routine QC of SIM microscopes - protocol?

[Cromey, Douglas W - (dcromey)]

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People who have SIM microscopes. Is there a set of quality control tests that you perform on your instrument on a regular basis (weekly/monthly) to ensure that things are working as expected? I've been tasked to come up with a regular testing protocol, and I would love to hear what others are doing.

I know there are some published QC articles, I have a stack about an inch thick to read.
Doug

------------------------------------------------------------------------------------------
Douglas W. Cromey, M.S. - Associate Scientific Investigator
Dept. of Cellular & Molecular Medicine, University of Arizona
1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA

office:  LSN 463              email: [hidden email]<mailto:[hidden email]>
voice:  520-626-2824       fax:  [phone]

http://microscopy.arizona.edu/learn/microscopy-imaging-resources-www
Home of: "Microscopy and Imaging Resources on the WWW"

UA Microscopy Alliance -  http://microscopy.arizona.edu<http://microscopy.arizona.edu/>

[Graham Wright-2]

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Hi Doug,

The SIMcheck paper and the follow-up with practical guidelines (cited and
linked below) provide an excellent starting point. It may be that it's not
possible to do all the test, but taking a selection can provide great
insight on the instruments performance.

Ball G, Demmerle J, Kaufmann R, Davis I, Dobbie IM, Schermelleh L.
SIMcheck: a
Toolbox for Successful Super-resolution Structured Illumination Microscopy.
Sci
Rep. 2015 Nov 3;5:15915. doi: 10.1038/srep15915. Erratum in: Sci Rep.
2016;6:20754
https://www.nature.com/articles/srep15915

Demmerle J, Innocent C, North AJ, Ball G, Müller M, Miron E, Matsuda A,
Dobbie
IM, Markaki Y, Schermelleh L. Strategic and practical guidelines for
successful
structured illumination microscopy. Nat Protoc. 2017 May;12(5):988-1010.
doi:
10.1038/nprot.2017.019
https://www.nature.com/articles/nprot.2017.019

Regards,
Graham

---
Graham Wright, PhD
Director, Microscopy Platform
A*STAR, Singapore


On 3 July 2018 at 00:05, Cromey, Douglas W - (dcromey) <
[hidden email]> wrote:
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> People who have SIM microscopes. Is there a set of quality control tests
that you perform on your instrument on a regular basis (weekly/monthly) to
ensure that things are working as expected? I've been tasked to come up
with a regular testing protocol, and I would love to hear what others are
doing.
>
> I know there are some published QC articles, I have a stack about an inch
thick to read.
> Doug
>
>
------------------------------------------------------------------------------------------
> Douglas W. Cromey, M.S. - Associate Scientific Investigator
> Dept. of Cellular & Molecular Medicine, University of Arizona
> 1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA
>
> office:  LSN 463              email: [hidden email]<mailto:
[hidden email]>
> voice:  520-626-2824       fax:  [phone]
>
> http://microscopy.arizona.edu/learn/microscopy-imaging-resources-www
> Home of: "Microscopy and Imaging Resources on the WWW"
>
> UA Microscopy Alliance -  http://microscopy.arizona.edu<
http://microscopy.arizona.edu/>

[Justin Demmerle]

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Hi Doug, thanks for asking.

And thanks, Graham, for highlighting our work.

As usual, it depends on what type of QC you want to do. There's not really
a canonical hard-and-fast protocol for SIM system maintenance because your
milage will vary by instrument / manufacturer / usage / facility, etc.
Other list members could perhaps provide more detailed instructions but
here's a short overview of some key calibration materials you can use.

I would separate this into 5 types of "reference" slide for SIM calibration
& maintenance:

1) A grid or solid fluorescent slide for laser/optical calibration - See
commercial offerings or a recent demonstration of custom-made slides
https://arxiv.org/abs/1806.05457v1

2) Bead slides for PSFs -  see the 2017 NatProt article mentioned by Graham

3) Bead lawn slides for SIM parameters - as above

4) multi-channel calibration slide for image registration. The optimal one
depends on what registration method you use, of which there are many
flavors with many trade-offs. See Kraus et al. 2017 Nat Prot
https://www.nature.com/articles/nprot.2017.020 or Matsuda et al. 2018
SciRep https://www.nature.com/articles/s41598-018-25922-7 , for some
suggestions.

5) Stereotypical cell/representative sample for your most common type of
experiment (medium/temp/modality/etc). For example, a DAPI/green/red
labelled cell with tubulin and actin, from which you can take FWHM
measurements and provides a nice training sample, or some other
stable/bright high-quality sample for demos and example images.

