Posted by
Alison J. North on
URL: http://confocal-microscopy-list.275.s1.nabble.com/confocal-detectors-and-deconvolution-tp7588223p7588241.html
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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
> +31 35 642 1626
> ***********************************************
--
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