Warning: Under construction!
Our JEOL JEM 3200FS transmission electron microscope (TEM) is an intermediate voltage (300 kV) electron microscope similar to the one shown in this image from the JEOL USA website. This electron microscope uses a thermal field emission gun (FEG) as its electron source, providing an extremely bright and coherent beam of electrons for use in imaging and analysis.
The 3200FS installed in Simon Hall during the last half of 2008 is equipped with an in-column energy filter and a Gatan UltraScan 4000 CCD camera. Note that the 3200FS is a different instrument from the JEOL JEM 3200FSC, which is the liquid helium cooled 300 kV TEM found in cryoEM facilities such the New York Structural Biology Center (NYSBC) and the National Center for Macromolecular Imaging (NCMI).
In addition to the TEM capabilities of the 3200FS, our instrument is also equipped with scan coils and detectors that allow it to function as a scanning transmission electron microscope (STEM). The dual capabilities of TEM and STEM makes such instruments significantly different from dedicated STEM machines like the Hitachi HD2700C or the VG HB501, and the designation (S)TEM or S/TEM is sometimes used to indicate that an instrument is capable of both STEM and TEM imaging.
In terms of physical appearance, the greatest differences between the instrument show here and our 3200FS are the presence of an Oxford EDS detector high on the right side of the column and a TV monitor to the left of the column for the TV rate camera located below the bottom-mount Gatan CCD camera. In addition, we have a pair of equal-sized computer monitors (instead of the smaller and larger ones shown above) connected to a PC that is in turn connected to the 3200FS's microprocessor.
In addition to the PC driving these monitors, there is a second (dual-monitor) PC connected to the Gatan UltraScan 4000 CCD camera and to DigiScan (Gatan's STEM control unit), and a third PC connected to the Oxford EDS detector. These PCs and their monitors are housed in a unit to the immediate right of the 3200FS and within easy reach of the operator. This bank of monitors is controlled by either the keyboard and mouse on the console of the 3200FS or the additional keyboard and mouse on this second desktop.
Field Emission Gun (FEG):
Transmission Electron Microscopy (TEM) Imaging:
Gatan UltraScan 4000 CCD Camera:
The 3200FS has a 4k x 4k Gatan UltraScan 4000 CCD camera mounted below the camera chamber. This camera has a dynamic range of 16-bits and utlizes 15 micrometer pixels with a 4 port readout. The multi-port readout makes it possible to record a full 4k x 4k image within 10-12 s (i.e., approaching the ease and speed of recording onto film), meaning that more time is spent examining the specimen and adjusting imaging conditions while less time is spent actually recording the images.
We have not explicitly determined either the modulation transfer function (MTF) or detector quantum efficiency (DQE) of this camera, but the images shown here demonstrate that there is considerable signal near the Nyquist frequency in 4k x 4k images recorded using the UltraScan camera.
In-column Energy Filter (aka "Omega Filter"):
Energy filters for EFTEM and EELS can be placed in two fundamentally different locations along the electron optics of any given electron microscope:
post-column energy filters: In this arrangement, the energy filter is below the specimen viewing chamber (if present) and below the cameras normally associated with a conventional TEM (i.e., the plate camera and most slow scan CCD devices). The Gatan Imaging Filter (GIF) is the most commonly encountered such device. The normal arrangement of a post-column filter is to bend the electron beam through 90° well below the normal film plane and to place the energy filter and its detectors along a vector running parallel to the floor and exiting the back of the electron microscope.
When a post-column filter is used, there is an appreciable "post-film plane" magnification factor (on the order of 10-15x) due to the additional path length through the energy filter and its detectors. Because of this additional path length, it can be difficult to record images that are identical except for the use of the filter (i.e., images that differ only by the wavelengths of the imaging electrons).
in-column energy filters: In this arrangement, the energy filter is below the specimen but above the viewing chamber and above the usual cameras. Such filters are often referred to as "omega filters" due to the path that the electron beam must follow as it passes through the filter.
The electron beam always passes through the in-column energy filter and "energy filtering" occurs only when a slit is inserted into the beam path. Because there is no additional path length when the slit is inserted, in-column energy filters make it extremely easy to record images that are identical except for the use of the filter.
On the other hand, because the electron beam always passes through the energy filter, any image degradation caused by the lenses in the energy filter will occur all the time.
The 3200FS uses an in-column filter that can be controlled either by TEMcon (JEOL's software that talks directly to the 3200FS) or by DigitalMicrograph (Gatan's software that talks to the microscope and to the various detectors attached to it). In addition to the software control for the detailed behaviour of the energy filter, there are several knobs and buttons on the left-hand knobset that control some fundamental aspects of the filter (i.e., whether the slit is inserted or not, the applied energy offset, etc.).
This ~30 cm long in-column filter is located just above the specimen chamber and is the main reason that the airlock for introducing specimens into the column of the 3200FS is more than 2 meters from the floor!
