

On Mon, Sep 28, 2015 at 2:53 AM, Shunsuke Miyamoto <[hidden email]> wrote:
Hi Mark

 I am sorry for delayed reply. I did not find your post, because I was not
familiar with this forum.

 I have developed a script for timelapse recording, but it does NOT work
properly. We made a script to
 1) take a series of snap with 50ms exposure,
 2) record a series of snaps for 10 second
 3) sleep 50 second

 As you point out, the current problem may be related to time interval. When
I start this script, unexpectedly, it took 500ms to take each snap. The
acutual time interval in time series of snaps was very strange; when I set 1
sec exposure in the script, the actual snap was taken with 2 sec sharp. When
I set 2 sec exposure, the actual snap was taken with 4 sec sharp.

The problem is not so much to do with your camera's readout time (though that is certainly one factor). It has more to do with the fact that "Snap" acquisitions are inherently slow, because they are done entirely in software. That is, the computer waits for some time, then sends a signal to the camera to expose; the camera exposes, then sends the image back to the computer. Every time the computer must take an action, there is a variable delay, because computers cannot guarantee that actions happen at a specific time.

If you want a consistent, high-speed time interval, then your best bet is to perform a "Sequence" acquisition, where the camera's onboard clock is responsible for all of the timing for each exposure, and it simply sends images to the computer as they are acquired. There is then of course some delay before the image is displayed and/or saved to disk, but while that delay is happening, the camera can be taking another image, so it does not really matter.

One way to do this is as Mark suggested in his earlier email: write a script that runs an MDA acquisition at periodic intervals. I've modified your script to do this. To use the script, simply set up the MDA dialog to do the 200-exposure series. Make certain that saving data is enabled in the MDA dialog. Depending on how large of a data acquisition you want to run, you may also want to toggle the "Hide MDA Display" option in the Options dialog under the Tools menu.

I hope this helps!

-Chris

 num2 = 2;
 exposure = 50; // ms
 mmc.setExposure(exposure);
 mmc.setConfig("20150925miyamoto","fastrecord") ;
 for (int j=0; j<num2; j++) {
   gui.runAcquisition();
 }


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Re: timelapse interval

Yukinobu
Dear all

I am a person who works with Shunsuke.

Owing to your valuable comments, we have overcome the problems and succeeded in recording timelapse with a certain interval.

Now we have a new problem.
The image windows that we captured in a recording before each interval remains on the desktop window. After a long time observation, too many windows suffer the memory of the computer.

We want to "Close" the window before the next timing of recording, but we can't find any command for that.

Does anyone know about a command to Close the windows in script.
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Re: timelapse interval

Philippe.POGNONEC
Hi person who works with Shunsuke,

Did you tick the "Save images" box in the "Multi-Dimensional
Acquisition" windows?

More here:
https://micro-manager.org/wiki/Micro-Manager_User's_Guide#Multi-dimensional_acquisition

Philippe


On 25/01/2016 04:05, Yukinobu wrote:

> Dear all
>
> I am a person who works with Shunsuke.
>
> Owing to your valuable comments, we have overcome the problems and succeeded
> in recording timelapse with a certain interval.
>
> Now we have a new problem.
> The image windows that we captured in a recording before each interval
> remains on the desktop window. After a long time observation, too many
> windows suffer the memory of the computer.
>
> We want to "Close" the window before the next timing of recording, but we
> can't find any command for that.
>
> Does anyone know about a command to Close the windows in script.
>
>
>
>
> --
> View this message in context: http://micro-manager.3463995.n2.nabble.com/timelapse-interval-tp7585561p7586563.html
> Sent from the Micro-Manager mailing list archive at Nabble.com.
>
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Re: timelapse interval

Yukinobu
This post was updated on .
Hi Philippe

We have ticked the box to direct the file to save, but no relation to Close the window.
Our program is as follows,
Record for 10 sec in 20ms interval, wait 50 sec. This sequence is reiterated in 6000 times.
Do you know how to close the window after each recording?

Best

Yuki, a person who work with Shunsuke
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Re: timelapse interval

JonD
Administrator
Check out this older thread: http://micro-manager.3463995.n2.nabble.com/How-to-close-the-acqusition-window-without-the-save-prompt-tt7584124.html.

I have had success doing something very similar to Chris' suggestion in that thread.  The variable "acqName" is the acquisition name used in a prior call to openAcquisition() in the ScriptInterface API.

gui.getAcquisition(acqName).promptToSave(false);
gui.closeAcquisitionWindow(acqName);

Jon

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Re: timelapse interval

Yukinobu
In reply to this post by Chris Weisiger
Hi Chris

Thanks for your code. It works.

Could you tell me one more thing: how to add a code for setting a save directory after
directory gui.runAcquisition()
?
I can set the save directrory in MDA but I now need to set it in in the Script Panel.

I look forward to hearing fromyou.

Best Yuki Arata
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