STXM and diffraction-imaging - the view from Stony Brook

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STXM and diffraction-imaging - the view from
Stony Brook

• Janos Kirz, Stony Brook University
• on leave for 2002-2003
• at the ALS
• With special thanks to Chris Jacobsen

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X-ray focusing Fresnel zone plates

• Diffractive optics radially varied grating
  spacing
• Largest diffraction angle is given by outermost
  (finest) zone width ?rN as ??/(2?rN)
• Rayleigh resolution is then ?t0.61 ?/(?)
• 1.22 ?rN
• Zones must be positioned to 1/3 width over
  diameter (10 nm in 100 ?m, or 1104)

Central stop and order sorting aperture (OSA) to
isolate first order focus
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Zone plates by electron beam lithography

• A. Stein, B. Hornberger, M. Lu, S. Spector (PhD
  1998), C. Jacobsen
• D. Tennant (Lucent)
• JEOL JBX-6000FS 1 nA into 7 nm spot, 2.5 nm over
  80 ?m, 50 keV
• JEOL JBX-9300FS 1 nA into 4 nm spot, 1.2 nm over
  500 ?m, 100 keV

A. Stein and JBX-9300FS
40 nm zones in 120 nm Ni
E-beam resist
RIE of Ge mask
RIE of polymer
Electroplating
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STXM IV the new room temperature microscope

• M. Feser et al., Stony Brook
• Two identical copies now in operation
• Sealed, helium-filled chamber makes Egt400 eV
  accessible
• Improved scanning stage higher resolution
• Motorized detector platform
• Laser interferometer and fast scanning upgrade
  underway

X-ray beam
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Why I like scanning?

• XANES spectroscopy
• Multi-channel detector
• Low dose, large area overview scans
• Convenient correlation to visible light
  microscopy
• Wet, dry, or cryo specimens
• Minimizes radiation dose
• Quantitative

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Drawbacks

• Slower than full-field microscopy
• Hungry for coherent photons
• (but note new STXM at ALS bending magnet!)
• Thickness restrictions in transmission mode

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Wet specimens

• One can get 50-80 transmission through 100 nm
  Si, Si3N4
• Place 1 ?l fluid droplet on 1 cm2, sandwich
  between two thin windows gives 10 ?m fluid
  thickness
• Let fluid wet one window (1-2 ?m thickness by
  wetting), place another 1 mm away to preserve air
  hydration

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Imaging of wet specimens
Human sperm (unfixed) S. Wirick, C. Jacobsen, Y.
Sheynkin

• NIL 8 fibroblast (glutaraldehyde fixed) V.
  Oehler, J. Fu, C. Jacobsen

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Spectromicroscopy by image stacks

• Acquire sequence of images over XANES spectral
  region automatically align using Fourier
  cross-correlations extract spectra.
• C. Jacobsen et al., J. Microscopy 197, 173 (2000).

Images at N150 energies are common.
IDL-based analysis tools are made available
Photon energy
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Analysis of stacks

• C. Jacobsen and students
• Singular Value Decomposition
• (components and model spectra known)
• Principal Component Analysis Cluster analysis
• (components unknown)

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Detector developmentsegmented, current mode
M. Feser, C. Jacobsen (Stony Brook) P. Rehak, G.
de Geronimo (BNL Instrumentation) L. Strüder, P.
Holl (MPI München)

• Silicon drift detector
• Simultaneous recording of bright field, dark
  field, differential phase and interference
  contrast (Polack Joyeux)
• No significant upper limit to signal rate.
  Acceptable dark noise (8 photons/msec
  equivalent room temperature)
• High quantum efficiency (gt90)

Assembly 40 mm across Active area 600 ?m
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Segmented silicon drift detector

• Corner of silicon nitride window silicon at 45
  wall slope forms a prism
• Refraction of x-ray beam in opposite direction
  from visible light prisms

X-ray refractive index n1-?-i?
All channels acquired simultaneously
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Amplitude, phase contrast imaging in STXM

• Use segmented detector for phase reconstruction.
  Finest features 30 nm.
• Beam noise is normalized out for free! Note
  organic crud
• M. Feser, PhD thesis

1 ?m
1 ?m
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Mapping protein and DNA in sperm

• X. Zhang et al.,
• J. Struct. Bio. 116, 335 (1996)
• New project to study human sperm just beginning!