Electron Energy Loss Spectroscopy (EELS):
Scanning Transmission Electron Microscope (STEM) Imaging:
Energy Dispersive X-Ray Spectroscopy (aka EDS, EDX or EDXS):
STEM combined with EELS or EDS:
Computers associated with the 3200FS:
As mentioned above and in several additional places on these web pages, the 3200FS is connected to a number of computers. The microscope itself has a microprocessor (referred to as the "VME") that controls its hardware (high tension, vacuum system, stage, apertures, etc.). This layer of computing is mostly invisible to the user, though there are certain occasions and conditions where it is important to understand that it exists and to make sure it is functioning properly.
There are three PCs which make up the conventional "user interface" to the 3200FS (and it's cameras/detectors) and two additional PCs that add functionality to the 3200FS and its computers. The diagram to the right shows how these computers are connected and highlights the fact that the only "internet connection" to the 3200FS is a dedicated line running from the 3200FS to the JEOL PC (described immediately below).
- JEOL PC: The JEOL PC (aka, the TEMcon PC) supports TEMcon (the user interface that controls the 3200FS), TEMserver (the communication agent that connects TEMcon to the microprocessor in the 3200FS), and JEOL's SimpleImageViewer (a program that controls the STEM detectors and displays the BF-STEM or HAADF-STEM images that the detectors acquire). Many of the microscope features are normally controlled via TEMcon (instead of the knobsets on the microscopes console) and all the information that a user needs (magnification, spot size, defocus, accelerating voltage, energy filter state, lens and deflector currents, etc.) are displayed for the user to see via TEMcon. This PC has two network cards, one that connects the PC to the microprocessor in the microscope and a second that connects the PC to the outer world (in our case, to the IU Bloomington network, but not to the world in general). This arrangement means that the microscope itself is isolated from everything except this particular PC.
- Gatan PC: The Gatan PC is physically connected to the UltraScan CCD camera and to DigiScan (Gatan's STEM control unit). It is networked to the PC that controls the Oxford EDS detector and to the JEOL PC. There is also a photo quality printer connected directly to the Gatan PC. The Gatan PC is the platform for both DigitalMicrograph (DM) (Gatan's user interface to virtually everything) and serialEM (the tomography data acquisition software from the Boulder Laboratory for 3-D Electron Microscopy of Cells). Both DM and serialEM can control the 3200FS, and DM can additionally control the Oxford EDS detector. In addition to the "permanent" and necssary network connections to the PCs in the microscope room, the Gatan PC has a similar required connection to a Linux PC (described below) in the room that houses the Vitrobot Mk3. The Gatan PC is connected via its single network card to the IU Bloomington network, and it is this network connection that allows the Gatan PC to communicate with the other computers.
- Oxford PC: The Oxford PC is directly connected to the Oxford EDS detector and networked to both the JEOL and Gatan PCs. In addition, the Oxford PC is directly connected to a small color document printer. This PC is also connected via its single network card to the IU Bloomington network.
Note: Because of all these interconnections between the PCs, the various cameras and detectors and the 3200FS itself, please do not attempt to reboot any of these machines. If you think that is necessary, please contact the director.
In addition to the three PCs that are in the room with the 3200FS, there are two other PCs involved in the daily operations of the 3200FS:
- Linux PC: The Linux PC is located in the room (032B) that holds the Vitrobot Mk3. The primary function of this PC is that it has the Lustre filesystem of the WAN area of the IU Data Capacitor directly mounted on it across the campus network. In this configuration, we are then able to put that same Lustre filesystem onto the Gatan PC as a "networked drive" (which appears as a single >400 TByte disk). This in turn allows the Gatan PC to save images and spectra directly to the Data Capacitor (which is the major reason every user of the 3200FS needs a computer account on Quarry). In addition, this PC has many of the image processing programs needed for data analysis installed on it (though it is not powerful enough to be a computational workhorse). Finally, the Linux PC is the only machine where USB devices can be used to download images and spectra.
- Sirius PC: The Sirius PC is currently located in the office of the director. The name "Sirius" derives from JEOL's "Sirius remote operation software" which allows a user with network access to the PCs that control the 3200FS to control all aspects of the microscope. The Sirius installation includes a partial knobset for microscope control and a track-ball for stage movement that are directly connected to the Sirius PC. These control devices and the software itself give a remote user access to anything the 3200FS can do (with the obvious exception of something like physical insertion of a specimen into the microscope). Because the JEOL, Gatan and Oxford PCs are available to the IU Bloomington campus network, it would be possible to move the Sirius PC to any location on the campus and to operate the 3200FS from there. If there are sufficient reasons to do so, we would also be able to make the JEOL, Gatan and Oxford PCs accessible from anywhere in the world and to operate the 3200FS from this Sirius PC (or a similarly enabled PC) anyplace with a (fast enough) network connection.
