1 Dear Electrophysiology Neuroscientists,
2 =======================================
4 As you might know, during November 13-17, the NeuroDebian team ran its
5 first Debian booth at the annual meeting of the `Society for
6 Neuroscience`_ (SfN2010_) in San Diego, USA. Our generic report `is
7 available from NeuroDebian website <http://neuro.debian.net/booth_sfn2010.html>`_.
9 In this post we want to summarize our findings on the status of Free
10 and Open Source Software (FOSS) in the domain of
11 neuro-electrophysiology.
13 - Majority of electrophysiology researchers are locked into software
14 platforms provided by the vendors of the used hardware
15 - There exist a number of FOSS platforms for all (?) stages necessary
16 for setting up the research workflow but their adoption in hindered
17 by difficulty to setup and maintain. That in turn results in the
18 absence of a set of commonly accepted and used ultimate FOSS
19 solutions in the field
20 - Majority of FOSS and some of the commercial data acquisition
21 solutions use Linux-based systems, relying on an additional stack
22 for real-time kernel support (e.g. RTAI_) and often the Comedi_
23 library for interfacing with the (most often proprietary) hardware
24 - Some commercial companies are interested in sharing their products
25 as FOSS (e.g. Ripple LLC: Trellis-Neuro) and getting them ready for
27 - Many labs develop their solutions and are willing to share but
28 - Nearly all researchers using Linux, already use Debian_ (or
29 Debian-derived such as Ubuntu_) Linux distribution as the platform
30 but primarily rely on manual deployment (download, build, install or
31 compose a custom Live media such as DVD or USB) of the 3rd-party and
34 Existing Electrophysiology FOSS
35 -------------------------------
37 We have initiated a `Debian Science Electrophysiology task page
38 <http://blends.alioth.debian.org/science/tasks/electrophysiology>`_
39 to collect all relevant FOSS for the field and signal their status in
40 respect to inclusion in Debian distribution or presence of not (yet)
41 official Debian packages. The list is constantly growing (and
42 changing), so if you spot some relevant FOSS absent, please `let us
43 know <team@neuro.debian.net>`_.
45 Here is a brief summary listing per application sub-domain:
47 XXX may be listing is just not needed and duplicate of what could be
48 found on the tasks page, although there it is not very
49 structured... so may be it is better to come up with a verbal
55 `Debian Science Data Acquisition task page
56 <http://blends.alioth.debian.org/science/tasks/dataacquisition>`_
57 provides similar summary for software such as RTAI_, Xenomai_, Comedi_
58 which enables data acquisition.
60 - Nspike -- electrophysiological and behavioral data collection
63 - provide verbal summary on existing solutions
64 - mention RT-Preempt kernel images being available
65 - point to 'cooked' solutions on how to build using RTAI-patches
66 - existing pre-built RTAI kernel packages:
68 http://www.linuxcnc.org/lucid/
69 carries for hardy and lucid
70 pointed there from http://hart.sourceforge.net/
75 - Relacs -- framework for closed-loop neurophysiological experiments
76 - RTXI -- real-time data acquisition and control applications in biological research
77 - Trellis-Neuro -- interface to neurophysiology data acquisition and stimulation instruments
80 - pointers to the SfN posters for RTXI, Mehmet's setups
86 - Chronus -- Matlab toolbox for analysis of neural signals
87 - KlustaKwik -- spike sorting tool
88 - Neurodata -- Octave/Matlab suite to analyze data acquired from electrophysiology experiments
89 - Openelectrophy -- data analysis framework for intra- and extra-cellular recordings
90 - Sigviewer -- GUI viewer for biosignals such as EEG, EMG, and ECG
91 - Spike -- information-theoretic spike train analysis techniques
92 - Stimfit -- viewing and analyzing of electrophysiological data
96 .. _chap_debian_booth_sfn2010: http://neuro.debian.net/booth_sfn2010.html
97 .. _blends_neuroscience_electrophysiology: http://blends.alioth.debian.org/science/tasks/electrophysiology
99 .. _annual meeting: http://www.sfn.org/am2010/
100 .. _SfN2010: http://www.sfn.org/am2010/
101 .. _Society for Neuroscience: http://www.sfn.org/
102 .. _RTAI: https://www.rtai.org
103 .. _Xenomai: http://www.xenomai.org
104 .. _Comedi: http://www.comedi.org
105 .. _Debian: http://www.debian.org
106 .. _Ubuntu: http://www.ubuntu.com