water window x-ray microscopy

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Hi ALL,

Water window soft X-ray microscopy is used successfully at Synchrotron
facilities to image bio samples. Water window is because water is
transparent to soft X-rays and only carbon constituents of the cell are
imaged. Could you please let me know how this techniques compares to other
microscopy techniques for bio applications.

Many thanks,
Otman BENALI, PhD

NANO-UV SAS, Paris/FRANCE
http://www.nanouv.com
http://www.mcxi.eu

[Lloyd Donaldson]

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Having just visited a Synchrotron where this approach was under development (they were still building the beam line and associated imaging equipment) resolution for x-ray tomography may reach sub 100 nm resolution. That is what they are aiming for but I don't think it has been achieved yet. However imaging in water may affect resolution and or contrast. Given the very intense beam it might also kill the cell since you are presumably interested in living tissue. This application is probably more suited to imaging materials.


Dr Lloyd Donaldson

Senior Scientist, Project Leader - Microscopy/Wood Identification
Scion - Next Generation Biomaterials
Private Bag 3020, Rotorua
New Zealand 3010

Ph: 64 7 343 5581



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Otman Benali
Sent: Wednesday, 27 October 2010 4:58 a.m.
To: [hidden email]
Subject: water window x-ray microscopy

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Hi ALL,

Water window soft X-ray microscopy is used successfully at Synchrotron
facilities to image bio samples. Water window is because water is
transparent to soft X-rays and only carbon constituents of the cell are
imaged. Could you please let me know how this techniques compares to other
microscopy techniques for bio applications.

Many thanks,
Otman BENALI, PhD

NANO-UV SAS, Paris/FRANCE
http://www.nanouv.com
http://www.mcxi.eu

Disclaimer: This e-mail and any attachments may contain information which is confidential or subject to copyright. If you receive this e-mail in error, please delete it.
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[DamirSudar]

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Researchers at the Advanced Light Source at Lawrence Berkeley National
Laboratory have been working on biological uses of soft X-ray microscopy
and tomography for a while and there are 2 beamlines set up for this at
the ALS. See: http://ncxt.lbl.gov/?q=technologies  for some info about
it and links to further reading. In brief, yes it works on cells and
other biological materials, resolution of about 50-60nm is achievable,
to reduce radiation damage from the X rays samples are fully hydrated
but kept at cryogenic conditions during imaging so no live cells.

- Damir

On 10/26/2010 12:11 PM, Lloyd Donaldson wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Having just visited a Synchrotron where this approach was under development (they were still building the beam line and associated imaging equipment) resolution for x-ray tomography may reach sub 100 nm resolution. That is what they are aiming for but I don't think it has been achieved yet. However imaging in water may affect resolution and or contrast. Given the very intense beam it might also kill the cell since you are presumably interested in living tissue. This application is probably more suited to imaging materials.
>
>
> Dr Lloyd Donaldson
>
> Senior Scientist, Project Leader - Microscopy/Wood Identification
> Scion - Next Generation Biomaterials
> Private Bag 3020, Rotorua
> New Zealand 3010
>
> Ph: 64 7 343 5581
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Otman Benali
> Sent: Wednesday, 27 October 2010 4:58 a.m.
> To: [hidden email]
> Subject: water window x-ray microscopy
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi ALL,
>
> Water window soft X-ray microscopy is used successfully at Synchrotron
> facilities to image bio samples. Water window is because water is
> transparent to soft X-rays and only carbon constituents of the cell are
> imaged. Could you please let me know how this techniques compares to other
> microscopy techniques for bio applications.
>
> Many thanks,
> Otman BENALI, PhD
>
> NANO-UV SAS, Paris/FRANCE
> http://www.nanouv.com
> http://www.mcxi.eu
>
> Disclaimer: This e-mail and any attachments may contain information which is confidential or subject to copyright. If you receive this e-mail in error, please delete it.
> Scion does not accept responsibility for anything in this e-mail which is not provided in the  course of Scion's usual business or for any computer virus, data corruption, interference or delay arising from this e-mail.

--
Damir Sudar - Staff Scientist and Deputy for Technology
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977R225A, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: [hidden email]
WWW: http://www.lbl.gov/lifesciences/labs/sudar_lab.html

[Ian Hallett]

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Lloyd

In terms of X-ray micro tomography resolution non synchrotron systems now claim resolutions down to 50 nm (for example the Ultra from Xradia).  I'm not sure how well these work in practice for wet biological material.