Of note, creating specific OTFs and testing bead lawns with SIMcheck (Ball
et al 2015) is important for optimal SIM performance. The frequency of
these various checks ranges from every session (i.e. image registration, if
you have multiple cameras), to infrequently in the case of optical
calibration, to whenever something seems off (i.e. bead lawns and typical
example slides). Making the PSF and bead lawn slides is particular to SIM
systems, and there are detailed instructions for preparing them in the
Protocols papers, so see those for more info, and feel free to contact us
off-thread.

Best,
Justin Demmerle
NIH-Oxford Scholar
Schermelleh Lab - University of Oxford / Biochemistry
Macfarlan Lab - NIH / NICHD
[hidden email]
<https://owa.nexus.ox.ac.uk/ecp/Customize/justin.demmerle@...>


On Wed, Jul 4, 2018 at 1:00 AM, CONFOCALMICROSCOPY automatic digest system <
[hidden email]> wrote:

> There are 6 messages totaling 456 lines in this issue.
>
> Topics of the day:
>
>   1. routine QC of SIM microscopes - protocol?
>   2. Release of Bio-Formats 5.9.0
>   3. LysoSensor and LysoTracker
>   4. LysoSensor and LysoTracker **Vendor reply**
>   5. Point Source/ Qioptic / Excelitas iFlex Viper 5 Line Laser System -
>      Control with Micromanager.
>   6. Point Source/ Qioptic / Excelitas iFlex Viper 5 Line Laser System -
>      Control with Micromanager
>
> ----------------------------------------------------------------------
>
> Date:    Tue, 3 Jul 2018 10:42:20 +0200
> From:    Graham Wright <[hidden email]>
> Subject: Re: routine QC of SIM microscopes - protocol?
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi Doug,
>
> The SIMcheck paper and the follow-up with practical guidelines (cited and
> linked below) provide an excellent starting point. It may be that it's not
> possible to do all the test, but taking a selection can provide great
> insight on the instruments performance.
>
> Ball G, Demmerle J, Kaufmann R, Davis I, Dobbie IM, Schermelleh L.
> SIMcheck: a
> Toolbox for Successful Super-resolution Structured Illumination Microscopy.
> Sci
> Rep. 2015 Nov 3;5:15915. doi: 10.1038/srep15915. Erratum in: Sci Rep.
> 2016;6:20754
> https://www.nature.com/articles/srep15915
>
> Demmerle J, Innocent C, North AJ, Ball G, Müller M, Miron E, Matsuda A,
> Dobbie
> IM, Markaki Y, Schermelleh L. Strategic and practical guidelines for
> successful
> structured illumination microscopy. Nat Protoc. 2017 May;12(5):988-1010.
> doi:
> 10.1038/nprot.2017.019
> https://www.nature.com/articles/nprot.2017.019
>
> Regards,
> Graham
>
> ---
> Graham Wright, PhD
> Director, Microscopy Platform
> A*STAR, Singapore
>
>
> On 3 July 2018 at 00:05, Cromey, Douglas W - (dcromey) <
> [hidden email]> wrote:
> >
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > Post images on http://www.imgur.com and include the link in your
> posting.
> > *****
> >
> > People who have SIM microscopes. Is there a set of quality control tests
> that you perform on your instrument on a regular basis (weekly/monthly) to
> ensure that things are working as expected? I've been tasked to come up
> with a regular testing protocol, and I would love to hear what others are
> doing.
> >
> > I know there are some published QC articles, I have a stack about an inch
> thick to read.
> > Doug
> >
> >
> ------------------------------------------------------------
> ------------------------------
> > Douglas W. Cromey, M.S. - Associate Scientific Investigator
> > Dept. of Cellular & Molecular Medicine, University of Arizona
> > 1501 N. Campbell Ave, Tucson, AZ  85724-5044 USA
> >
> > office:  LSN 463              email: [hidden email]<mailto:
> [hidden email]>
> > voice:  520-626-2824       fax:  [phone]
> >
> > http://microscopy.arizona.edu/learn/microscopy-imaging-resources-www
> > Home of: "Microscopy and Imaging Resources on the WWW"
> >
> > UA Microscopy Alliance -  http://microscopy.arizona.edu<
> http://microscopy.arizona.edu/>
>
> ------------------------------
>
> Date:    Tue, 3 Jul 2018 15:19:11 +0000
> From:    "David Gault (Staff)" <[hidden email]>
> Subject: Release of Bio-Formats 5.9.0
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear all,
>
> Today we are releasing Bio-Formats 5.9.0 which included the following
> changes:
>
> File format fixes and improvements:
>
>   *   MetaMorph
>      *   fixed a NullPointerException when a stage label in not present
