Development of a Cryo Scanning Transmission
X-Ray Microscope at the NSLS
Jörg Maser, Chris Jacobsen, Janos Kirz, Angelika Osanna, Steve Spector,
Steve Wang, Jan Warnking
Physics Department, State University of New York at Stony Brook, Stony Brook,
NY 11794–3800, USA
Abstract. We have developed a cryo Scanning Transmission X-ray Microscope at the X1A beamline at the NSLS. The system is designed to
image hydrated biological objects of a thickness of several micrometers
at temperatures of around 110 K at a resolution of ultimately 30 nm
or less. A description of the setup of the cryo-STXM is given. We have
started to commission the system and present some results, including
first images of biological samples.
1
Introduction
The Scanning Transmission X-ray Microscope (STXM) at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL) uses
soft X-rays of wavelengths between 2 nm and 5 nm from the X1 undulator [10].
It is capable of imaging specimens of several micrometer thickness, mostly of
biological objects, with a spatial resolution of currently around 50 nm. Its main
operation mode is bright field absorption contrast. It is also well suited to performing spectroscopic measurements such as elemental and chemical state mapping and spectroscopy of small sample areas (≈ 0.2µm) [2, 20, 4]. Its flexible
setup allows the use of other image acquisition modes such as dark field contrast
[5], differential phase contrast [14], microdiffraction imaging [15], or of other
contrast mechanisms such as X-ray induced luminescence [9, 3] and dichroism
contrast [1].
A major application of X-ray microscopy is the investigation of hydrated,
biological samples (see e.g., [11]). Many of these objects suffer structural damage from the irradiation by X-rays (see e.g., [19, 16]). To address the problem of
radiation damage, we have developed and are commissioning a cryo-STXM [13].
This system is designed to image hydrated objects at a temperature of around
110 K in expectation of increased radiation hardness of the samples at these
temperatures. Cryo techniques have been extensively researched by electron microscopists, and a significant increase of radiation hardness of biological objects
has been demonstrated (see e.g., [6, 7]). Theoretical calculations show that a
significant reduction of structural damage can also be expected in cryo X-ray
microscopes [16], and recent experiments have confirmed this [17].
X-Ray Microscopy and Spectromicroscopy
Eds.: J. Thieme, G. Schmahl, D. Rudolph, E. Umbach
c Springer-Verlag Berlin Heidelberg 1998
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J. Maser et al.
There are several advantages in using the cryo method in a STXM. Increased
radiation hardness will allow us to image radiation sensitive objects at high spatial resolution without chemical fixation, and hence without artifacts stemming
from this preparation method. The ability to record multiple images of the same
sample area will allow us to obtain elemental and chemical state contrast at high
spatial resolution, and to experiment with tomographic methods on biological
objects. Finally, use of fast-cooling methods will allow us to freeze dynamical
processes with a time constant in the millisecond range.
2
2.1
Instrumental Setup of Cryo-STXM
Concept of Cryo-STXM
In most X-ray microscopes in use, the sample is placed in an ambient environment. This allows easy access to the sample area, a rather fast exchange of the
sample, and is well suited for imaging samples in a wet state. It also makes
changes to the sample area or a change of detectors relatively straightforward
and enhances the flexibility of the system. On the other hand, absorption of the
X-rays by air or a replacement gas such as helium can reduce the usable spectral
range of the system, and even small variations in the ratio of the replacement
gas and residual air in the beam path can cause a considerable increase of noise
in spectroscopic measurements. Also, when cooling the sample to low temperatures, convectional heat exchange between the cold sample and its environment
significantly contributes to thermal drifts. Therefore, we have decided to place
the sample in a high vacuum. This reduces the sensitivity of the cryo-STXM to
thermal drifts, gives us a good control of contamination of the cold sample, and
allows us full use of the water- -window spectral range.
2.2
Optical Setup
A Fresnel zone plate (FZP) is used to focus the spatially coherent part of the
undulator beam into a diffraction-limited spot on the sample (see e.g., [13]). A
central stop on the zone plate and an order sorting aperture (OSA) are used
to block out unwanted light. For imaging, the sample is scanned through the
spot. The transmitted signal is collected by a detector and the measured value
stored pixel by pixel in a computer. For focusing, the FZP and the OSA are
moved together along the optical axis. For spectral scans, the monochromator is
scanned instead of the sample, and FZP and OSA are moved along the optical
axis to keep the sample in focus at all times.