Ian

Ian Hallett
Senior Scientist
Team Leader: Microscopy and Cell Walls

T: [phone]
F: [phone]
[hidden email]
www.plantandfood.co.nz
The New Zealand Institute for Plant & Food Research Limited

Postal Address: Plant & Food Research Mt Albert
Private Bag 92169, Auckland, 1142, New Zealand
Physical Address: Plant & Food Research Mt Albert
120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Lloyd Donaldson
Sent: Wednesday, 27 October 2010 8:11 a.m.
To: [hidden email]
Subject: Re: water window x-ray microscopy

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Having just visited a Synchrotron where this approach was under development (they were still building the beam line and associated imaging equipment) resolution for x-ray tomography may reach sub 100 nm resolution. That is what they are aiming for but I don't think it has been achieved yet. However imaging in water may affect resolution and or contrast. Given the very intense beam it might also kill the cell since you are presumably interested in living tissue. This application is probably more suited to imaging materials.


Dr Lloyd Donaldson

Senior Scientist, Project Leader - Microscopy/Wood Identification
Scion - Next Generation Biomaterials
Private Bag 3020, Rotorua
New Zealand 3010

Ph: 64 7 343 5581



-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Otman Benali
Sent: Wednesday, 27 October 2010 4:58 a.m.
To: [hidden email]
Subject: water window x-ray microscopy

*****
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*****

Hi ALL,

Water window soft X-ray microscopy is used successfully at Synchrotron
facilities to image bio samples. Water window is because water is
transparent to soft X-rays and only carbon constituents of the cell are
imaged. Could you please let me know how this techniques compares to other
microscopy techniques for bio applications.

Many thanks,
Otman BENALI, PhD

NANO-UV SAS, Paris/FRANCE
http://www.nanouv.com
http://www.mcxi.eu

Disclaimer: This e-mail and any attachments may contain information which is confidential or subject to copyright. If you receive this e-mail in error, please delete it.
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 Food Research Limited.

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Dear Ian,

Many thanks. The X-radia system is based on hard X-rays. Water window
refers to microscopy at wavelength between 2 and 4nm where water is
relatively transparent and only Carbon and Nitrogen constituents of the
cell are imaged. The technology exists using Synchrotron light but there
are a few tabeltop system being developed based on discharge and laser
produced plasma light sources.

Regards,

Otman BENALI, PhD

NANO-UV SAS

16-18, Avenue du Quebec Bat. Neflier

91961 Courtaboeuf cedex FRANCE

Tel: [phone]

Fax: [phone]

http://www.nanouv.com <http://www.nanouv.com/>

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that endows resources with a new capacity to create wealth*"

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On 26/10/2010 23:07, Ian Hallett wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Lloyd
>
> In terms of X-ray micro tomography resolution non synchrotron systems now claim resolutions down to 50 nm (for example the Ultra from Xradia).  I'm not sure how well these work in practice for wet biological material.
>
> Ian
>
> Ian Hallett
> Senior Scientist
> Team Leader: Microscopy and Cell Walls
>
> T: [phone]
> F: [phone]
> [hidden email]
> www.plantandfood.co.nz
> The New Zealand Institute for Plant&  Food Research Limited
>
> Postal Address: Plant&  Food Research Mt Albert
> Private Bag 92169, Auckland, 1142, New Zealand
> Physical Address: Plant&  Food Research Mt Albert
> 120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Lloyd Donaldson
> Sent: Wednesday, 27 October 2010 8:11 a.m.
> To: [hidden email]
> Subject: Re: water window x-ray microscopy
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Having just visited a Synchrotron where this approach was under development (they were still building the beam line and associated imaging equipment) resolution for x-ray tomography may reach sub 100 nm resolution. That is what they are aiming for but I don't think it has been achieved yet. However imaging in water may affect resolution and or contrast. Given the very intense beam it might also kill the cell since you are presumably interested in living tissue. This application is probably more suited to imaging materials.
>
>
> Dr Lloyd Donaldson
>
> Senior Scientist, Project Leader - Microscopy/Wood Identification
> Scion - Next Generation Biomaterials
> Private Bag 3020, Rotorua
> New Zealand 3010
>
> Ph: 64 7 343 5581
>
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Otman Benali
> Sent: Wednesday, 27 October 2010 4:58 a.m.
> To: [hidden email]
> Subject: water window x-ray microscopy
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi ALL,
>
> Water window soft X-ray microscopy is used successfully at Synchrotron
> facilities to image bio samples. Water window is because water is
> transparent to soft X-rays and only carbon constituents of the cell are
> imaged. Could you please let me know how this techniques compares to other
> microscopy techniques for bio applications.
>
> Many thanks,
> Otman BENALI, PhD
>
> NANO-UV SAS, Paris/FRANCE
> http://www.nanouv.com
> http://www.mcxi.eu
>
> Disclaimer: This e-mail and any attachments may contain information which is confidential or subject to copyright. If you receive this e-mail in error, please delete it.
> Scion does not accept responsibility for anything in this e-mail which is not provided in the  course of Scion's usual business or for any computer virus, data corruption, interference or delay arising from this e-mail.
>
> The contents of this e-mail are confidential and may be subject to legal privilege.
>   If you are not the intended recipient you must not use, disseminate, distribute or
>   reproduce all or any part of this e-mail or attachments.  If you have received this
>   e-mail in error, please notify the sender and delete all material pertaining to this
>   e-mail.  Any opinion or views expressed in this e-mail are those of the individual
>   sender and may not represent those of The New Zealand Institute for Plant and
>   Food Research Limited.
>
>    

