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<p class="MsoNormal"><span style="color:#1F497D">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Best Regards<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Fredrik<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="SV" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Från:</span></b><span lang="SV" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Feinstein, Timothy N [mailto:tnf8@pitt.edu]
<br>
<b>Skickat:</b> den 7 oktober 2015 17:17<br>
<b>Till:</b> Fredrik Ek; openspim@openspim.org<br>
<b>Ämne:</b> Re: [OpenSPIM] aquisition speed<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Hi Fredrik, <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">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. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">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.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Forgive me if you have tried all this already. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">All the best, <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Tim<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Timothy Feinstein, Ph.D. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">Research Scientist<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black">University of Pittsburgh Department of Developmental Biology<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black"><<a href="mailto:openspim-bounces@openspim.org">openspim-bounces@openspim.org</a>> on behalf of Fredrik Ek <<a href="mailto:fredrik.ek@med.lu.se">fredrik.ek@med.lu.se</a>><br>
<b>Date: </b>Wednesday, October 7, 2015 at 10:50 AM<br>
<b>To: </b>"<a href="mailto:openspim@openspim.org">openspim@openspim.org</a>" <<a href="mailto:openspim@openspim.org">openspim@openspim.org</a>><br>
<b>Subject: </b>[OpenSPIM] aquisition speed<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">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.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Thanks again for a great project!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">BR<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black">Fredrik <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Fredrik Ek, PhD,
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Researcher, Chemical Biology & Therapeutics
</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Department of Experimental Medical Science
</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Lund University, BMC D10
</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">S-221 84 Lund, SWEDEN
</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">------------------------
</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
</span><span lang="SV" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><a href="mailto:Fredrik.Ek@med.lu.se"><span lang="EN-US" style="font-family:"Arial","sans-serif"">Fredrik.Ek@med.lu.se</span></a></span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><br>
</span><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Phone: +46-727 17 22 05
</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:black"> <o:p></o:p></span></p>
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