2.3
Hardware Setup
The cryo-STXM is contained in a vacuum chamber which is pumped by an ion
pump. A turbo station is used for evacuation and for prepumping of the sample
in an airlock prior to insertion into the chamber. The vacuum chamber sits
Development of a Cryo Scanning Transmission X-Ray Microscope
I - 37
on a frame which is supported by kinematical mounts. These allow positioning
of the chamber in 3 directions and along 3 rotational axes. The stages for the
coarse scanning motion of the sample and for detector positioning are outside the
vacuum, with bellows for bringing the motion inside the chamber. The vacuum
chamber is presently separated from the beamline by a Si3 N4 window and can,
therefore, be vented without venting the downstream section of the beamline.
Two viewport doors give fast access to the optics and to the detector area. The
ultimate pressure of the system is designed to be on the order of 10−7 torr.
Setup of the Scanning Motions
Fig. 1. Front view of the cryo-STXM. The X-rays impinge perpendicular to the plane
of the figure. The sample is mounted on a LN2 -cooled sample holder (A). The holder
interfaces with an airlock (B) which can move in x and y against a bellows and is
guided by a lever mechanism. The sample holder rests in a socket on the fine scanning
stage (E). For coarse scans, stepping motors (D) drive the fine scanning stage and with
it sample holder and airlock in x an y. For fine scans, only sample holder and airlock
are moved. A cold trap (C) reduces contamination of the sample.
Figure 1 shows a front view of the vacuum chamber with the sample holder
(A), the airlock (B) and the scanning stages (D and E). For image acquisition,
the sample is scanned in a plane perpendicular to the optical axis. A coarse
scanning motion (D) allows imaging of large fields, and a fine scanning motion
(E) is used to obtain high spatial resolution. The coarse motion is provided
by stepping-motor driven linear translation stages, located outside the vacuum,
with a minimum step size of 1 µm and a range of several millimeters. To avoid
off-center loads, a true vertical translation stage (Newport UZM160) is used for
the vertical motion. The fine scanning motion is performed by an in-vacuum
aluminum flexure stage which is mounted atop the coarse stage through bellows.
Fine scans are driven by Queensgate piezoelectric actuators with capacitance
micrometers which allow minimum steps of a few nm and have a range of 70 µm.
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J. Maser et al.
First tests give a mechanical resolution of the fine stage of better than 20 nm.
The flexure stage has been designed using a concept developed by S. Lindaas,
M. Howells and C. Jacobsen [12].
The sample is held in a cryo holder (A) which is inserted into the vacuum
chamber through an airlock (B). The airlock is suspended at two points from
a lever mechanism with pivot points formed by Lucas hinges. The airlock is
connected to the vacuum chamber with bellows. This allows it to move freely
in a plane orthogonal to the optical axis. After inserting the cryo holder into
the vacuum chamber, it is mechanically connected to the airlock with a lock
nut, such that airlock and cryo holder move as one unit without slip. The tip
of the cryo holder ends in a sapphire ball which is placed in a cone-shaped hole
on a socket on the scanning stage. It is held in place by vacuum force which is
partly balanced by adjustable springs to yield a small preload. The socket on the
scanning stage, in which the cold tip of the sample holder rests, is made of invar
to reduce thermal drifts. A thermocouple is installed on the socket to monitor
its temperature.
Cryo Sample Holder
Placing the sample in a vacuum enables us to make use of equipment developed for cryo transmission electron microscopes (cryo-TEM). To hold the
sample, we use a modified cryo-TEM specimen holder built by E. A. Fischione
Instr. [13]. The holder is cooled by LN2 to a temperature of around 110 K. It is
designed to interface with the airlock of a JEOL-100 CX TEM; we use such an
airlock to allow a quick transfer of the sample into the vacuum chamber. The
temperature of the cryo holder is continuously monitored, and can be raised by
activating a heating circuit. This allows us to maintain temperatures between
110 K and 370 K. Controlled heating is particularly useful to investigate manifestation of radiation damage or ice crystal formation by comparing images of
samples taken at different temperatures.
