simephys icon

   SimePhys    

The virtual electrophysiology lab

This is an application to learn and simulate basic electrophysiological experiments of in vivo preparations based.
Current version is V1.1 from 06-Sep-2015.

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Table of Content

Welcome - a brief introduction about the program

License - terms of use

Requirements - what is needed to run this program?

Installation - installation of the program

Usage - how to use the programm

*.fly viewer - a tool to monitor your recorded data

FAQ - frequently asked questions

Download - get your copy here

History - history and future develoment

Welcome

This is an application to learn and simulate basic electrophysiological experiments of in vivo preparations. While the main purpose of this software is teaching and learning, it is also some kind of test ballon for neuronal coding and signaling models.

The software simulates experiments like performed on the visual system of the fly. There are several well characterized cells (currently H1 of both hemispheres, V1 and V2) implemented inside the software that respond to moving grating patterns. Moreover there are many not exactly specified cells implemented counting to a total of 45 cells. Cell recordings are done extracellularly.
The software provides several basic experiments:

  • you can apply simple visual stimuli to characterize cells.
  • do basic speed adaptation experiments
  • determine cell response tuning curves to different grating speeds

  • For background information about the adaptation experiments please refer to T. Maddess and S.B. Laughlin (1985): Adaptation of Motion-Sensitive Neuron H1 is Generated Locally and Governed by Contrast Frequency. Proc. R. Soc. Lond. B. 225: 252-275 DOI:10.1098/rspb.1985.0061

    For further information don't hesitate to contact me. I am happy for any feedback.

    License

    This software currently is free for personal use. You may use it on your own risk. You are free to copy and distribute the archive. When distributing and/or spreading the program you must not:

  • charge money
  • modify the archive
  • Note: If you want to use this software for teaching purposes in lectures, classes or courses (for schools, universities or other educational institutions) it is required to obtain a license from the author (please mail to ulrich.beckers|at|web.de)

    Requirements

    This software is written in the Hollywood programming language and thus available for many systems. There is no additional software required and it should run on bog standard computers running one of the supported operating systems. You may need a processor better not less than 1000 MHz and maybe a few MB (roughly about 25, depends on the particular system) of available RAM. To sum it up, if you don't use something very special or antique you probably will be able to run this program.

  • a screen resolution of at least 1024x768 is required
  • soundcard and speakers or headphones
  • a processor of at least 1000 MHz
  • internet connection for help files and update notifications
  • The operating systems supported are:

  • MorphOS (any version will do, ppc binary) >> Download
  • Windows (minimum: Win 2000, x86 binary) >> Download
  • OS X (minimum 10.4 aka Tiger, ppc or x86 binary)
  • Linux (ppc or x86 binary)
  • AmigaOS (68k or ppc binary)
  • AROS (x86 binary)
  • AmigaOS (minimum V3.0, 68k or ppc binary)
  • AROS (x86 binary)
  • Binaries for OS X, Linux, AmigaOS and AROS and are not provided on this site but are available upon request only.

    If you run the *.fly viewer without Simephys you need less processor power and a resolution of 1024x600 is sufficient (ideal for usual netbooks).

    Installation

    Once you've downloaded the archive for your operating system, unpack the archive and copy it to any destination you like. You may put it on your harddsik or on a usb key or even on a server. There is no special installation process required

    Note: If you want to use the *.fly viewer from within Simephys (recommended) you need to create a subdirectory called flyview inside the directory where you have copied the Simephys binary to.

    Usage

    Just doubleclick the icon named Simephys to launch the program. Once the splash screen disappeared (usually quick, but can take a few seconds) the progam launches three windows as shown in the screen shots below (MorphOS version):

    1st window: Simephys - main window, program control center and preparation

    simephys main window

    There are some buttons and sliders to use the program. Note, that all sliders can only be moved when the mouse pointer is over the red bar and the right mouse button is clicked while moving the slider bar. All buttons are operated by the left mouse button though.

    The fuctions of main window's buttons are:

  • help - shows some online help within your standard browser
  • flyview - opens the additional data analysis program *.fly viewer if found and not opened already. If the *.fly program is not found the button does notify this with red characters.
  • hide fv - hide or show flyview window (doesn't quit)
  • hide osci - hide or show the oscilloscope window
  • hide visstim - hide or show the visual stimulus window
  • reset - provides a new preparation
  • quit - quits the program (w/o further requester)
  • rec - records data until hit again (redly tinted when recording)
  • adapt - starts a velocity adaptation experiment
  • speed tune - starts a velocity tuning experiment

  • Moving the sliders will wander the electrode along the preparation. The string below the buttons shows the name and path of the last recorded file (*.fly files). Filename consists of current calendar date and gets incremented each recording by one. If a filename does exists already the name gets incremented acoordingly until no file of identical name exists. If the full path of the filename is too long to get shown at the display the left part of the name gets cut. A cut name is indicated by two dots "..".
    If an update to the installed version is available a notification about that will appear just below the file name area. A mouse click on that message will open a browser window that leads to the download of the new version.

    2nd window: Visual Stimulus visual stimulus and control of it

    simephys visual stimulus




    The fuctions of the visual stimulus window buttons are:

  • run - start/stop movement of the grating pattern
  • turn - turn the grating pattern 90 degrees
  • help - shows some online help within your standard browser

  • With the sliders of that window the speed of the grating pattern is adjustable. The slider with the "d" is for downward speed whereas the "u" dentes the slider for the upward speed. The string field gadget the grating pattern speed additonally.

