*****
To join or leave the confocal microscopy listserv or to change your email address, go to:
https://lists.umn.edu/cgi-bin/wa?SUBED1=confocalmicroscopy&A=1
Post images on http://www.imgur.com and include the link in your posting.
*****

Dear Radek,

I've carefully considered the issue you've described, and it indeed strikes me as peculiar. 
Throughout the evolution of the LZ1 machine and software, swift single-plane acquisition has consistently been feasible. 
With sCMOS cameras, in particular, achieving speeds of up to 15 fps for full chip and 33-35 fps when cropping to 800x800 dexels has been routine. 

The "as fast as possible" option, though seemingly advantageous, may actually be exacerbating the problem in your specific setup. 
I suggest disabling this option to see if it alleviates the issue. If not, consider expediting the dual-side fusion during post-processing. 
Although pivoting incurs a slight time overhead, given your relatively long exposure time, its impact should be negligible.

In any case, I recommend consulting with your local service engineer to assess the system's efficiency.
 
I hope this helps.

Best,

D.
--
Davide Accardi, PhD.
Champalimaud ABBE Platform
Advanced BioImaging and BioOptics Experimental Platform
Scientific and Managing Leader

Champalimaud Centre for the Unknown
Av. Brasilia, Doca de Pedroucos
1400-038 Lisbon, Portugal
T (+351) 210 480 139

www.fchampalimaud.org
[log in to unmask]



