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It is common knowledge that neuroscience -- particularly experimental neuroscience -- uses MATLAB more than any other programming language. I have always just taken this as a given, and pointed to existing toolboxes, legacy lab codebases, and social pressure as the reasons why this continues to be the case, even though concrete reasons to switch are widely known.

I want to go past these general reasons and pin down the exact causes of MATLAB's stronghold in Neuroscience. Things like

  • file formats that can only be read in MATLAB
  • acquisition systems that are highly coupled to MATLAB
  • toolboxes that are widely regarded as the "gold standard" for something
  • labs or companies that train many researchers on MATLAB and advocate for it
  • introductory neuroscience programs / textbooks that teach concepts through MATLAB examples

or any other tangible things to point to would be excellent.

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    $\begingroup$ At least for EEG, fMRI and MEG analysis, the dominant toolboxes - SPM, EEGLAB, Fieldtrip - are all MATLAB-based. These toolboxes are all dominant most likely because they combine 1. open-source tech, 2. being the first to provide, or at least make accessible, a long range of now gold-standard analysis tools, 3. allowing both basic and advanced analyses. Also, the most typical form of data for multivariate neuroscience stuff is matrices, which the MATrix LABoratory happens to handle adequately. $\endgroup$ – jona Sep 17 '14 at 19:53
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    $\begingroup$ And then, aren't we all praying every day for the adequate Python-based solution to finally arrive?.. $\endgroup$ – jona Sep 17 '14 at 19:53
  • $\begingroup$ @jona Yes, but who'll pay for it? MATLAB toolboxes represent man years of software development. I'd love to see more in Python. $\endgroup$ – James Sep 19 '14 at 10:59
  • $\begingroup$ @James, Many labs are already producing modernized versions of Matlab toolboxes, written in Python. They're certainly years behind, but there's a huge momentum behind Python for both ideological reasons and practical (read: monetary) ones. In short, the answer to your question is "labs are rerouting funds for Matlab licenses towards Python development and supplementing it with grant money." Exhibit A. Exhibit B. $\endgroup$ – blz Sep 25 '14 at 13:39
  • $\begingroup$ @blz Certainly the toolboxes licensed by my employer would have cost many times their fee in development for us to have done that but none the less I am very pleased organisations are doing this. $\endgroup$ – James Sep 26 '14 at 0:35
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I think the major reason is inertia, in the sense that many labs use Matlab, so many Matlab toolboxes are available, so many labs train people in the use of Matlab...

However, as a trained software engineer turned Neuroscientist who has been programming in various languages for close to 30 years, there are several reasons why I actually enjoy using Matlab. One can also make arguments for why it's a good fit for labs filled with people who aren't programmers.

(As an aside, the .mat file format is actually a standard file format called "HDF". So I don't think that file format lock-in is a real reason.)

Things Matlab does well

  1. Very good cross-platform support. Matlab runs out of the box on every major platform. In research, when you want something to just work, spending days getting a python distribution configured with a mutually-compatible set of package versions is just ridiculous. Caveat: I haven't tried anaconda, which hopefully has solved this problem.

  2. Very low housekeeping overhead. No other serious language (is BASIC a serious language?) lets you start writing code without having to include headers, define namespaces, allocate memory... For biologists without programming experience, this is a godsend.

  3. Integrated debugging environment. Non-programmers will not easily be able to learn a language that does not come with an IDE. R, I'm looking at you. Python has very nice options now.

  4. Intrinsic vectorisation of operations. for loops are kind of ugly and error-prone, when what you really want to do is perform an operation on every element of a matrix or perform matrix operations. I know that Python has some add-ins to accomplish matrix operations, but Python itself is not vectorised.

  5. Support for object-oriented software design. As a legacy language, Matlab has a whole bunch of baggage. Mathworks is slowly improving the design of the language and adding other niceties (the parallel computing toolbox is pretty great): the class system; tables with named columns; the ability to ignore return and input arguments in function calls; function handles; namespaces...

  6. Ability to work across machine abstraction levels. Matlab used to be slow, but the JIT compilation works wonders and keeps improving. You can operate at a very high level of abstraction with classes and objects; if you need something fast and low-level, you can write a small amount of C code and call it natively from Matlab.

