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.

The forest for the trees

As you might have guessed from reading JK’s recap of the last few years, the progression through the chain of Emispec, FEI and Enoetic that has now led to AppFive has been a pretty wild ride.  I was a fairly public face of Emispec — if you received either ES Vision field service or a demo, there’s a good chance we met personally — so I should chime in as well.

As JK indicated, everyone at Emispec was very much forward-looking.  We’re looking to renew that vision in AppFive, with a focus on developing software applications.  Yes, we put great effort into designing good architectures and platforms, but what got all of us excited at the end of the day was making programs that manifested themselves in the physical world — whether that was through automation of the column and its associated detectors, analyzing experimental data to reveal new insights, or relieving users of some microscopy workflow tedium.

Times have changed since the Emispec days, and pulling back from the microscopy world for a few years to work as Enoetic was the “forest for the trees” moment that made this crystal clear.  From end-users to programmers, what people expect from software has changed.  If nothing else, the web’s collaborative-mashup culture has introduced the concept of “reuse through interaction” as opposed to “reuse through inheritance.”  That’s significant.

Now I’m not advocating a Facebook or even a web-application for EM, but what I am saying is that AppFive is excited about helping our customers:

• Break their big jobs into smaller tasks
• Picking the best tools to get those tasks done
  • The best tools might be software applications you’re already using
  • Or we can make custom software for you
• Unifying any disparate tools into a single experience

So even if you don’t need all-new, custom software — if you’ve ever been sitting in front of your computer working on a microscopy experiment or analysis and wished your software worked a little differently — we want to hear from you.