> On 16 Feb 2024, at 09:35, Radek Machan (Dr) <[log in to unmask]> wrote:
> 
> *****
> To join or leave the confocal microscopy listserv or to change your email address, go to:
> https://lists.umn.edu/cgi-bin/wa?SUBED1=confocalmicroscopy&A=1
> Post images on http://www.imgur.com and include the link in your posting.
> *****
> 
> Hi Kimmo,
> 
> Thanks for the suggestions. I've checked all the file-saving and streaming settings - that didn't seem to be the problem. I've looked at your Z-stack idea and indeed by replacing time points with slices I can accelerate the acquisition, the limitation is that the minimal spacing of slices that I can set in ZEN is 0.65um, so I can't do enough slices without running out of focus.
> 
> A few people reported they can get much higher frame rates at Z1 lightsheet without employing any special tricks. I don't know if it could be a matter of software version or hardware configuration. Or if it is a matter of some settings, it must some well hidden settings as I've tested all I could find and followed all the suggestions I've received without getting past the 800 ms/frame.
> 
> If anybody has any more suggestions, I'm still looking for a solution.
> 
> Best wishes,
> Radek
> 
> Radek MACHAN, Ph.D. | Senior Research Fellow
> NOBIC<https://imsva91-ctp.trendmicro.com/wis/clicktime/v1/query?url=https%3a%2f%2fwww.nobic.sg%2fFacilities.html&umid=5908DDF6-D932-C505-99E6-6F45C828DC29&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-219949b1ff29e0988e9bb1e4be7da3af80bd8ace> Imaging Facilities<https://imsva91-ctp.trendmicro.com/wis/clicktime/v1/query?url=https%3a%2f%2fwww.nobic.sg%2fFacilities.html&umid=5908DDF6-D932-C505-99E6-6F45C828DC29&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-219949b1ff29e0988e9bb1e4be7da3af80bd8ace> Manager
> www.nobic.sg<https://imsva91-ctp.trendmicro.com/wis/clicktime/v1/query?url=http%3a%2f%2fwww.nobic.sg&umid=5908DDF6-D932-C505-99E6-6F45C828DC29&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-15d93b3a000587a7445a2cc38707575b5cb3407a> | [log in to unmask]
> 
> SCELSE, Nanyang Technological University
> #B2, 60 Nanyang Drive, SBS-01N-27
> Singapore 637551
> ________________________________
> From: Confocal Microscopy List <[log in to unmask]> on behalf of Tanhuanpää, Kimmo K <[log in to unmask]>
> Sent: Tuesday, February 13, 2024 15:02
> To: [log in to unmask] <[log in to unmask]>
> Subject: VS: Time/frame in lightsheet Z1
> 
> [Alert: Non-NTU Email] Be cautious before clicking any link or attachment.
> *****
> To join or leave the confocal microscopy listserv or to change your email address, go to:
> https://lists.umn.edu/cgi-bin/wa?SUBED1=confocalmicroscopy&A=1
> Post images on http://www.imgur.com and include the link in your posting.
> *****
> 
> Hi Radek,
> My first guess is that you are saving each timepoint to a separate file and initializing file writing causes the overhead. Is there a tick mark on separate files tab - time? If yes, remove it. If that does not help, try imaging in xyz mode infinitely thin stack with as many z-levels as you want to have timepoints.
> Best,
> Kimmo
> 
> 
> _________________________________________________
> 
>                               Mr. Kimmo Tanhuanpää
> 
>            Docent (Biological Microscopy), PhD (Biochemistry)
> 
>                       Head of Light Microscopy Unit
> 
>               Institute of Biotechnology, University of Helsinki
> 
> https://www.helsinki.fi/en/infrastructures/bioimaging/light-microscopy-unit
> 
>       office +358 50 4484 000 [log in to unmask]
> 
> 
> 
> ________________________________
> Lähettäjä: Confocal Microscopy List <[log in to unmask]> käyttäjän Radek Machan (Dr) <[log in to unmask]> puolesta
> Lähetetty: tiistai 13. helmikuuta 2024 7.25
> Vastaanottaja: [log in to unmask] <[log in to unmask]>
> Aihe: Time/frame in lightsheet Z1
> 
> *****
> To join or leave the confocal microscopy listserv or to change your email address, go to:
> https://lists.umn.edu/cgi-bin/wa?SUBED1=confocalmicroscopy&A=1
> Post images on http://www.imgur.com and include the link in your posting.
> *****
> 
> Dear Colleagues,
> 
> a user of our Z1 lightsheet wanted to do a fast (10 fps at least) time-lapse at a single plain, single channel. I thought it would be no problem as with a widefield, until we tested it. When we selected the "as fast as possible" option in time series settings and measured the speed, the time/frame was about 800 ms, despite the exposure time being only 50 ms. I found this very surprising as in my experience the lightsheet is very fast in acquiring large stacks, which is only possible if the time/slice is not excessively long. I probed this a little further. For stacks of 2 slices, the time/stack was about 1.2 s (hence about 600 ms/individual image), for stacks of 3 slices it was about 1.5 s (about 500 ms/individual image) and eventually for large stacks the time/individual image approaches quite close to the limit of the exposure time. It seems therefore that the overhead doesn't apply to individual images, but to whole time points in a time series. Does anyone know what is the reason for the rather large overhead? Or even better, does anyone know of a way around it that would allow to acquire a fast time series?
> 
> Thank you,
> Best wishes,
> Radek
> 
> Radek MACHAN, Ph.D. | Senior Research Fellow
> NOBIC<https://imsva91-ctp.trendmicro.com/wis/clicktime/v1/query?url=https%3a%2f%2fwww.nobic.sg%2fFacilities.html&umid=5908DDF6-D932-C505-99E6-6F45C828DC29&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-219949b1ff29e0988e9bb1e4be7da3af80bd8ace> Imaging Facilities<https://imsva91-ctp.trendmicro.com/wis/clicktime/v1/query?url=https%3a%2f%2fwww.nobic.sg%2fFacilities.html&umid=5908DDF6-D932-C505-99E6-6F45C828DC29&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-219949b1ff29e0988e9bb1e4be7da3af80bd8ace> Manager
> www.nobic.sg<https://imsva91-ctp.trendmicro.com/wis/clicktime/v1/query?url=http%3a%2f%2fwww.nobic.sg&umid=5908DDF6-D932-C505-99E6-6F45C828DC29&auth=6e3fe59570831a389716849e93b5d483c90c3fe4-15d93b3a000587a7445a2cc38707575b5cb3407a> | [log in to unmask]
> 
> SCELSE, Nanyang Technological University
> #B2, 60 Nanyang Drive, SBS-01N-27
> Singapore 637551
> ________________________________
> 
> CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete it, notify us and do not copy, use, or disclose its contents.
> Towards a sustainable earth: Print only when necessary. Thank you.