SSRL Workshop, 10/8-9/2002 1

STXM and diffraction-imaging - the view from Stony Brook

Janos Kirz, Stony Brook Universityon leave for 2002-2003

at the ALS

With special thanks to Chris Jacobsen

SSRL Workshop, 10/8-9/2002 2

SSRL Workshop, 10/8-9/2002 3

X-ray focusing: Fresnel zone plates

• Diffractive optics: radially varied grating spacing

• Largest diffraction angle is given by outermost (finest) zone width rN as =/(2rN)

• Rayleigh resolution is then t=0.61 /()=1.22 rN

• Zones must be positioned to ~1/3 width over diameter (10 nm in 100 m, or 1:104)

Central stop and order sorting aperture (OSA) to isolate first order focus

SSRL Workshop, 10/8-9/2002 4

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

E-beam resist RIE of Ge mask RIE of polymer Electroplating

40 nm zones in 120 nm Ni

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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 E>400 eV accessible

• Improved scanning stage: higher resolution

• Motorized detector platform• Laser interferometer and fast

scanning upgrade underway

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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

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

Human sperm (unfixed): S. Wirick, C. Jacobsen, Y. Sheynkin

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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 N=150 energies are common.

IDL-based analysis tools are made available

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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 development:segmented, current

mode

•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 (>90%)

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

Assembly: 40 mm acrossActive 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: n=1--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 1 mm 1 1 mm

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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 @ 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)Real space:•Finite support:

object fills only part of the field

•Histogram•Positivity?

Fourier space:•Re-impose

the measured intensities while letting the phases evolve

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!

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

Live bacteria

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Radiation damage resistance in cryo

Left: frozen hydrated image after exposing several regions to ~1010 GrayRight: after warmup in microscope (eventually freeze-dried): holes indicate irradiated regions!

Maser et al., J. Microscopy 197, 68 (2000)

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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 temperature:XANES spectra

• T. Beetz, SUNY Stony Brook• Peak at 531.4 eV: C=0 bond• Plateau at 540 eV: total mass (plus some

emphasis on oxygen * bonds)

C=0 peakC=0 peak

Plateau

Plateau

Room temperature Liquid nitrogen 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 C=0 bond in PMMA)

Plateau at 540 eV:total mass

Peak at 531.4 eV:C=0 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 TennantMany collaborators…