[OpenSPIM] aquisition speed

[Fredrik Ek]

Thanks for your reply suggestions Tim. We are performing volume scans so I refer to fps as each xy-projection and in our case we have 10 of those in each volume. We are running with camera link option for theoretical 100 fps.

Best Regards

Fredrik

Från: Feinstein, Timothy N [mailto:tnf8 at pitt.edu]
Skickat: den 7 oktober 2015 17:17
Till: Fredrik Ek; openspim at openspim.org
Ämne: Re: [OpenSPIM] aquisition speed

Hi Fredrik,

Are you imaging volumes or a fixed 2D plane?  If imaging a volume then I would be impressed with 3 FPS.  If you want to visualize a fixed plane, acquisition speed is simply the frame rate of your camera.  To optimize speed you should look into buying a CameraLink adapter card rather than using USB (does your computer have a USB 3.0 port and cable?).  You can speed it up right now by only using a sub-region of the sensor chip.  Click the 'ROI' button in uManager while viewing live and the camera will image a smaller area twice as fast.  Click the button without live view and it will give you an adjustable rectangle to choose how much of the sensor you want to use.  Only the number of vertical lines determine acquisition speed so the cropped area can be as wide as you want.

With a Flash 4.0 v2, CameraLink and ROI enabled we image a beating zebrafish larva heart at about 400 fps.  Naturally you need an acquisition time of 2 ms or so to do that, meaning more laser power.

Forgive me if you have tried all this already.

All the best,


Tim

Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology


From: <openspim-bounces at openspim.org<mailto:openspim-bounces at openspim.org>> on behalf of Fredrik Ek <fredrik.ek at med.lu.se<mailto:fredrik.ek at med.lu.se>>
Date: Wednesday, October 7, 2015 at 10:50 AM
To: "openspim at openspim.org<mailto:openspim at openspim.org>" <openspim at openspim.org<mailto:openspim at openspim.org>>
Subject: [OpenSPIM] aquisition speed

Hi all,

We have started to use the SPIM system for calcium imaging and thus would like increase acquisition speed. What frame rates can be achieved with the OpenSPIM setup? What are the major limitations, considering software (micromanager) versus hardware (stage). I have noticed that the speed is ok in the beginning of a time laps exp but reduces over time (7-10 fps down to 3 fps). The system is has an Flash 4 so far from theoretical camera frame rates. I have a good workstation with +100 gb physical memory. I have increased the buffer memory in micromanager to 20 Gb (even tested with 50 Gb but no additional effect), writing data to a virtual harddrive generated in the physical memory, deselected xy and twister during acquisitions (noticed some effects) and uses short exposure times. Any other tips how to improve the speed.

Thanks again for a great project!

BR

Fredrik

Fredrik Ek, PhD,
Researcher, Chemical Biology & Therapeutics
Department of Experimental Medical Science
Lund University, BMC D10
S-221 84 Lund, SWEDEN
------------------------
Fredrik.Ek at med.lu.se<mailto:Fredrik.Ek at med.lu.se>
Phone: +46-727 17 22 05

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