[OpenSPIM] OpenSPIM-related stuff

Fri Dec 20 03:32:17 CST 2013

Hey Veli-Pekka,

This sucks!! They have a good selection of wavelengths too... I wonder if
there is anything we can do.

Have a nice weekend and a Merry Christmas/Happy New Year!!

Best Regards!
Pete

-- 
Peter Gabriel Pitrone - TechRMS
Microscopy/Imaging Specialist
Prof. Dr. Pavel Tomancak group
Max Planck Institute for
Molecular Biology and Genetics
Pfotenhauerstr. 108
01307 Dresden

"If a straight line fit is required, obtain only two data points." - Anon.

On Fri, December 20, 2013 10:14 am, Veli-Pekka Ronkainen wrote:
<|> Hi all,
<|>
<|> FYI, I just got an email from Coherent: Unfortunately the Obis
cannot be
<|> controlled  with the MicroManager up to now. There are plans to make it
<|> work but this will be out at least 6 more months.
<|>
<|> Regards,
<|> Veli-Pekka
<|>
<|> From: openspim-bounces at openspim.org
<|> [mailto:openspim-bounces at openspim.org] On Behalf Of Veli-Pekka Ronkainen
<|> Sent: 13. joulukuuta 2013 11:30
<|> To: Michael Weber
<|> Cc: openspim at openspim.org
<|> Subject: Re: [OpenSPIM] OpenSPIM-related stuff
<|>
<|> Thanks Michael for the answers and ccing!
<|>
<|> Our initial plan is to build up a SPIM with a dual side simultaneous
<|> excitation by one laser wavelength at the time, and image colors
<|> sequentially. Laser (either 488nm or 561nm) is divided into two
identical
<|> illumination pathways to reduce shading and the need of rotation. So at
<|> least in the first version we have to replace the laser head between the
<|> channels. Maybe later well try to modify it so that we could use two
<|> lasers installed at the same time and control the excitation wavelength
<|> with µManager, if that appears to be possible. Do you think it is
<|> generally worth building a two sided illumination set-up compared to
<|> single sided illumination, or can we assume some unexpected problems
<|> arising from reflections or difficulties in aligning overlapping
<|> lightsheets etc.?
<|>
<|> So anyone please, do you have any further information about controlling
<|> Coherent OBIS lasers with OpenSpim µManager? I havent got any answers
<|> from Coherent. Would you like to share your experiences with sCMOS
<|> cameras as well?
<|>
<|> Regards,
<|> Veli-Pekka Ronkainen
<|> Biocenter Oulu, University of Oulu
<|> Finland
<|>
<|> From: Michael Weber [mailto:weber at mpi-cbg.de]
<|> Sent: 12. joulukuuta 2013 11:49
<|> To: Veli-Pekka Ronkainen
<|> Cc: openspim at openspim.org<mailto:openspim at openspim.org>
<|> Subject: Re: OpenSPIM-related stuff
<|>
<|> Dear Veli-Pekka,
<|>
<|> it was my pleasure to give the lecture in Oulu and I enjoyed my time in
<|> Finland! It's great to hear that you are moving into the SPIM field as
<|> well and I am happy to answer part of your questions. However, when it
<|> comes to software integration, I rather leave that to the guys on the
<|> mailing list, which is why I also put them on CC.
<|>
<|> So if I get it right you want to build a two-color setup with
<|> double-sided illumination? Do you want to detect both colors
<|> simultaneously or sequentially? And how do you plan to use the
<|> double-sided illumination, also simultaneously or sequentially?
<|>
<|> Using a camera with a bigger sensor like sCMOS is possible and should
not
<|> be limited by the microscope objective or the emission filter, so no
<|> optical redesign is necessary here. However, additional components could
<|> be problematic and block light from reaching the edges of your chip.
<|> Those components are namely camera adapters with additional
<|> (de)magnification or image splitter. On the other hand, an image
splitter
<|> is a neat way to capture two colors simultaneously, especially on a big
<|> camera chip which has plenty of pixels to share. Some companies are now
<|> also modifying their splitters for sCMOS chips.
<|> Compared to a camera with a smaller chip, you lower your effective
<|> magnification (or in other words, you increase your field of view) if
you
<|> use the entire chip of an sCMOS camera. If there are components which
<|> limit the field of view (adapters, splitters), you end up with smaller
<|> useable area. But maybe that does not matter and you simply crop to the
<|> center of the chip, which would also increase your maximum frame
rate. It
<|> really depends on what you want to image and which spatial and temporal
<|> resolution you wish to get.
<|>
<|> Regarding the integration of camera and laser into the software, as I
<|> said, I am not up to date. But probably someone else from the mailing
<|> list can help here?!
<|>
<|> Best regards,
<|> Michael
<|>
<|>
<|> On Dec 12, 2013, at 10:05 AM, Veli-Pekka Ronkainen
<|> <veli-pekka.ronkainen at oulu.fi<mailto:veli-pekka.ronkainen at oulu.fi>>
<|> wrote:
<|>
<|> Hi Michael!
<|>
<|> I still want to thank you for your visit here in Oulu in June. Your
<|> lecture was confirming our researchers that we need SPIM here as well,
<|> and happily we just got nice funding for the build-up costs of OpenSPIM!
<|>
<|> We are planning the set-up now, and it wed like to have some laser and
<|> camera modifications to the dual side illumination version of OpenSPIM.
<|> Our plan is mainly clear with a few unsolved issues and Id
appreciate if
<|> you had time to answer couple of my questions? Ive browsed through the
<|> mailing list archives (and µManager discussions too), but have not find
<|> clear answers yet. So wed like to use Coherent OBIS-series lasers
<|> instead of CUBE (to get the 561 nm laser as well), and in one mailing
<|> list thread you and Peter Pitrone discussed that OBIS and other series
<|> have been used successfully in OpenSPIM. µManager has drivers for CUBE,
<|> but not a clear support for OBIS, so do you know how replacing the
lasers
<|> should work? Another question is related on the camera. Wed like to use
<|> Orca-Flash 4 (or Andor Zyla 5.5) camera and we are mainly aware of the
<|> camera-drivers-computer related things, but do you know how people have
<|> fitted this larger sensor type camera to the detection pathway? Do we
<|> need some optical redesign to fill the whole sensor area, or is that
<|> smaller sensor size Orca-ER just cropping the signal and the original
<|> pathway design would fill the larger chip as well? Of course I could
<|> reform and write these questions to the mailing list if you prefer?
<|>
<|> Best Regards,
<|> Veli-Pekka
<|>
<|> _____________
<|>
<|> Michael Weber
<|> PhD Student, Huisken lab
<|> Max Planck Institute of Molecular Cell Biology and Genetics
<|> Pfotenhauerstrasse 108, 01307 Dresden
<|> Tel. 0049 351/2102837
<|>
<|> http://www.mpi-cbg.de/huisken
<|>
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