Things Matlab does badly

  1. Graphics and GUIDE. Oh my god. Handle graphics is pretty horrible. I know they are working on version 2, and it can't come soon enough. matplotlib in Python looks much better, and R makes amazing graphs out of the box. GUIs are pretty ugly to design in any language, but GUIDE makes it very easy to write some really horrible code.

  2. Global namespace. This is sort-of true, and sort-of makes sense for convenience's sake. It's an inherent tradeoff between ease of use and nice encapsulation. Matlab does provide namespace support now, but I think it's still true that the vast majority of toolboxes don't use it.

  3. First-class functions. If the anonymous function system could be upgraded slightly to handle multiple return arguments and to handle currying... Also, intrinsic support for named arguments and parameters would be greatly helpful, especially considering that many Matlab functions accept named parameters as part of their calling syntax.

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  • $\begingroup$ Absence of namespace is is generally considered to be a Very Bad Thing, and forgoing these (small) hurdles is only a win in the most near-sighted sense; it's akin to saying a car without seatbelts is better for novice drivers because remembering to buckle up is a pain in the ass. I would also have placed the OOP support under the heading of "Things Matlab does badly" ;) Lastly, the Anaconda distributions have made it so that Python Just Works, so that is by and large a problem of the past. (In all fairness though, I agree with your other points!) $\endgroup$ – blz Sep 24 '14 at 15:57
  • $\begingroup$ As another extensive MATLAB user, I don't agree with many of your claims. Just some examples: 1, Python and R, being Open Source and free, are practically easier to deploy. 2, neither R nor Python require any of these. 3, RStudio is arguably better than the MATLAB IDE (which I personally never use). 4, The appropriate comparison is Numpy, which offers all the vectorization MATLAB does; R also vectorizes easily. 5, MATLAB tends to get these (e.g., formula syntax, DataFrame formats) after other languages. 6, MATLAB is slower than R and Python in many benchmarks. $\endgroup$ – jona Sep 24 '14 at 20:46
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    $\begingroup$ Sorry, I don't agree with free == easy to deploy. Matlab is trivial to deploy: run an installer, everything just works. Anaconda aside, Python has been miserable to deploy at least until very recently. I don't see how Anaconda can possibly resolve the issue Python has with Python package incompatibilities and the tangled web of requirements. R seems pretty straightforward to deploy, but I haven't used it much. Numpy is the matrix-operation Python add-in I referred to. The core language of Python is not vectorised. $\endgroup$ – Dylan Richard Muir Sep 24 '14 at 21:12
  • $\begingroup$ Point 5. So? Like I said, Matlab comes from the era of Fortran. 6. The benchmarks I've seen (Python vs Matlab: wiki.scipy.org/PerformancePython; R vs Matlab: sciviews.org/benchmark but I can't find a more recent benchmark) don't show a huge difference. They should all be using low-level optimised BLAS routines anyway. Besides, if you want blinding speed you should be writing everything in C. Which is not going to happen in Neuroscience. $\endgroup$ – Dylan Richard Muir Sep 24 '14 at 21:13
  • $\begingroup$ @DylanRichardMuir, Concerning your response to jona's 5th point: Matlab's heritage is not an excuse. The complaint is that Matlab is a poorly-designed and slow-to-evolve language. Of course there are reasons for this, but it doesn't change the end result! :) Your argument is akin to driving a Ford Model T and exclaiming "Of course my car sucks! It's from the 1900's!" The issue isn't that of machine time, but that of developer time. That's what matters in the overwhelming majority of cases, and it's why nobody uses Fortran anymore. [Note: no disrespect intended! I'm enjoying the arg!] $\endgroup$ – blz Sep 25 '14 at 9:51
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I completely agree with most the factors you've identified, but before I suggest some additional points, I'd like to correct one of yours:

file formats that can only be read in MATLAB

Unless you're talking about some obscure format that I'm unaware of (entirely possible!), MATLAB files are readable by non-MATLAB tools. In particular, scipy.io provides flawless I/O from/to .mat files (especially since yours truly submitted a minor patch ;) ).

