Running Digital Micrograph on Linux or Mac OSX

As recently published in March 2012 issue of Microscopy Today,  It is possible to run Digital Micrograph without any virtualization software on Linux or Mac OSX.  The guide is freely available directly from the Microscopy Today website. The introduction of the article reads:

"Digital Micrograph (DM), the core software of Gatan’s Microscopy suite, is considered an industry standard among microscopists. The offline DM application is freely available from Gatan [1]. Unfortunately, DM software has been designed to run only on Microsoft Windows operating systems, thus distancing the microscopy community from popular Unix based systems such as Linux or Mac OSX. An ad hoc solution to this problem has required a virtualized Windows operating system running on top of the users native operating system. This is not only slow, having to emulate each processor instruction, but also requires installation and licensing of Windows and the virtualization software. However, with the aid of open source resources, it is possible to run DM natively on Linux and Mac OSX (Figure 1). This article was written as a guide with easy- to-follow installation instructions to liberate users from the Windows emulation pidgeonhole and enable them to freely analyze data on Unix based systems. 

Running Digital Micrograph (32-bit) on Linux and Mac OSX is accomplished with the use of Wine, an open source application that allows Unix-like operating systems to execute programs written for Microsoft Windows. Wine provides a compatibility layer that allows Windows system calls to be run on a substitute operating system. As stated by internal Wine admins, “You can start your Windows application straight from your regular desktop environment, place that application's window side by side with native applications, copy/paste from one to the other, and run it all at full speed” [2]. After installing Wine and the necessary Microsoft components, DM runs readily on Linux or OSX. The software has been tested using the offline DM V2.01 demo provided by Gatan."

Accessing Journals in Papers2 via Cornell Proxy

Papers2 is a fairly nice way to manage your scientific articles. At least nice enough for me to purchase, although I am not convinced it is vastly superior to the cross-platform alternatives like Zotero and Mendeley. Nonetheless, it has become my software of choice for the moment.

My library institution is Cornell University and accessing articles off campus requires circumventing the pay-wall via a proxy. I spent the time figuring out how to do this from within Papers via the Cornell proxy. Unfortunately, this guide will reach a small audience and may be redundant with information already on the internet - however, I would have found it very useful two hours ago.

So, to get Papers2 setup for the Cornell system,

go to: File -> Preferences

Then select the "Access" menu:

Select Cornell University from the dropdown menu:

Lastly, and most importantly, you will need to specify Cornell's proxy in the region circled below:

In the circled region put: http://proxy.library.cornell.edu

You will now be able to access MOST journal services and articles. Note that Web of Science will probably not work, so you will need to locate your journals through other services such as Google Scholar, PubMed, IEEExplore, etc.

Rotating a Figure or Plot in Matlab

So, if you would like to rotate / invert a figure or plot in Matlab by 90 degrees or by any other specified amount, it is very easy. Simply use:

>> view(90,90)

...and you can go from this:


...to this:


Normally I would not post such a simple tutorial on my blog, however I wasted over a half an hour trying to find out this simple solution. After sifting through a multitude of poor documentation, blog posts, and forum threads, I ended up figuring it out on my own. I would like to say that there are many other ways to achieve this, and I was aware of most of them. I just wanted to know the easiest way and now hopefully the internet finds this useful as well.

A New Equals Sign - Dot Equals

I think that mathematics could use a new commonly used character to describe certain types of equalities. Typically, the equals sign, = , is used to denote the equality of two quantities. A simple example of this would be



A lot of times, algebraic manipulations of expressions are made and the equals sign is also used. An example of this would be:



In this latter example, I think a unique equality character should be used to distinguish equalities made solely from mathematical manipulation.

So I propose the following a dot equals to denote equalities made solely from mathematical manipulation or evaluation. A simple example being:



Or




Although this symbol is available in unicode and Latex, if the character does not exist an equal with a period ( .= ) could be used. I must note that I have seen this to denote "in the limit of". I do not think this is a common use, and as an alternative a dot underneath the equals sign could be used or anything else similar to an equals sign. This symbol and many others exist in Unicode or Latex. For inspiration, check out all of the unicode symbols here.

MIT Photonic Bands (MPB) on Cygwin

MIT Photonic Bands (MPB) on Cygwin
how to run MPB on windows
-Robert Hovden, Jul 30 2008

[View PDF]

This is a quick rundown / summary of what I did to compile and install MPB using Cygwin on my Windows Vista machine. There are many dependencies and libraries that are needed to get MPB up and running. It is not comprehensive but at the very least, this should save you some time.

Installing Cygwin

Cygwin is a Linux-like environment for Windows which can be used to run software written for Linux distributions. After downloading Cygwin and running setup.exe you will be prompted with a couple hundred optional packages to install. You will need many of these packages to run MPB, let’s go through what dependencies can be installed using setup.exe.

gcc : C compiler
> Devel
gcc-g++: C++ compiler
> Devel
gcc-g77: Fortran compiler
> Devel
gettext: GNU Internationalization development utilities
> Devel
guile: The GNU extension language and Scheme interpreter – executables
> Interpreters
guile-devel: The GNU extension language and Scheme interpreter – development
> Libs
hdf5: HDF5 Hierarchical Data Format
> Utils
lapack: Comprehensive FORTRAN library for linear algebra operations.
> Math
libhdf5-devel: HDF5 Hierarchical Data Format – (development)
> Utils
libgmp-devel: Development library for GMP arbitrary precision arithmetic library
> Libs
libiconv: GNU character set conversion library and utilities
> Libs
libtool: A shared library generation tool
> Devel
make: The GNU version of the ‘make’ utility
> Devel
 

FFTW 2.1.5

FFTW version 3 is available through the cygwin setup but you will need version 2 which must be downloaded and compiled. Versions 2 and 3 will not conflict if both are simultaneously installed on your machine.

LIBCTL

Libctl is written by the authors of MPB and it can be found on their website. This must be compiled and installed.

MPB

With all of the above dependencies you should have enough to compile, install, and run MPB. Note that in order to install MPB using Windows Vista you will have to run cygwin as an administrator.