The specimen is placed on an electron microscope grid, which in turn is mounted
on a seat in the tip of the holder. Additional seats are provided in the tip to
allow mounting of a test pattern and of a pinhole for alignment purposes and resolution tests. A shutter, operated by an out-of-vacuum actuator, can be placed
around the sample to protect it from contamination during all phases of sample
transfer and between taking images. To further reduce contamination, we have
also installed a cold trap around the sample. This so-called “anticontaminator”
(Fig. 1C) consists of two copper blades, cooled to a temperature of below 110 K,
which are placed around the sample.
Zone Plate and OSA
The FZP and OSA each sit on a support which is mounted to 3-axis translation stages. This allows rather convenient positioning of both components with
respect to each other. We use remotely controlled, vacuum-compatible PMAs
(Piezo Micrometer Actuators, New Focus) as actuators. The PMAs allow po-
Development of a Cryo Scanning Transmission X-Ray Microscope
I - 39
sitioning at a speed of around 1 mm/min which has proven sufficient for all
practical purposes. Since the OSA is closest to the cold sample, its support is
made of invar, and a thermocouple for temperature monitoring attached. We
have also kept open the option of heating the OSA to prevent thermal drifts,
but the drifts encountered so far are comfortably small.
Both the FZP and the OSA translation stages are mounted on a vacuumcompatible linear z-stage which is driven by a DC motor along the optical axis
for focusing and spectral scans. The stage is bolted to the bottom of the vacuum
chamber. Alignment of the z-motion parallel to the optical axis is accomplished
by tilting the vacuum chamber with its kinematical mounts.
Detector Arrangement
Figure 2 shows a side view of the vacuum chamber with the scanning stages
for the sample (A, B) and the positioning stage for the detector (E). The detector assembly for the transmitted X-ray flux (F) is mounted on a platform
in the vacuum chamber, downstream of the sample area. The platform can be
positioned in x, y and z with manual micrometer stages outside the chamber.
The X-ray detector is mounted inside a small steel can. Electrical connections
and water cooling are provided through a long, flexible tube to the detector.
X-rays are admitted to the evacuated front area of the detector through a Si3 N4
window. The whole detector can is mounted on a slide mechanism on top of the
platform and can be moved in and out of the beam (in x) with a wobble stick.
Fig. 2. Side view of the cryo-STXM. Coarse (A) and fine (B) scanning stages move the
sample through the micro probe. FZP and OSA (C) are moved parallel to the optical
axis by a separate z-stage (D) for focusing and spectral scans. The X-ray detector (F)
is contained in a steel can inside the vacuum chamber. It can be moved out of the
beam and replaced by infinity-corrected visible light objectives (G) using slides on the
platform. The platform is positioned with a micrometer stage (E). The head of the
visible light microscope (H) is placed outside vacuum.
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J. Maser et al.
To preview the sample optically, we have installed a Nikon OptiPhot microscope head (H) with infinity-corrected objectives inside the vacuum (G). The
lenses are mounted on the same in-vacuum slide as the detector box, and are
moved in position when the detector is moved out of the beam. The position of
the detector is defined by a kinematical mount, while the position of the lenses
is defined by stops. Once the detector is aligned on the optical axis, all components can be moved in and out of position with the wobble stick using the
kinematical mount and the stops, and no readjustment of the detector position
with the micrometer stage is needed.
In our first experiements, we have used a photomultiplier tube (PMT) with a
phosphor-covered entrance window as an X-ray detector. The phosphor converts
the X-rays to visible light, and the PMT converts the visible light pulses to a
TTL signal. We plan to use an avalanche photo diode system (APD) with active
quenching circuit from EG&G in the future [13].
