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Propagating population signal from the turtle visual cortex. Provided by Jim Prechtl, Larry Cohen and David Kleinfeld, Yale University and UCSD.

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                                                                                           User Interface | Data Aquisition | Data Analysis
New Features
We incorporate approximately 90% of users suggestions about new features and improvements to the software.
 
The Software
The software consists of 2 distinct sections, Analysis and Acquisition. The analysis section runs under Windows95 or Unix (we have tested only Sun Solaris 7). The acquisition sections of the program are specific to the hardware used for the NeuroPDA and NeuroCCD systems and run only on PC's. NeuroCCD runs under WindowsNT and NeuroPDA under Windows95 or WindowsNT. The software for both camera systems is called NeuroPlex.
 
For those who would like a NeuroPlex display larger than that provided by a 1600x1280 21 inch monitor, two monitors can be used simultaneously (Brian Salzberg and AnaLia Obaid, personal communication). A video card that supports two monitors is the Matrox, G200MULTI-MONITOR (DUAL); part number G2/DUALP-PL (for PCI slot). $499.
 
User Interface
Analysis
User Interface 1 NeuroPlex's first user interface (shown at left, Enlarge) for analysis contains two windows for viewing data. The right window, called the Page Display, displays data from all photodiodes as they are positioned in the array. The Trace Display (left window) provides a larger view of data from a reduced number of photodiodes or electrode inputs. Photodiodes can be selected for this more detailed examination by pointing and clicking on the traces in the Page Display. A variety of low- and high-pass filters and display adjustments are available for each display. User Interface 2 The Trace Display also provides additional controls for averaging over diodes, superimposing and scaling traces.

The second analysis interface within NeuroPlex provides pseudocolor displays of the data (shown at right, Enlarge). Options for pseudocolor image displays include single frame, multiple frame, and movie displays of the time series. For anatomical reference, the pseudocolor images can be overlaid on an image of the preparation. A variety of color schemes, scaling, and filtering options are available.

Aquisition
Acquisition also has its own interface. A variety of options exist for acquisition, including three major acquisition/averaging protocols.

NeuroPlex software also controls various aspects of the experiment, such as the shutter, the stimulator, and the camera fans (NeuroCCD).

NeuroPlex provides a comprehensive package of data acquisition and analysis software for optical recordings with the WuTech 464 element photodiode array or the NeuroCCD camera. The software is written in the high-level language IDL (Research Systems, Inc.) and runs under Windows95, WindowsNT and Unix. The software has two main functions: Data Acquisition and Data Display & Analysis.

Data Acquisition
The data acquisition software is specific to a particular PC based analogue-to-digital converter card. Some capabilities of the acquisition section are:

Signal Averaging:
Three types of averaging are available.
  1. Averaging from a trigger provided by the computer.
  2. Averaging from the occurrence of a spike on one of the recorded channels.
  3. Averaging from the occurrence of an external event such as the EKG. (NeuroPDA only)
    In this mode, alternate trials with and without a stimulus can be subtracted to reduce heart-beat artifacts.
 
Subset:
For the Photodiode array system a Subset or Binning of the diodes can be selected for acquisition. Using a subset allows an increase in the frame rate above 1.6 kHz and/or a reduction in the size of the resulting data file. For NeuroCCD 2x2 binning can be used to increase the frame rate, reduce the data storage requirements, and/or reduce the relative dark-noise contribution
 
Resting Light Intensity:
The DC level of the amplifier output can be measured directly or can be measured after subtracting the DC level with no light.
Other parameters under the user's control are:
  1. file name,
  2. number of points (frames) per detector,
  3. frame interval,
  4. number of trials (for averaging),
  5. interval between trials (for averaging),
  6. and interval between light on and start of sampling.
 

Data Display & Analysis
Two different kinds of data display are provided. The first is intensity vs. time for the individual detectors and the second is a simultaneous pseudocolor display of intensity for all detectors at a particular time. A long series of such pseudocolor frames can be played as a movie.

Intensity VS. Time:
There are two display windows on the main NeuroPlex widget. The Page Display displays intensity versus time for
all detectors (plus 8 BNC channels) in the arrangement of the photodiode array. The individual traces can be displayed with a enlargement on the Trace Display by clicking them individually on the Page Display. The two displays can be filtered and processed separately. In addition to the usual X and Y gain adjustments, the following kinds of high- and low- pass filtering are available:
  • Gaussian,
  • Butterworth,
  • median,
  • RC,
  • and binomial.

The traces can be displayed as intensity vs. time or as intensity/(resting intensity) vs. time.

The Page Display can be modified by a fudge array (replaces bad detectors with the average of the four adjacent detectors) or an omit array (replaces detectors with no signal with a flat line).

The Trace Display can display:

  1. the spatial averages of selected traces
  2. the FFT of selected traces
  3. the correlation between traces
  4. spaced or superimposed traces
  5. superimposed traces can be scaled to equal height for comparing time courses.
  6. Both the Page display and the Trace display can be exported as a TIFF file, a PostScript file or an ASCII file.
Pseudo-Color Frames:
The filtered data can be made into pseudocolor movie frames and then be viewed as individual frames, or multiple frames in one window, or as an animated movie. The color of the frames can manipulated by using different color tables and four different scaling schemes.

The scaling schemes are:

  1. variable (each detector will have the maximum and the minimum color at some time in the trial),
  2. fixed; using the trace with the largest signal,
  3. fixed; using a user chosen detector, and
  4. manual.

(When you've tried all these options, it will be clear why it is called pseudo-color).

The movie frames can also be overlayed onto a high resolution CCD image of the preparation by importing its TIFF or BMP file. The movie can be saved as a movie file and the file can then be read and replayed by NeuroPlex. The display on the movie window can be exported as a TIFF file.