    3rd window: Oscilloscope - the oscilloscope with some functions

    simephys oscilloscope

    The fuctions of oscilloscope window's buttons are:

  • hold - hold data on the oscilloscope screen, release on next click
  • help - shows some online help within your standard browser

  • The oscilloscope shows the actual cell signal recorded at the elelectrode in green. Red dashes denote detected action potentials (AP). Use the slider to apply a threshold for AP detection. The threshhold is shown as gray line at the oscilloscope screen. The string gadget shows the sum of all detected APs (spikes) within the shown 175ms time window.


    To start an experiment you must move the recording electrode. The electrode will move according to the coordinates of the sliders.
    Once you found a cell signal you can use the slider bar at the oscilloscope window to use a threshold detector to determine action potentials (APs) against background noise. The detected APs are shown as red dashes.
    Note: For beginners it may seem hard to find cells, but that is part of the program's intenton since it simulates an actual in vivo electrophysiology experiment where finding cells is one of the difficulties of the entire experimental work. You need some patience to find cells.

    The button run starts a visual grating pattern that is used for cell search and cell type discrimination. The button turn toggles the alignment of the visual grating (either horizontal or vertical).
    With the sliders to the right of these buttons the speed of the grating pattern can be manipulated.

    The adaptation named button at the main window starts an adaptation experiment. The grating pattern is moved for 0.75s with one velocity and for 0.25s with another velocity for a total of 9 times. Detected APs are recorded to harddisk for later evaluation (for example with the *.fly viewer. Data is stored in files with the .fly extension at a program's subdirectory called data. The record process is indicated by a redly tinted record button.

    The reset button resets the current preparation and provides another preparation and new electrode (i.e. different noise behaviour, slightly different cell positions and intrinsic properties). Don't push that button by accident, you'll lose your current preparation!

    To quit the application click on the quit button, the close gadget of the main window or just by press Ctrl-C.

    *.fly viewer

    The *.fly viewer (stardotfly viewer) is a little tool to monitor and average recorded .fly data from the experiments performed with the Simephys software.
    The program can be run stand alone or directly from Simephys. It needs a screen resolution of at least 1024x600.
    If run from Simephys the binary must:

    - be named fly_view.exe or just fly_view
    - stay in a directory called fly_view that resides in the same directory the Simephys binary is located.

    *.fly viewer

    There are three buttons on the bottom of the program window. The left button add trial opens a file requester and asks you for a .fly file. Once a data file is chosen, the data gets displayed as a PSTH (20 ms bin width) to monitor the action potential rate over the experiment (upper diagram).
    The bottom diagram shows the average over all yet loaded data sets. It gets updated and newly averaged as soon as another data file gets loaded by the add trial button.

    If you don't want to add a data file to your average, chose the button show tr.. A file requester opens and asks you once again for a file. This time the chosen data set will not get included to the average. The current trial will be displayed in the upper trace, the average without the current trial once again in the bottom diagram.

    The right button reset resets the current average.

    Note: The *.fly-viewer is currently not part of the simephys archieve. Check out this dedicated page.

    FAQ

    Windows says this program is potentially dangerous Well, it's not dangerous, but the binary is not signed and hence, the Windows smart screen warns about that issue. I don't want to judge whether that behaviour of Windows is good or bad in general but signing the program costs money. If you don't want Windows to annoy you with warnings you may self sign the program or ask me for a copy on a CD or usb stick.

    I found a bug, want to discuss the data or methods, have a feature request or want to donate you a bag of gold ducates? Well, in that case don't hesitate to contact me.

    Note: V1.1 is still in rather early development state and may contain functional bugs. Stability of the programm is rather good though.
    The cell models and particularly the adaptation behaviour is not finished yet.

    Download

    Grab your copy from here:

    V1.1 - Download (Windows x86 version)
    V1.1 - Download (MorphOS version)
    V1.1 - Download (Amiga 68k version)

    Note: Versions for OS X (x86 or ppc), Linux (x86 or ppc), and AROS (x86) are available upon request only, please mail for a copy.

    History

    V1.1 released on 06-Sep-2015
    - new: automatic update availability notification (if online)
    - new: splash screen
    - new: moving the electrode along the z-axis now graphically shown, too
    - fixed: no more graphics issues with the oscilloscope
    - improved: better spatial cell distribution
    - improved: no more internal OS dependencies
    - UI slightly changed and improved

    V1.0 released on 08-Dec-2013
    - completely new and much improved user interface and design
    - new: the data evaluation program flyview can be launched from Simephys directly now
    - new: velocity tuning experiment
    - new: spike counter added
    - new: online help added
    - new: threshhold gets shown at oscilloscope's display
    - new: last recorded file name and path gets diplayed
    - new: grating pattern speed gets shown at string gadget
    - fixed: no more corrupted recorded data as with last release

    V0.10 released on 29-Feb-2012
    - new: support for Linux and AROS
    - improved: noise is more naturalistic now
    - fixed: no stuttering soundoutput anymore
    - fixed: removed a bug at calculation of new cell properties for a new preparation
    - new: added a test cell at a fixed position

    V0.9 released on 24-Jan-2011
    - new: auto offset for the oscilloscpe
    - fixed: issues with precise threshold detection
    - threshold detection now for entire oscilloscope range
    - improved layout
    - speed improvement of about 10%

    V0.8 released on 28-Oct-2010
    - initial public release

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    Cheers!

    Document history:

    08-12-2013 update to V1.0
    29-02-2012 update to V0.10
    01-08-2011 *.fly viewer information updated
    24-01-2011 update to V0.9
    28-10-2010 Documentation started


    Back to main page and contact information or to files page
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    © U. Beckers