[James Pawley]

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>*****
>To join, leave or search the confocal microscopy listserv, go to:
>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>*****
>
>Hi ALL,
>
>Water window soft X-ray microscopy is used successfully at Synchrotron
>facilities to image bio samples. Water window is because water is
>transparent to soft X-rays and only carbon constituents of the cell are
>imaged. Could you please let me know how this techniques compares to other
>microscopy techniques for bio applications.
>
>Many thanks,
>Otman BENALI, PhD
>
>NANO-UV SAS, Paris/FRANCE
>http://www.nanouv.com
>http://www.mcxi.eu

Dear Otman,

After 50 years, x-ray microscopy remains a shimmering promise on the
fringes of biological microscopy.

I believe that it will always remain there.

Initially, the argument was the Abbe Limit of 200nm in light
microscopy that could only be overcome with shorter wavelengths.
Hence x-rays. The problem was that there were no sources bright
enough and no lenses. In the mean time, electron microscopy and later
cryo-electron microscopy filled the void, and filled it pretty well.

No matter, it always made it easier to get massive Congressional
appropriations for physics toys if one could hold out the promise of
improved biological imaging. So x-ray microscopy refused to die. Over
time, the sources got brighter and rudimentary lenses were developed.
Although these devices were very clever in themselves, their
performance parameters were vastly inferior to those of their
electron-optics counterparts (For instance, although a zone plate can
indeed focus about 10% of a parallel, monochromatic x-ray beam into a
small spot, the other 93% scatters all over the place.) There was
always progress and a new idea on the horizon, but if you will permit
a personal observation, these ideas were often pushed by people who
seemed to have very little understanding of what was already being
done in other fields of biological microscopy (I know, I went to some
of their meetings. In the early, they were still talking about EM at
the level it was practiced in the early 1960s).

As time went on it became obvious that both EM  and x-ray microscopy
were not in the end limited by the lenses or the sources but by the
interaction of the beam with the specimen. In particular, both use
ionizing radiation that produced inelastic interactions that
deposited energy in the specimen and they did so at a high enough
energy that covalent bonds were broken. This became increasingly
important as the resolution improved (more damage to smaller area).
Looking at living specimens beyond normal LM resolution was a mirage.
(My definition is that you only look at living cells to see some
change. This means at least two images with some hope that the
damage created by making the first is so slight that the second image
has some interest. This excludes both EM and XM)

Once one understands this, the parameter of interest is how to get
the most information for the least damage and this leads us to the
details of the scattering and the contrast of the specimen. The full
description would require a short book but in short, EM has better
(cheaper, smaller more available) sources, better lenses (now they
have corrected the aberrations MUCH better) and the interactions have
higher intrinsic contrast (even in the fabled water window, where the
x-ray contrast is indeed better but the claimed resolution is
relatively worse) and far more of the interacting quanta can be
collected in the final data.

In short, be very careful not be be swept away by all the shiny
stainless steel and compare any results you see with other methods of
looking at dead tissue (like cryo-electron tomography or for living
cells: STED?).

And don't forget the time element. Most microscopy studies in biology
are limited first and foremost not by "resolution" by not looking at
enough specimens. There is a big difference between a scope down the
hall and one across the country.

Grumpy Jim Pawley
--
James and Christine Pawley, 21 N. Prospect Ave. Madison, WI, 53726
Phone: [phone]

[Geoffrey Guttmann]

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Jim and Otman and others with an interest in SXM

As one who did their dissertation on soft x-ray microscopy (SXM) many years
ago, I realized that confocal microscopy was much more effective at
recording changes in living biological samples and seeing what may occur
when prodded by some external stimulus or environment. Yes, EM and SXM are
very limited in that they can only really look at dead tissues or cells.