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Applications _at_ NSLS X1A

• Sperm morphology / infertility Jacobsen, USB
• Interplanetary dust, meteoritics Flynn,
  SUNY/Plattsburgh
• Organic geochemistry / wood, coal Cody,
  Carnegie Inst.
• Nuclear waste transport Schaefer, Karlsruhe
• Marine organic matter Brandes, U. Texas
• Bacteria and uranium chemistry Gillow, BNL
• Humic acid aggregates Rothe, Karsruhe
• Humic and fulvic acids Scheinost, Zurich
• Biofilms Thieme, Goettingen
• Emulsion stability Urquhart, Saskatchewan
• PMMA damage as fn of temperature Jacobsen, USB

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Applications - elsewhere

• ALS 5.3.2 Polymer STXM (BM) Ade, Hitchcock
• ALS 11.0.2 EMS STXM (EPU) Shuh, Warwick
• BESSY II Soil, colloid STXM (U) Thieme
• New, 2002
• Under construction, 2002

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STXM higher energy 1-4 KeV

• APS 2ID-B McNulty
• ESRF ID 21 Susini
• Attractions Na, Mg, Al, Si, P, S, Cl edges
• Challenges High aspect ratio for zone plate
• Need for phase contrast or fluorescence

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Imaging using x-ray diffraction from
non-periodic specimens

• Diffraction pattern can be recorded with no
  optics-imposed resolution limits
• Proposed by Sayre (in Schlenker, ed., Imaging and
  Coherence Properties in Physics, Springer-Verlag,
  1980)
• Previous experiments by Sayre, Yun, Chapman,
  Miao, Kirz
• Reconstruction iterate between real and Fourier
  space (Gerchberg-Saxton, Fienup, Elser)

• Fourier space
• Re-impose the measured intensities while letting
  the phases evolve

• Real space
• Finite support object fills only part of the
  field
• Histogram
• Positivity?

?FT?
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Diffraction imaging present efforts

• New experimental chamber rotate frozen hydrated
  specimen through ?80
• In-vacuum CCD, placement of optics/pinholes
  upstream and downstream of sample
• Diffraction tomography in biology T. Beetz et
  al.
• Diffraction in biology D. Shapiro, E. Lima et
  al.
• Magnetic speckle T. Mentes, C. Sanchez-Hanke,
  C.-C. Kao (BNL)

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Diffraction patterns from yeast cells
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Damage!
Live bacteria

• V. faba chromosomes fixed in 2 glutaraldehyde.
  S. Williams et al., J. Microscopy 170, 155 (1993)

Previously unexposed damage timescale longer
than msec-range pixel time
Repeated imaging of one chromosome shows mass
loss, shrinkage
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Radiation damage resistance in cryo
Maser et al., J. Microscopy 197, 68 (2000)
Left frozen hydrated image after exposing
several regions to 1010 Gray
Right after warmup in microscope (eventually
freeze-dried) holes indicate irradiated regions!
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PMMA at room, LN2 temperature

• T. Beetz, Stony Brook
• Repeated sequence dose (small step size, long
  dwell time), spectrum (defocused beam)
• Images dose region (small square) at end of
  sequence

Room temperature mass loss immediately visible
LN2 temperature no mass loss immediately visible
After warm-up mass loss becomes visible
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PMMA at LN2, room temperatureXANES spectra

• T. Beetz, SUNY Stony Brook
• Peak at 531.4 eV C0 bond
• Plateau at 540 eV total mass (plus some emphasis
  on oxygen ? bonds)

C0 peak
Plateau
C0 peak
Plateau
Liquid nitrogen temperature
Room temperature
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Results from fitting spectra

• T. Beetz, SUNY Stony Brook
• LN2 temp protection against mass loss, but not
  against breaking bonds (at least C0 bond in PMMA)

Plateau at 540 eV total mass
Peak at 531.4 eV C0 bond
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Group effort!

• Stony Brook group
• Faculty Chris Jacobsen and Janos Kirz
• Senior research support specialist Sue Wirick
• Postdoc Michael Feser
• Students Tobias Beetz, Holger Fleckenstein,
  Benjamin Hornberger, Mirna Lerotic, Enju Lima,
• Ming Lu, David Shapiro, Aaron Stein
• Guest scientist David Sayre
• Recent alumni Sven Abend, Mary Carlucci-Dayton,
  Konstantin Kaznacheyev, Jianwei Miao, Ulrich
  Neuhäusler, Angelika Osanna, Thorsten Schäfer,
  Stefan Vogt, Steve Wang, Barry Winn
• Lucent Don Tennant
• Many collaborators