Parameter Files

Generic file name: base.xml

Format: XML

The parameter file is a generic file which contains information required by many related programs; Klusters only needs a subset of this information. Note for advanced users: the schema describing the parameter file can be found in the source archive (src/parameter.xsd). Here is an example:

<parameters creator="par2xml" version="1.0" >	
  <acquisitionSystem>
    <nBits>16</nBits>
    <nChannels>16</nChannels>
    <samplingRate>20000</samplingRate>
    <voltageRange>20</voltageRange>
    <amplification>1000</amplification>
    <offset>0</offset>
  </acquisitionSystem>
  <fieldPotentials>
    <lfpSamplingRate>1250</lfpSamplingRate>
  </fieldPotentials>
  <anatomicalDescription>
    <channelGroups>
      <group>
        <channel>0</channel>
        <channel>2</channel>
        <channel>7</channel>
      </group>
      <group>
        <channel>3</channel>
        <channel>4</channel>
        <channel>5</channel>
        <channel>6</channel>
      </group>
      <group>
        <channel>8</channel>
        <channel>10</channel>
        <channel>15</channel>
      </group>
      <group>
        <channel>11</channel>
        <channel>12</channel>
        <channel>13</channel>
        <channel>14</channel>
      </group>
    </channelGroups>
  </anatomicalDescription>
  <spikeDetection>
    <channelGroups>
      <group>
        <channels>
          <channel>0</channel>
          <channel>2</channel>
          <channel>7</channel>
        </channels>
        <nSamples>32</nSamples>
        <peakSampleIndex>16</peakSampleIndex>
        <nFeatures>4</nFeatures>
      </group>
      <group>
        <channels>
          <channel>3</channel>
          <channel>4</channel>
          <channel>5</channel>
          <channel>6</channel>
        </channels>
        <nSamples>32</nSamples>
        <peakSampleIndex>16</peakSampleIndex>
        <nFeatures>3</nFeatures>
      </group>
      <group>
        <channels>
          <channel>8</channel>
          <channel>10</channel>
          <channel>15</channel>
        </channels>
        <nSamples>32</nSamples>
        <peakSampleIndex>16</peakSampleIndex>
        <nFeatures>4</nFeatures>
      </group>
      <group>
        <channels>
          <channel>11</channel>
          <channel>12</channel>
          <channel>13</channel>
          <channel>14</channel>
        </channels>
        <nSamples>32</nSamples>
        <peakSampleIndex>16</peakSampleIndex>
        <nFeatures>3</nFeatures>
      </group>
    </channelGroups>
  </spikeDetection>
</parameters>

As mentioned earlier, Klusters belongs to a larger framework for neurophysiological data analysis, also comprising NeuroScope. If you use NeuroScope to create your spike extraction groups, a basic parameter file will be created for you and you will only need to add the nSamples, peakSampleIndex and nFeatures tags.

Most tags are self-explanatory, but some tags may need clarification:

Each group tag inside the spikeDetection tag identifies a group of electrodes used for spike extraction and sorting. Notice that the order of these group tags is relevant: the first tag describes the first electrode group (i.e., files base.clu.1, base.fet.1 and base.spk.1), the second tag describes the second electrode group (i.e., files base.clu.2, etc.) and so on. When loading wide-band signals recorded from a group of electrodes in Klusters, the traces appear in the Trace View in the same order as the channels are listed in the channels tag.

Starting from version 1.5, the parameter file format was changed from two flat text files to the single XML file described in the previous section (as mentioned in the documentation for previous versions of Klusters, the flat text format was temporary - it was mostly used for backwards compatibility with legacy software - and destined to be replaced with a more flexible one). However, Klusters is backward compatible and can still read these parameter files, which are described in the following paragraphs.

16 16          # total number of electrodes, resolution of the acquisition system (in bits)
50 800         # sampling interval (in microseconds), high-pass filter frequency (in Hz)
4              # number of electrode groups
4 0 1 2 3      # number of electrodes for the 1st group, electrode IDs
4 4 5 6 7      # number of electrodes for the 2nd group, electrode IDs
3 8 9 10       # number of electrodes for the 3rd group, electrode IDs (in this example, electrode 11 was discarded)
4 12 13 14 15  # number of electrodes for the 4th group, electrode IDs

16 4 50     # total number of electrodes, number of electrodes for this group,  sampling interval (in microseconds)
0 1 2 3     # electrode IDs
10 2        # refractory sample index after detection, RMS integration window length
90          # approximate firing frequency in Hz
16 8        # number of samples in each waveform, sample index of the peak
12 6        # window length to realign the spikes, sample index of the peak (detection program)
4 4         # number of samples (before and after the peak) to use for reconstruction and features
3 16        # number of principal components (features) per electrode, number of samples used for the PCA
800.        # high pass filter frequency (in Hz)