I did do some experiments to image living biological cells using a technique
called soft x-ray contact microscopy (SXCM), which is akin to the
semiconductor techniques used to make the chips used in computers. I used
both a x-ray C target tube source using supposedly only C x-ray lines and a
laser plasma x-ray source. The static system such as the C target x-ray tube
source killed the biological sample after a short period of time and didn't
make much of a useful image on the resist. I did get some images but they
were rather questionable. To solve this problem, I used some rather hearty
cell samples. The cells ended drying up and what was left was a fine
cytoskeletal framework with maybe a remnant of the cell membrane. The hazard
with doing SXCM is the resist must be read by another microscope, in this
case the SEM. When I realized I couldn't really image a living biological
cell with a x-ray C target tube source, I moved to using a laser plasma
source. Problem, at the time I did this work there were not many laser
plasma sources available. I did find a friend and colleague to help me out
and I managed to image a number of living cell samples using the laser
plasma source. There were a number of trials and tribulations until I got a
protocol that worked. Even then the living cell was not alive once the laser
plasma source had been fired. Thus one could not go back and look at the
cell again. I was able to capture the cells in movement and also during
mitosis. To verify mitosis however would have required that I kill the cell
and inject an antibody that could carry gold to the microtubules found in
the spindle fibers. Gold would be necessary to create contrast within the
cell. Essentially one creates a circular argument to justify doing these
experiments, when other light microscopy techniques may work better.

In short, soft x-ray microscopy is a technique in search of a problem to
solve. Biological tissues and cells are not that type of problem that can be
resolved by SXM very easily. Confocal microscopy can do a much better job in
this case. I have seen a number of physics tools being developed for SXM but
none have made an impression on me in the last twenty years. There are a
number of issues that need to be solved. One of these is radiation dose,
which is extremely high in SXM and SXCM, and will have a major effect on the
tissues or cells. Radiation dose is also a concern in doing transmission
x-ray microscopy because the question is, "Is the cell responding to the
radiation or to the environment acting as a stimulus?" Another issue is the
necessity to use an EM to view the resist in SXCM.

So, what biological issue can be resolved with SXM or SXCM? Well, one can
look at the botanicals or plant cells. Plant cells can handle high radiation
doses to a point before they die and they may not have much movement or be
static.

Cheers from someone who was converted from soft x-ray to confocal microscopy.

Geoff Guttmann, Ph. D. (Univ. of California, Berkeley 1989)
Professor of Anatomy
The Commonwealth Medical College
Scranton, PA 18509

[Fred Perry]

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Click
http://www.cvent.com/EVENTS/Info/Summary.aspx?e=29b2ee80-516e-451a-b21c-afd8a8d1a576 
to view the agenda etc.

The 8th Advanced Imaging Methods (AIM) Workshop,
January 19-21, 2011, is organized by the UC
Berkeley Molecular Imaging Center in conjunction
with Becker & Hickl GmbH, and focuses on the
latest techniques, results, and technology in
laser scanning confocal microscopy, especially
time resolved, presented by world-renowned scientists.

Topics this year include: fluorescent lifetime
imaging, FRET, multi-photon microscopy, adaptive
optics, super resolution, physiological
measurements, in-vivo imaging, spectroscopy,
single molecule detection, and more. In addition
to lectures and discussions, there is a poster
session and manufacturer demonstrations.

AIM is geared to researchers of all levels –
students, postdocs, and primary investigators
looking to learn more about the most recent
advances in microscopy. Imaging techniques are
one of the most useful tools in scientific
discovery today, making this conference useful to
researchers in almost any field: biology,
chemistry, engineering, physics, vision science,
astronomy, stem cell studies, optics, and more.

While advantageous to have some experience in
microscopy to get the most out of AIM, it is not
essential. Primer talks on session topics will be
given at the start of the major sessions. There
is ample opportunity to meet with others in the
field and engage in discussions in an informal,
friendly setting. Morning pastries, lunch and
coffee breaks will be included in the
registration price, as well as evening receptions and optional tours.

Click
http://www.cvent.com/EVENTS/Info/Summary.aspx?e=29b2ee80-516e-451a-b21c-afd8a8d1a576 
to view the agenda etc.

- Fred Perry

=====================

Fred Perry
Boston Electronics Corporation
91 Boylston Street, Brookline MA 02445 USA
[phone] or [phone];  fax [phone]
[hidden email]          http://www.boselec.com
*********************************************