Here are a number of the additions to the Electron Microscopy Center (EMC) that have been discussed since the facility officially began. Some have yet to be started (marked as Open), some are true works-in-progress (marked as On-going) and others have been fully accomplished (marked as Done).
NOTE: This is an accordion with expandable folds. Click on a fold to expand it. Each item has a "Status" line and a detailed description of what the EMC has done. Finished items will have links to other pages in our website. The first time you visit this page, all the lists will be collapsed. You can collapse and expand the different items and leave them in mixed states. All expanded entries will still be expanded the next time you visit this page within a single web browser session. However, if you reload the page or revisit it after closing your browser, all the lists will again be collapsed.
In the spring of 2017, the EMC received an IU Research Equipment Fund (REF) grant for the purchase of a Fischione model 1070 NanoClean Ar/O plasma cleaner. The plasma cleaner can be used to burn away contaminating hydrocarbons both from all our specimen holders and from actual specimens that contaminate badly while examining with TEM and/or STEM. Cleaning the holder is especially important when using the Poseidon liquid cell holder. Included in the plasma cleaner purchase was a model 9020 vacuum pumping station for maintaining up to five specimen holders under vacuum. The pumping station replaces the Gatan model 655 Dry Pumping Station in the Simon Hall EM area and allows us to move that system to the Myers Hall EM area where it can be used in conjuction with the JEOL JEM 1400plus.
Several groups have developed tools that allow modern electron microscopes to collect image data in an automated fashion. Leginon has been developed by Bridget Carragher, Clint Potter and others in the National Resource for Automated Molecular Microscopy (NRAMM) based at the Simons Electron Microscopy Center (formerly known as the New York Structural Biology Center) and is primarily designed to interact with FEI electron microscopes. However, there are several ports of the software to JEOL instruments similar to our 3200FS and we hope that Clint and Bridget will begin to support JEOL instruments more fully. We are exploring the possibility of installing Leginon here, but nothing concrete is being done before there are assurances of long-term support from the NRAMM group.
More recently, the JADAS project (a collaboration between Wah Chiu at NCMI and JEOL USA) has been developed specifically for JEOL instruments. This is a commercial product and we would need to find the funds to purchase it if we were to decide to go that route.
It is also possible to use the tomography data collection program serialEM to do automated data collection. We already have serialEM running on both the JEOL JEM 3200FS and 1400plus, and using it for automated data collection is simply a matter of obtaining (or writing) and testing the appropriate scripts. We expect to have this running sometime during the summer of 2017.
We hope to revive a Balzers BAF 400D which has been in storage for many years. The last time this device worked was more than fifteen years ago. It was almost revived around 2007 or 2008, but was returned to storage before the final testing of repairs was accomplished.
The Electron Microscopy Center is in the process of amassing many common TEM/SEM supplies and consumables for resale to users. The intent is to make working in the EMC as simple as possible, including obtaining some of the items specific for EM work. The EMC currently has certain commonly used items for resale to users. The EMC is also considering making reagents for freeze-substitution available at cost to users. If you have suggestions for additional items, please let the EMC staff know.
In August and September of 2015, the EMC tested a Direct Electron DE-12 (a 3k by 4k sensor) on our JEOL JEM 3200FS. We also did demonstrations of a DE-20 (a 4k by 5k sensor) on a JEOL microscope with Kristen Parent at Michigan State University and Gatan's K2 Summitt on a Krios in the Cryo-EM Facility at Purdue University. After these demos, the EMC wrote several grant proposals for the purchase of a DED. With the help of Craig Pikaard in the Biology Department, the EMC received an equipment grant from the Howard Hughes Medical Institute (HHMI) for the purchase of a DE-64 (an 8k x 8k sensor). The DE-64 was installed in the spring of 2017.
Part of the equipment package that allowed us to purchase the JEOL JEM 1400plus also allowed us to upgrade the EDX system on the JEOL JEM 3200FS. Installation of the detector was slowed by the need for a different cryo-fin for the 3200FS that would accomodate the much larger EDX detector, but in the summer of 2017, we replaced the existing system (an Oxford INCAx-sight detector) with an Oxford AZtek X-MaxN 100-TLE system. This windowless silicon drift detector (SDD) is more sensitive and faster than the previous detector and does not need to be filled with liquid nitrogen every few days.
We have both a Wohlwend HPF Compact 2 high pressure freezer and a Leica EM AFS-2 freeze substitution machine. These machines are currently available for use and both the staff of the Electron Microscopy Center and several research groups are beginning to understand how best to use them. We hope to have additional information about these devices on the website in the near future. At this time, we are not charging for the use of this equipment (but we are charging for the liquid nitrogen required to cool the machines). The EMC keeps various consumables needed for this work on hand (and is also considering making reagents for freeze-substitution available). Such consumables are available for resale at cost to users.
The Leginon automated data acquisition system described briefly elsewhere automatically creates an image database that can be used to examine the images and help track microscope parameters used for image acquisition. An "add-on" to Leginon called Appion marries this database structure to an image processing pipeline, where the user interacts with the pipeline using any web browser. If we are able to get Leginon running smoothly here (and this depends on whether the group at NRAMM supports the use of Leginon on JEOL microscopes), the next step would be to add the data processing pipeline.