>      *   ensured that reported domain is now consistent with the existence
> of a Plate in OME-XML
>      *   fixed Metamorph RGB series channel count (thanks to Jeremy
> Muhlich)
>   *   Leica LIF
>      *   improved handling of dimension order for non-RGB channels
>   *   Imspector OBF
>      *   added support for FLIM datasets
>   *   Inveon
>      *   updated to attempt to locate renamed data files
>   *   Volocity
>      *   expanded image names to include the stack parent names
>   *   Olympus OIR
>      *   added a fix for slow tag reading and a potential infinite loop
>   *   TIFF
>      *   added support in TiffWriter for the writing of DEFLATE (zlib)
> compression
>      *   deprecated getIFDs()  in TiffParser and added getMainIFDs() and
> getSubIFDs()
>   *   Zeiss CZI
>      *   fixed an issue with big images when tiling is present but a
> pyramid is not
>   *   Nikon NIS-Elements ND2
>      *   prevented integer overflow exception when reading a tile from a
> large image
>   *   Amersham Biosciences Gel
>      *   prevented overflow issue when reading unsigned integer values
>   *   Cellomics
>      *   fixed indexing when the field counts are variable
>   *   Trestle
>      *   updated to ensure consistent ordering of used files
>
> Bug fixes and improvements:
>
>   *   enabled building and testing with Java 9 and 10
>   *   added CI testing with Java 10 on AppVeyor and Travis
>   *   removed Java 7 from Appveyor matrix
>   *   updated a number of Maven plugins to current versions
>   *   corrected warnings in Maven configuration in sub-components
>   *   added a warning to clarify the behavior when passing metadata with
> dimensionOrder in bfsave as part of the Bio-Formats MATLAB toolbox (thanks
> to Jonathan Armond)
>   *   improved robustness in the detection of patterns as part of the file
> stitching
>   *   fixed a bug relating to dimension order in the Bio-Formats plugins
> Exporter
>   *   fixed download URLs in Bio-Formats command-line tools
>   *   updated use of 'static final' to match Oracle's recommendations and
> convention
>   *   disabled upgrade checker when running unit tests
>   *   added support to data repo test suite for unconfigured tests
>
> Documentation improvements:
>
>   *
>   *   fixed unstable links flagged by automated link checking
>   *   begun adding testing for breakages to memo files
>   *   clarified ordering expectation in getUsedFiles Javadocs
>   *   added documentation for dimensionOrder in bfsave with the MATLAB
> toolbox<https://docs.openmicroscopy.org/bio-formats/5.9.0/developers/
> matlab-dev.html>
>   *   fixed broken links in previous release notes
>   *   expanded documentation for command-line tools to cover undocumented
> options<https://docs.openmicroscopy.org/bio-formats/5.9.0/users/
> comlinetools/display.html> and environment variables<https://docs.
> openmicroscopy.org/bio-formats/5.9.0/users/comlinetools/index.html>
>   *   added a new license/copyright section to the About Bio-Formats<
> https://docs.openmicroscopy.org/bio-formats/5.9.0/about/index.html> page
>   *   updated the public format page for the Vectra QPTIFF format
>
>
> Full details can be found at https://docs.openmicroscopy.
> org/bio-formats/5.9.0/about/whats-new.html
>
> The software is available at:
> https://www.openmicroscopy.org/bio-formats/downloads/
> and will shortly be available from the Java-8 update site for Fiji users.
>
> Any problems or comments, please use the OME Forums or mailing lists:
>
> http://www.openmicroscopy.org/support
>
>
> Regards,
>
> The OME Team
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> ------------------------------
>
> Date:    Tue, 3 Jul 2018 11:27:53 -0400
> From:    Feriel P <[hidden email]>
> Subject: LysoSensor and LysoTracker
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hello everyone,
>
> I am looking for papers that have evaluated the degree of toxicity of
> LysoSensor and LysoTracker Probes. I was unable to find details on the
> product pages or the references they mention. I have not yet used these
> probes, but I am aware that the mechanism of action is that they work by
> being protonated and retained in lysosomes. I have been told that these
> probes can exhibit an alkalinizing effect on the lysosomes, such that
> longer incubations increase pH and lower total lysosomal capacity.
>
> Does anyone have references they have turned to in the past that elucidate
