(COMMERCIAL) How do you define what is acceptable for a microscope ?

[Gautier Papon]

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Hello to all,



We are a small company manufacturing tools for performance assessment of fluorescent imaging systems. We have some feedbacks from users that ask us to define what values are acceptable for their systems (our products do not “judge” systems, we just characterize them) – We are uncomfortable with giving a clear answer because of the lack of established consensus.



So I have two questions for the community  :

  *   Would you be interested in having this “acceptable” values for your systems ?
  *   Who/what would be an acceptable source to define those values ?



SO, we are trying to establish a somehow comprehensive list of the organized initiatives performed to advance standardization in the field of non-coherent imaging. By that we mean actions, programs, that included several people in an effort to define metrological terms/elements for fluorescence microscopy.



We already know some of them, listed below.



In France :
·         The RTmfm  (http://rtmfm.cnrs.fr/)  - A French network of core imaging facilities involved in the development of "MetroloJ": an ImageJ plugin to help track the quality of microscopes. http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:metroloj:start.<http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:metroloj:start> They have also edited metrology protocols, together with acceptation criteria.

In the USA :
·         The Light Microscopy Research group (LMRG) from ABRF has been continuously working  on creating a 3D biologically relevant test slide and imaging protocols. https://abrf.org/research-group/light-microscopy-research-group-lmrg
·         The NIST is working on an ASTM Guide about performing quantitative fluorescence intensity measurements for WF system (https://www.astm.org/DATABASE.CART/WORKITEMS/WK59530.htm)

In Germany :
·         The German Bioimaging consortium has been discussing a DIN/ISO norm about confocal microscopes in 2016 (http://www.germanbioimaging.org/wiki/index.php/Annual_community_meeting_2016 in the minute document)



Do you know other initiatives or papers about it ?



Sorry for the long mail 😉

Best regards,
Gautier from Argolight.

[Sathya Srinivasan]

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Hi Gautier,
This volume in:  Methods in Cell Biology on "Quantitative Imaging In Cell
Biology", Edited by Jennifer C. Waters, Torsten Wittman
Volume 123, Pages 2-568 (2014) is a great compilation on the topics which
covers various aspects in microscopy and calibration standards. (
https://www.sciencedirect.com/bookseries/methods-in-cell-biology/vol/123/suppl/C
)

Jennifer and Torsten (the editors of that volume) would be a fantastic
source (hope they are reading this!). I have a collection about the various
calibration methods for different types of systems and you can contact me
personally and I can lead you to the articles that I have if you think it
would be useful for your mission. Good luck!

Sathya Srinivasan
ONPRC
Imaging and Morphology Support Core

On Fri, May 18, 2018 at 2:38 AM, Gautier Papon <[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.
> *****
>
> Hello to all,
>
>
>
> We are a small company manufacturing tools for performance assessment of
> fluorescent imaging systems. We have some feedbacks from users that ask us
> to define what values are acceptable for their systems (our products do not
> “judge” systems, we just characterize them) – We are uncomfortable with
> giving a clear answer because of the lack of established consensus.
>
>
>
> So I have two questions for the community  :
>
>   *   Would you be interested in having this “acceptable” values for your
> systems ?
>   *   Who/what would be an acceptable source to define those values ?
>
>
>
> SO, we are trying to establish a somehow comprehensive list of the
> organized initiatives performed to advance standardization in the field of
> non-coherent imaging. By that we mean actions, programs, that included
> several people in an effort to define metrological terms/elements for
> fluorescence microscopy.
>
>
>
> We already know some of them, listed below.
>
>
>
> In France :
> ·         The RTmfm  (http://rtmfm.cnrs.fr/)  - A French network of core
> imaging facilities involved in the development of "MetroloJ": an ImageJ
> plugin to help track the quality of microscopes.
> http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:metroloj:start.<
> http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:metroloj:start>
> They have also edited metrology protocols, together with acceptation
> criteria.
>
> In the USA :
> ·         The Light Microscopy Research group (LMRG) from ABRF has been
> continuously working  on creating a 3D biologically relevant test slide and
> imaging protocols. https://abrf.org/research-group/light-microscopy-
> research-group-lmrg
> ·         The NIST is working on an ASTM Guide about performing
> quantitative fluorescence intensity measurements for WF system (
> https://www.astm.org/DATABASE.CART/WORKITEMS/WK59530.htm)
>
> In Germany :
> ·         The German Bioimaging consortium has been discussing a DIN/ISO
> norm about confocal microscopes in 2016 (http://www.germanbioimaging.
> org/wiki/index.php/Annual_community_meeting_2016 in the minute document)
>
>
>
> Do you know other initiatives or papers about it ?
>
>
>
> Sorry for the long mail 😉
>
> Best regards,
> Gautier from Argolight.
>
>

[Arnaud ROYON]

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Dear all,

We would like to inform the community that our products can be used to
benchmark deconvolution softwares regarding the intensity quantification.

More particularly, thanks to a fluorescent pattern consisting of 16
intensity levels following a linear evolution (pattern C: 4x4 intensity
gradation / http://argolight.com/argo-hm/), one can easily and quickly
check if deconvolution preserves the ratio between the intensity levels,
the linearity and the dynamic.

