Where are all the TEM Applications?

If you have anything to do with the field of computer software, you know that there have been monumental changes in the accessibility to developers over the last 10 years.  When I started doing commercial programming almost 20 years ago, your choices were limited.  There were only a few compilers, they were fairly expensive, difficult to use, and they still always seemed to be missing important things that you needed.  I’m not exaggerating that there was a several month learning curve to do anything useful.

These barriers don’t exist any more, at least not in the web world.  The number of tools, languages and IDE’s, most of which are free, has led to thousands, if not millions of applications available, again mostly for free.  But there must be some kind of barrier remaining in the TEM world, because I don’t see very many new applications having come out in the approximately 5 years I’ve been “out” of TEM.  So I feel the need to ask the question:

Where are all the TEM Applications from the last 5 years?

I should first describe what I mean by a “TEM Application”.  To me a TEM application is anything that improves the efficiency or simplicity of running the instrument and/or manipulating your data from the instrument.  This doesn’t include the basic software that runs the instrument and its detectors, like Gatan’s Digital Micrograph, or EDAX’s Genesis, or FEI’s Tecnai/TIA, which I refer to as “platforms”, because they provide basic functionality (although it may be fairly high level) through manual operation.  Applications generally involve some level of automation – doing with software what you would normally do manually – and/or integration – giving access through a single interface what is otherwise done through several interfaces.

So what applications are out there?  Here’s what I found from commercial vendors that I would classify as “TEM applications” and not just functionality of their standard system:

• Gatan:  About 10 applications written for Digital Micrograph, including TEM AutoTune, Digital Montage, HoloWorks and EELS Advisor.
• Thermo Scientific:  COMPASS (Multivariate Statistical Analysis),  XPhase Compositional Analysis, Spectral Match, EDS Feature Sizing.
• Oxford Instruments:  INCAEnergy TEM phasemap, spectrum matching and Cameo+
• Olympus Soft Imaging Solutions:  8 iTEM Solutions, including strain analysis with CBED, diffraction analysis and Virology.
• FEI:  Inspect3D and Explore3D, electron tomography acquisition and reconstruction.
• JEOL:  TEMography 3-D acquisition, reconstruction and visualization software, JEOL Automated Data Acquisition System (Jadas) and JEOL Archive Management System (Jams).

Additionally, there are several applications available which were developed in the academic community:

• SerialEM – tomography tilt series acquisition from the Univ. of Colorado.
• Leginon – automated acquisition of TEM images from the Scripps Research Institute.
• NCMIR – National Center for Microscopy and Imaging Research has a number of applications for biological imaging, including a number developed at various research centers around the country.

There are also a number of small, highly-specialized (any often very old) applications available at a number of government labs:

• National Institute of Standards and Technology
• Argonne National Laboratory

Beyond that, I’ve only found a few small, usually very limited distribution apps done in individual labs.  Of course I’m sure I forgot about or missed some, so if you have or know of other significant applications, please let me know about them by posting a comment.

Many of the above apps already existed 5 years ago, and most of the new ones are centered around electron tomography.  I don’t see much new out there in other areas like spectroscopy, lattice imaging, automation/productivity, database archiving, etc.   I have a hard time believing that TEM users out there aren’t doing anything but tomography, and that they don’t need significant new software to help them with their work.

When I effectively left the field 5 years ago, there was huge promise for applications.  Microscopes were just getting stable, advanced, open software interfaces (Tecnai and FasTEM), and there were a number of equally suitable platforms for application development (Digital Micrograph, TIA and iTEM).  Based on our intentions at the time with Emispec, and based on what we heard from other manufacturers and from customers, we expected to see a flood of new application come out.

So what happened?  Well, my guess is that major hardware developments, including FEI’s Titan, JEOL’s in-column filter and FIB’s, silicon drift EDX detectors and new CCD cameras took so much development to get to the market that applications development was put on the back burner.  Unfortunately, I don’t see much effort to move applications to the front burner, but if I have anything to say about it, we’re going to cook up lots of new applications now that we’re back in the TEM game.