I mention this because it's an excellent argument for making the switch towards the scientific python stack; my Ph.D advisor only knows MATLAB, but she has become much less reluctant to work with Python since I explained that everything I did could be trivially made to interact with existing MATLAB code.

Additional (Python-centric) reasons why MATLAB remains king:

  1. There's what I call "battered spouse syndrome": researchers are used to the pain and suffering caused by MATLAB and wrongly assume that it's just part of the programming landscape. In other words, they don't know any better. They don't realize that there are tools that are more pleasant to use, more robust, (often) faster, more reliable, free and extensible. It's a classic case of thinking that all programming languages (eligible bachelors) are as abusive as your current tool (spouse).
  2. Researchers are put off by IDLE and aren't aware of such great tools as:
    1. IPython
    2. IPython Notebook (this will really rock your socks if you haven't seen it yet)
    3. Spyder (for those seeking a MATLAB-esque graphical interface)
  3. People haven't seen the Pandas library in action. I know it's a bit presumptuous to claim that a single library can convert steadfast MATLAB users, but Pandas, especially when combined with the IPython notebook, makes dealing with labeled matrices downright enjoyable. It offers such things as:
    • string-labeled columns and/or rows
    • groupby, split & merge operations
    • baked-in plotting with fine-grained control
    • baked-in summary & inferential statistics
  4. Python has historically been quite a pain in the ass to install on windows and OSX, and most potential users are still unaware that the Anaconda distribution has all but completely solved the problem.

My reason for bringing up point 3 is more than just a shameless plug for the Pandas library. I wanted to draw your attention to the fact that Pandas manages to combine MATLAB's most sought-after features (fast numerical arrays, logical indexing, plotting & myriad 3rd party libraries) with some of the most useful features of the R language (DataFrame-like structures, summary stats, split/combine/apply operations, missing data management (e.g. fill-forward, interpolation, etc). With this library, you can essentially make the argument that you're replacing two languages for most common purposes.


And now a real shameless plug: I'm one of the moderators on Reddit's /r/pystats. Anybody trying to ditch Matlab is more than welcome around these parts ;)

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  • $\begingroup$ I really like Pandas, but regardless of how great Pandas is, it's a long way from having scipy.io and Pandas to performing SPM or doing EEG analyses. To say otherwise would honestly be nothing but ignorant of the great work done by Friston, Makeig/Delorme, et. al. Yes, somebody could implement all of that in Python; but "could" means something like "spend half a decade or more coding". Thanks for fixing .mat IO in scipy either way! $\endgroup$ – jona Sep 23 '14 at 20:31
  • $\begingroup$ @jona, I don't disagree with your statement, and I certainly didn't mean to insinuate that every use-case was covered in Python. There are some very clear use-cases for using Matlab, especially in the neurosciences. This having been said there are very promising projects for SPM and EEG analysis that aren't far from giving Matlab a good run for it's money; I'm of course referring to NIPy and py-MNE. But I share your sentiment insofar as programming tools should make the job easier, not harder, and in any case, half a decade is only 5 years ;) $\endgroup$ – blz Sep 23 '14 at 21:33
  • $\begingroup$ IPython Notebook is very awesome, and looks like it should make Python more accessible to non-programmers and the Mathematica crowd. $\endgroup$ – Dylan Richard Muir Sep 24 '14 at 14:47
  • $\begingroup$ I think there is a bit of a dogmatic push to move to Python, which has started (and continued) by re-implementing huge chunks of Matlab functionality. While there are issues with the design of Matlab's language (it comes from the Fortran era, after all), I'm not convinced that the whole sphere of Python is so much more appealing to justify the huge reimplementation project. $\endgroup$ – Dylan Richard Muir Sep 24 '14 at 14:49
  • $\begingroup$ @DylanRichardMuir while I certainly agree that there's (what I would call) an ideological push for Python, it's also hard to deny that Python is not a better-designed language. Matlab has a tendency to generate illegible code beyond what one expects from novice programmers. Again, I want to stress that this is because of language design: Matlab is designed with the (false) premise that all data is best represented as matrices. PHP's double-clawed hammer analogy seems appropriate, here. $\endgroup$ – blz Sep 24 '14 at 15:54

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