More information can also be found in the section 4 of our applications
guide:
http://argolight.com/wp-content/uploads/2017/05/Argolight-solutions_Applications-guide.pdf

Hope that helps,
Best regards,
Arnaud.

--
Arnaud ROYON, Ph.D.
CTO, board member & co-founder
Argolight
Cité de la Photonique, Bat. Elnath
11 avenue de Canteranne
33600 Pessac, FRANCE
Email:[hidden email]
Tel: [phone]
Web site:www.argolight.com
                                       


    Re: Addition to post on "confocal detectors and deconvolution"

Posted by *Alison North* on /May 11, 2018; 6:35pm/

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Dear all,

I am a big fan of carefully performed deconvolution, and we have used
Huygens, Autoquant and GE's SoftWoRx deconvolution packages on many
types of microscope images (widefield, confocal, spinning disk, light
sheet etc.) with great success.  However, I'm not sure I agree fully
with George's comment that every confocal microscope should have
deconvolution running immediately downstream, unless the manufacturers
are going to do a better job of educating every single user about what
goes on in their black box of deconvolution.  As we all know, some
deconvolution softwares are more quantitative than others.  I am
particularly concerned after a talk I just heard about the new Leica
LIGHTNING software, which uses different parameters for each voxel in
the image.  Here is a direct quote from Leica's web page:

"Maximize the information you extract from your specimen and get
in-depth answers to scientific questions with the LIGHTNING detection
package for image information extraction."

LIGHTNING fully automatically detects the finest structures and details,
which are otherwise simply not visible. The key technology of LIGHTNING
is an adaptive process for extraction of hidden information in the
image. Unlike traditional technologies, that use a global set of
parameters for the full image, *LIGHTNING calculates an appropriate set
of parameters for each voxel *to uncover every detail with the highest
fidelity."

I think we need to impress upon the microscope manufacturers very
strongly that we are in the business of collecting quantitative
scientific data, not just pretty pictures.  At their presentation of
this new software at the ABRF meeting last week, I asked whether it
would be possible for them to flash up a big red warning on the screen -
"Pretty picture ONLY!" - every time somebody uses this operation, to
warn the user that this is a non-quantitative operation and therefore
the user will never be able to perform any kind of quantitative image
analysis on those images.  I'm not sure they took my comment seriously,
but I was indeed being perfectly serious!  I also think the same should
be implemented for any kind of operation that turns a quantitative raw
image into one that is not, such as the use of the High Dynamic Range
button on some of the confocal systems. Since many journals require
authors to declare any nonlinear operations to images, including gamma
adjustments, it's critical for every researcher to be aware of any such
operations.  It may be acceptable to perform this kind of operation
after the fact, as long as one understands what has been done and states
it clearly in the methods or figure legend, but I am very nervous about
acquiring RAW data that has already been changed in a nonlinear way.

I'm not meaning to pick on Leica - they are not the only ones with evil
buttons and options in their software! - but I do believe we need to
point out how worrying this trend is.

Best,
Alison


On 5/11/2018 8:55 AM, Vincent Schoonderwoert wrote:

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***Vendor message***


Dear all,


Without getting involved in a discussion about the need for
deconvolution (although we are tempted), we feel a profound need to
inform you about the status of the collaboration between SVI-Huygens and
Leica to prevent any misunderstanding if you are considering a new
confocal microscope.

Per December 1, 2017,  despite its success, Leica stopped selling
Hyvolution2 with Huygens as its computing engine. As George kindly
mentioned, Hyvolution2 includes "the SVI Huygens software under the
hood". New Leica customers are now offered another option in LASX that
does NO LONGER involve the Huygens software and SVI.

We will maintain our high level of support to customers who already
purchased a Huygens license via Hyvolution or directly with their SP8.
Like before, we also keep offering Huygens for the latest microscope
types and file formats.  Also the new and fully automated on-the-fly
deconvolution tool "Batch Express" will offer this functionality.

We welcome any further questions and will respond offline. Apologies to
Mike for using your interesting post.

With kind regards,
Vincent


Get the best out of your microscopy images with Huygens Batch Express:

https://urldefense.proofpoint.com/v2/url?u=http-3A__www.svi.nl_BatchExpress&d=DwIDaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=RBx0-WJrAO5vwSOLNmFbqYvikvIZS5ns3-USwvMOuLo&m=otc_bgF6TO_iCl4lyz-BEkOTqW9EsRGuiTXpZHmRB3U&s=EAEoN_a12grsO5QrEbCKFIa1T8P_LjFnR_rzGasiUpk&e= 



***********************************************
Vincent Schoonderwoert, PhD
Senior Imaging Specialist/Account Manager
Scientific Volume Imaging
www.svi.nl
[phone]
***********************************************

--
Alison J. North, Ph.D.,
Research Associate Professor and
Senior Director of the Bio-Imaging Resource Center,
The Rockefeller University,
1230 York Avenue,
New York,
NY 10065.
Tel: office ++ 212 327 7488
Tel: lab     ++ 212 327 7486
Fax:         ++ 212 327 7489