| Virtual Retina: biological retina simulator, with contrast gain control (Wohrer and Kornprobst 2009) |
| Accession: 118524 |
"We propose a new retina simulation software, called Virtual Retina, which transforms a video into spike trains.
Our goal is twofold: Allow large scale simulations (up to 100,000 neurons) in reasonable processing times and keep a strong biological plausibility, taking into account implementation constraints.
...
This software will be an evolutionary tool for neuroscientists that need realistic large-scale input spike trains in subsequent treatments, and for educational purposes."
Reference: Wohrer A, Kornprobst P (2009) Virtual Retina: a biological retina model and simulator, with contrast gain control. J Comput Neurosci 26:219-49 [PubMed] |
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Virtual Retina - Download
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Technical
prerequisites
- Runs under linux Compiled with gcc version 3.4 or more.
- Also runs under mac
(thanks to Horacio.Rostro_Gonzalez@sophia.inria.fr).
- Required helper softwares (included in the archive)
- MVASpike , an event-driven
neural network simulation software
- CImg, an image processing
library
- libxml++ , an xml parsing
software
- xmlParameters++ , a small
helper library producing an interface between c++ parameters and an xml
tree.
Download
retina_package.tar.gz
is the archive with Virtual
Retina
and other required libraries. It also
contains the tutorial explaining in details both installation and usage
of the software.
Installation
A shell comand performs an automatic installation of all libraries.
Basic directions are also provided in the tutorial (included in the
archive; also available here)
for those wishing to perform a custom, manual installation.
Tutorial
A tutorial
is available,
explaining both installation procedure and usage of the software in
detail. Some README files in the archive also contain some information.
Typically, the program is called under a
LINUX shell, with a syntax that looks like this:
Retina
path/to/my/test_sequence*.pgm -ret my_retina.xml -r
10 -outD path/to/my/saving/directory
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with possible options:
- test sequences can
be 2d frames under any usual format (as here), or directly a .inr
3-dimensional file.
- -ret gives
the path to the retina definition
file in
xml format.
- -r 10 : each input
frame is presented to the retina for a duration of 10*(retinal time
step) = 50 ms in this case.
- -outD : path to the
directory where all simulation files will be saved.
- etc. Full list of options by typing -h.
Virtual Retina
contains
a number of customized retina definition files
that you can directly use to start your first simulations.
Log
file
A log file has
been created to keep track of the succesive changes in the format
required for the XML definition file.
Retina schema
If you want to create a Retina configuration file, you can find a RelaxNG schema of the options you must provide there : retinaSchema.rng.
So you should be able to valide your Retina configuration file with a command like that (xmllint is part of libxml package) :
xmllint your_xml_file.xml --noout --relaxng retinaSchema.rng
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