3
3.1
Operation and Initial Results
Sample Preparation and Transfer
The objective during sample preparation and transfer is to cool a hydrated sample without formation of ice crystals, and keep it at a temperature where no
crystallization can take place during sample transfer and imaging. Ice crystallization during cooling can be prevented by either fast cooling methods or by
high pressure cooling methods. In order to prevent formation of ice after cooling, the sample has to be kept at temperatures of around 130 K or below during
all steps of sample preparation, transfer and observation. At low temperatures
on this order, the sublimation rate of water in vacuum is also very slow which
helps prevent freeze drying of the sample during imaging. We chose to cool the
sample with a plunge freezing method (see e.g., [7]), where the sample is rapidly
plunged into liquid ethane, which in turn is cooled by LN2 to a temperature of
around 90 K. Cooling speeds on the order of 104 − 106 K/s can be obtained by
this method, and it should be possible to cool samples of several micrometers
thickness with minimal formation of ice crystals.
After plunge cooling, the EM grid with the sample is mounted to the cryo
holder in a workstation, and the shutter on the cryo holder is closed to prevent
contamination of the sample. The workstation is cooled with LN2 , and all operations take place under cold boil-off nitrogen gas. For transfer of the sample
holder into the vacuum chamber, an airlock is used. The cryo holder is removed
from the workstation and inserted into the airlock, where the area around the
tip is immediately pumped down. During pumpdown, the sample temperature
is monitored. After few minutes of prepumping, a gate valve to the main chamber is opened, the cryo holder inserted onto the socket on the scanning stage
and secured with the locknut to the airlock. If the FZP, OSA and detector are
aligned, the shutter can be opened and experiments with the sample can begin.
Development of a Cryo Scanning Transmission X-Ray Microscope
3.2
Measurements and First Images of Biological Samples
3u
A
I - 41
1u
B
Fig. 3. Ge test pattern, imaged with a zone plate of drN = 60 nm, D = 160 µm. Figure 3A shows good orthogonality and linearity of the scanning stage. Figure 3B shows
the central part of the test pattern. Periodic lines and spaces as small as 40–50 nm can
be detected, corresponding well to the frequency cutoff of the zone plate used.
The cryo-STXM was commissioned in May and June 1996, and experiments
resumed after completion of the upgrade of the X1A beamline. Most of our
beam time was dedicated to testing general functions such as vacuum issues,
alignment and sample transfer, and to characterize the cryo-STXM mechanically
using a test pattern. However, we have been able to take some first images of
plunge-cooled biological specimens as well.
All experiments were performed at a wavelength of λ = 2.4 nm. We used a
zone plate of germanium with a diameter of 160 µm and an outermost zone width
of 60 nm, corresponding to a focal length of 4 mm at λ = 2.4 nm. This reduced
the risk of mechanically damaging sensitive components during commissioning,
and helped to ease the alignment of the optical components. The zone plate
was made by S. Spector using electron beam lithography and a tri-layer etching
process [18]. The exit slits of the new X1A beamline were set to 20 µm in the
vertical direction and 25 µm in the horizontal, corresponding to a product of
zone plate diameter D and full angular acceptance θ of D · θ ≈ 0.5 λ · rad,
providing spatially coherent illumination of the zone plate.
Figure 3 shows images of a test pattern which was also made by S. Spector.
A full view of the test pattern, Fig. 3A, demonstrates that the scanning stage
is orthogonal and linear. Figure 3B is taken from the central region of the test
pattern at a higher resolution (step size: 25 nm). We can detect periodic lines
and spaces of around 40–50 nm, which corresponds well to the frequency cutoff
at of 1/0.06µm for the zone plate used. The test pattern is made of 180 nm thick
Germanium, the low contrast of this object at λ = 2.4 nm being the reason for
a relatively high noise level in the image.
To measure thermal drifts, we have cooled the test pattern to 130 K, imaged
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J. Maser et al.
it repeatedly over the course of one hour and recorded the change of position over
time. We have found an average drift of around 1.3 nm/sec, with a maximum of
2.5 nm/sec. This corresponds to a shift of few pixels per total image. Since the
image is recorded in a serial fashion, drifts of this magnitude have no effect on
the resolution, and an acceptably small effect on the linearity of the image.
199u
A
C
4u
B
8 µm 15mar015.eps
Fig. 4. First images taken with the
cryo-STXM of biological samples. Figure 4A is taken with the coarse scanning stage from a 1 mm × 1 mm area
of the sample. Figure 4B and Fig. 4C
are taken taken with the fine scanning
stage with a step size of 100 nm. Figure 4B shows an image of a frozen hydrated V79 fibroblast (Chinese hamster
lung), Fig. 4C an image of a frozen hydrated 3T3 fibroblast (Fig. 4C). Both
samples were imaged at a temperature
of 110 K.