> the mechanism of LysoSensor and LysoTracker Probes and the toxic effects of
> prolonged use in live cell imaging? I'd be very grateful if you could
> direct me to author(s) or papers that have studied this.
>
> Many thanks,
> -Feriel
> --
>
> ------------------------------
>
> Date:    Tue, 3 Jul 2018 21:16:22 +0000
> From:    "Kilgore, Jason A." <[hidden email]>
> Subject: Re: LysoSensor and LysoTracker **Vendor reply**
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
>
> ** Vendor reply **
>
> Hi, Feriel,
>
> It's an important question.
>
> I've used the LysoTracker dyes many times and haven't seen any signs of
> cellular toxicity in the timeframes of my imaging experiments, though I
> don't think I've ever imaged beyond about an hour or so.
>
> I don't have references to the effect, but our internal researchers (Nick
> Dolman and Yu-Zhong Zhang, who originally helped develop these dyes) looked
> at this question and performed some controlled experimentation.  I've cc'd
> them with their approval.
>
> Here's how they responded:
>
> Low dose they aren't toxic, and they aren’t retained well for the time
> periods that would cause toxicity. Though all organic dyes can perturb in
> some manner if you incubate for long periods or high concentrations, or
> over-expression (in the case of fluorescent proteins). Using the
> LysoTrackers as they are intended doesn’t give conditions that are
> generally toxic. As always the researcher should control for any
> experimental manipulation, including label.
>
> Please let us know if you need further information.
>
> Jason
>
> Jason A. Kilgore
> Technical Application Scientist
> Molecular Probes / EVOS Tech Support
> Thermo Fisher Scientific
>
> 1-800-955-6288 then option 4, then option 3, then option 2.
> Or dial direct at [phone]
> [hidden email]
>
> This communication is intended solely for the individual/entity to whom it
> is addressed. It may contain confidential or legally privileged
> information.  Any unauthorized disclosure or copying is prohibited and may
> be unlawful. If you have received this communication in error, please
> notify the sender immediately and delete it from your system.
>
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Feriel P
> Sent: Tuesday, July 03, 2018 8:28 AM
> To: [hidden email]
> Subject: LysoSensor and LysoTracker
>
> CAUTION: This email originated from outside of the organization. Do not
> click links or open attachments unless you recognize the sender and know
> the content is safe.
>
>
> *****
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> pyTrvhv4oPCz8qS2E3La70fbz2jJXQscXx3ME2UGM8w&e= and include the link in
> your posting.
> *****
>
> Hello everyone,
>
> I am looking for papers that have evaluated the degree of toxicity of
> LysoSensor and LysoTracker Probes. I was unable to find details on the
> product pages or the references they mention. I have not yet used these
> probes, but I am aware that the mechanism of action is that they work by
> being protonated and retained in lysosomes. I have been told that these
> probes can exhibit an alkalinizing effect on the lysosomes, such that
> longer incubations increase pH and lower total lysosomal capacity.
>
> Does anyone have references they have turned to in the past that elucidate
> the mechanism of LysoSensor and LysoTracker Probes and the toxic effects of
> prolonged use in live cell imaging? I'd be very grateful if you could
> direct me to author(s) or papers that have studied this.
>
> Many thanks,
> -Feriel
> --
>
> ------------------------------
>
> Date:    Tue, 3 Jul 2018 16:56:16 -0500
> From:    Brandon Lee <[hidden email]>
> Subject: Point Source/ Qioptic / Excelitas iFlex Viper 5 Line Laser System
> - Control with Micromanager.
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi everyone,
>
> We acquired a Point Source iFlex Viper 5 Line Laser System.  Here are some
> pictures:
>
> https://imgur.com/a/jXnnD9f
>
> We do not have the USB controller for it.  We are trying to see if we can
> get it somehow from Qioptic/Excelitas.
>
> In the meantime though, we were trying to figure out how to control the
> laser with Micromanager via the AUX1 input.
>
> Here is a PDF instruction set for the iFlex Viper System:
>
> <a href="https://www.dropbox.com/s/464m4fvssl7qbeh/PSB1042%">https://www.dropbox.com/s/464m4fvssl7qbeh/PSB1042%
> 20iFLEX%20Viper%20Five-Line%20Laser%20Engine.pdf?dl=0
>
> Also, here is a PDF instruction set for the iFlex Viper System's USB