It would be theoretically possible to implement Appion independently of Leginon, but that involves creation of an image database that reproduces what Leginon creates automatically. This second option is not currently under consideration by the Electron Microscopy Center (EMC), but if users think this option might be useful, please contact the EMC staff.
Another possibility would be an OMERO database for images recorded using the EMC's electron microscopes. This would give users access to all the tools contained in imageJ and would greatly simplify some things normally done with images recorded using the JEOL JEM 1010, JEOL JEM 1400plus and JEOL JEM 3200FS. While this approach does not lead into the sort of intensive image processing required for most cryoEM images recorded using the 3200FS, it would still be a significant step forward. Again, the EMC is not currently considering this option, but would do so if there is enough user interest.
Our twenty year old 100 kV JEOL JEM 1010 is a very useful and robust TEM for routine work at moderate resolution. However, it is old and it will eventually become impossible to maintain its service contract. Both in anticipation of this eventuality and in the expectation that the EMC will need more total imaging capability in the near future, we have worked for several years to obtain an additional low voltage TEM. After a number of grant submission cycles that did not yield positive results, the EMC obtained a block of money through the IU College of Arts and Sciences to "improve electron microscopy on the IU Bloomington campus." This was used for the purchase of a new electron microscope, several new specimen holders, an upgrade to the EDX system on the JEOL JEM 3200FS and an accessory for the 3200FS that allows us to collect brigth field and high angle annular dark field STEM images simultaneously.
After discussions with several TEM vendors, the EMC decided to purchase a JEOL JEM 1400plus equiped with a Gatan OneView camera and an Oxford AZtek X-MaxN 65-T EDX detector. The advantage that this instrument had over other vendors is that it can be used with any of the existing specimen holders for the JEOL JEM 3200FS (and any of the new specimen holders that we purchase for the 1400plus can also be used with the 3200FS). In addition, the EMC receives a service contract discount based on the number of JEOL instrument we have under service, and the additional discount from having a third JEOL microscope makes it difficult to switch vendors.
The 1400plus was installed starting in January, 2017. It did take a while to sort out various issues with the OneView camera and overall instrument performance, but we are happy with the decision to purchase this instrument.
Another part of the package for the JEOL JEM 1400plus allowed the purchase of a liquid cell holder. Our decision to purchase the Poseidon Select (the latest model from ProtoChips) was driven by three factors: ProtoChips has demonstrated several versions of their liquid cell holders using our JEOL JEM 3200FS, members of the Sara Skrabalak group have used an early model Poseidon holder at Oak Ridge National Laboratory several times and Xingchen Ye, our newest materials science faculty member, had extensive experience with a Poseidon from his time at UC Berkeley. The Poseidon Select uses the same platform for all their liquid cell applications (2-port or 3-port flow, heating and electrochemistry) and we purchased the accessories necessary for 3-port flow and heating. The liquid cell technology is new enough that no-one really knows what can be done with it, and we hope to explore numerous biological and materials science applications. The Poseidon Select is now available for use, though it requires significant training.
Another part of the package for the JEOL JEM 1400plus allowed the purchase of a single tilt beryllium holder that can be used with both the 1400plus and the JEOL JEM 3200FS. Beryllium specimen holders are used when a low background signal is needed for EDX work, and the only beryllium holder the EMC has had until this purchase was a dual tilt holder. That holder can be difficult to load and is prone to damage, and the EMC had been interested in a single tilt beryllium holder for several years. The new Single Tilt Beryllium holder is now available for use.
An ongoing collaboration between David Morgan here at IUB, Jacob Brink with JEOL USA and David Mastronarde from the Boulder Laboratory for 3-D Electron Microscopy of Cells resulted in new releases of the tomography data collection program serialEM which support STEM tomography (spring, 2011). We are working to develop STEM imaging conditions that will be more useful for biological applications and refining our ability to record tomographic data from a variety of materials science samples. Contact David for more information about STEM tomography.
Since we have not been able to make much progress installing Leginon and Appion, we continue to explore ways to make image browsing and analysis easier. Our rappture-based Graphic User Interfaces (GUI's) that collect information for image processing jobs that run on the Indiana University computer center clusters are one such attempt to make dealing with EM data processing more user friendly.
The Electron Microscopy Center has been working with several staff members from the Scientific Applications and Performance Tuning group within the IU Pervasive Technology Institute on the creation of a scientific portal (aka, scientific gateway) that would allow easy access to images recorded using our microscopes. This portal is an off-shoot of the One Degree Imager - Pipeline, Portal and Archive (ODI-PPA) project which was designed to give researchers around the world access to images recorded using a new instrument at the Kitt Peak National Observatory. The portal for EM images initially allows users to browse their data using any web-browser and to search through images based on a variety of tag words. The portal also includes some simple tools for image exploration and processing (e.g., measurement tools and a variety of image filtering and display options). We hope eventually to include some of the initial steps for cryoTEM single particle image processing and three-dimensional reconstruction. If this overall concept proves useful, we hope to extend the portal to images acquired using the FEI Teneo. Here are the official plan for this portal and an official description of the project. The EMC maintains updates on the status of this project.
aberration corrected TEM for materials science
dedicated cryo-TEM for structural biology
dedicated glow discharge apparatus
electro-chemistry upgrade to Poseidon liquid cell holder
in situ heating specimen holder
combining all the EMC equipment into a single location