In Fig. 4, some images of plunge-cooled biological specimens are shown. All
images were taken at a wavelength of λ = 2.4 nm, with the sample at a temperature of around 110 K. Figure 4A shows an image taken with the coarse scanning
stage of a large area of the grid with the samples. This allows us to get an
overview of the whole sample grid, and to select specific areas for further study.
Figure 4B and Fig. 4C show images of frozen hydrated specimens. The samples by plunging into liquid ethane, without prior fixation or other treatment.
Figure 4B is taken of a frozen hydrated fibroblast (transformed V79 fibroblast
cell from Chinese hamster lung). Figure 4C is taken of a frozen hydrated 3T3
fibroblast. Both samples show good preservation of structural features.
As can be seen from these first experiments with sample preparation, blotting
of the specimen prior to plunging allows us to easily obtain an ice thickness of a
Development of a Cryo Scanning Transmission X-Ray Microscope
I - 43
few micrometer, as required for imaging with soft X-rays. Also, use of both the
coarse and the fine scanning stage allows previewing of the whole sample at low
dose (Fig. 4A) for selection of different areas of interest, and subsequent imaging
of the selected sample areas at higher resolution (Fig. 4B, C).
4
Conclusions and Outlook
We have developed and are commissioning a cryo Scanning Transmission X-Ray
Microscope. This system is capable of imaging specimens of a thickness of several micrometers at a temperature of around 110 K. The temperature is stable
to ±0.5 ◦ C. The sample is kept in a vacuum of 10−7 torr or better, allowing good
control of thermal drifts and of contamination, and full use of the water window spectral range for imaging and spectroscopic measurements. An airlock on
the vacuum chamber allows a sample exchange within few minutes. The sample
temperature is monitored and can be raised in a controlled way with a built-in
heater to well above room temperature. The computer control of the system
records data from up to 8 analog and 8 digital channels which allows the use
of configured detectors, e.g., and recording of the temperature of the sample
and other parts of the microscope. An optical microscope with infinity-corrected
lenses for previewing of the sample and prefocusing of zone plate and OSA is
installed.
The first tests of the cryo-STXM show good orthogonality of the fine scanning stage. In coarse scanning mode, a field of up to several millimeters can be
imaged, whereas the fine scanning mode allows a mechanical resolution of 20 nm
or better. Alignment and focusing procedures have been successfully tested, and
first test of the spatial resolution were done using a zone plate with an outermost zone width of 60 nm. We were able to detect periodic lines and spaces of
40 nm–50 nm in a test pattern, corresponding well to the exptected frequency
cut-off of the zone plate. Thermal drifts were measured to be on the order of
around 1.3 nm/s which is small enough not to distort the image or reduce the
resolution. We have obtained first images of frozen hydrated specimens.
We plan to pursue two lines of work in the near future. The first is dedicated to fully characterizing the cryo-STXM mechanically and optically, and to
improving some of the components. This involves installing an avalanche photodiode with active quenching circuit as an X-ray detector, and implementing
a rotary motion on the airlock to allow recording of tomographic data sets. We
also want to reduce the rate of thermal drifts further. The experimental program
will focus at first on taking 2D images of frozen hydrated objects, on improving the sample preparation protocol, and on determining the radiation hardness
of biological cryo-objects. We also plan to perform spectromicroscopy on those
samples. One application is to take spectra of samples with vitrified and samples
with crystalline ice at the oxygen absorption edge with the intention of using
differences in the spectra to help determine the degree of crystallinity of frozen
hydrated samples. After installing the rotation mechanism, we will also start
experimenting with tomography.
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J. Maser et al.
Acknowledgments
We want to thank Sue Wirick for her continuous help at X1A. This work was
supported by the Office of Health and Environmental Research, Department of
Energy, under contract FG02-89ER60858, by the National Science Foundation
with Presidential Faculty Fellow award RCD-9253618 (CJ), and by the Alexander von Humboldt Foundation through a Feodor Lynen Fellowship (JM). The
experiments were performed at the NSLS which is supported by the Department
of Energy.
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