> Controller (we do not have this):
>
> <a href="https://www.dropbox.com/s/nryzwtqazf50kli/PSB1068%20iFLEX-Viper%20USB%">https://www.dropbox.com/s/nryzwtqazf50kli/PSB1068%20iFLEX-Viper%20USB%
> 20Controller%20Software%20Installation%20and%20Operating%20I....pdf?dl=0
>
> According to this USB controller PDF instruction, this USB controller uses
> a Velleman K8061 DAQ, which MicroManager seems to have support for (written
> by Austin Blanco):
>
> https://micro-manager.org/wiki/Velleman_K8061
>
> However, what is strange is that MicroManager also has support for the
> iFlex Viper System separately (written by Tom Porter of Excelitas/QiOptic):
>
> https://micro-manager.org/wiki/USB_Viper_QPL
>
> And it seems like this version of the Viper uses the Measurement Computing
> USB-3101 DAQ.
>
> We also found this:
>
> https://valelab4.ucsf.edu/svn/micromanager2/trunk/
> DeviceAdapters/USB_Viper_QPL/
>
> If we had to take a guess, it seems as though the Viper system has an
> updated USB controller with the USB-3103 DAQ.  We were wondering though:
>
> 1.) If anyone has successfully controlled the iFlex Viper System with
> Micromanager
>
> 2.) If so, which USB controller they had
>
> If we can't obtain the USB controller, we will try to make a custom set up
> for the iFlex Viper System using a DAQ, as the pin outs for the AUX 1 input
> (see PDF instruction for the IFlex Viper System with the pin out diagram)
> seem to be fairly straightforward.
>
> Any and all input would be immensely appreciated.
>
> Thank you all so much.
>
> ------------------------------
>
> Date:    Tue, 3 Jul 2018 16:59:13 -0500
> From:    Brandon Lee <[hidden email]>
> Subject: Point Source/ Qioptic / Excelitas iFlex Viper 5 Line Laser System
> - Control with Micromanager
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Hi everyone,
>
> We acquired a Point Source iFlex Viper 5 Line Laser System.  Here are some
> pictures:
>
> https://imgur.com/a/jXnnD9f
>
> We do not have the USB controller for it.  We are trying to see if we can
> get it somehow from Qioptic/Excelitas.
>
> In the meantime though, we were trying to figure out how to control the
> laser with Micromanager via the AUX1 input.
>
> Here is a PDF instruction set for the iFlex Viper System:
>
> <a href="https://www.dropbox.com/s/464m4fvssl7qbeh/PSB1042%">https://www.dropbox.com/s/464m4fvssl7qbeh/PSB1042%
> 20iFLEX%20Viper%20Five-Line%20Laser%20Engine.pdf?dl=0
>
> Also, here is a PDF instruction set for the iFlex Viper System's USB
> Controller (we do not have this):
>
> <a href="https://www.dropbox.com/s/nryzwtqazf50kli/PSB1068%20iFLEX-Viper%20USB%">https://www.dropbox.com/s/nryzwtqazf50kli/PSB1068%20iFLEX-Viper%20USB%
> 20Controller%20Software%20Installation%20and%20Operating%20I....pdf?dl=0
>
> According to this USB controller PDF instruction, this USB controller uses
> a Velleman K8061 DAQ, which MicroManager seems to have support for (written
> by Austin Blanco):
>
> https://micro-manager.org/wiki/Velleman_K8061
>
> However, what is strange is that MicroManager also has support for the
> iFlex Viper System separately (written by Tom Porter of Excelitas/QiOptic):
>
> https://micro-manager.org/wiki/USB_Viper_QPL
>
> And it seems like this version of the Viper uses the Measurement Computing
> USB-3101 DAQ.
>
> We also found this:
>
> https://valelab4.ucsf.edu/svn/micromanager2/trunk/
> DeviceAdapters/USB_Viper_QPL/
>
> If we had to take a guess, it seems as though the Viper system has an
> updated USB controller with the USB-3103 DAQ.  We were wondering though:
>
> 1.) If anyone has successfully controlled the iFlex Viper System with
> Micromanager
>
> 2.) If so, which USB controller they had
>
> If we can't obtain the USB controller, we will try to make a custom set up
> for the iFlex Viper System using a DAQ, as the pin outs for the AUX 1 input
> (see PDF instruction for the IFlex Viper System with the pin out diagram)
> seem to be fairly straightforward.
>
> Any and all input would be immensely appreciated.
>
> Thank you all so much.
>
> ------------------------------
>
> End of CONFOCALMICROSCOPY Digest - 2 Jul 2018 to 3 Jul 2018 (#2018-149)
> ***********************************************************************
>

--
Justin Demmerle
NIH-Oxford Scholar
Schermelleh Lab - University of Oxford / Biochemistry
Macfarlan Lab - NIH / NICHD
[hidden email]
<https://owa.nexus.ox.ac.uk/ecp/Customize/justin.demmerle@...>