SCRC Data Capture and Analysis System

Help Facility for Analysis Program

Copyright © 1984-2019, Gilles Detillieux, Spinal Cord Research Centre, University of Manitoba. All Rights Reserved.

Initial actions

Analysis Methods

Analysis Parameters

Analysis Menus

Maintenance

^ top

Analysis Methods

^ top

Analysis Parameters

^ top

Hierarchy of Analysis Menus

^ top

Analysis: Trace averaging by frame list

A single bin is set up for each trace in the "Trace # list". All frames in the "Frame list", which fall in the range to be analysed, are added in to obtain a single average for each trace. Deleted frames, and frames whose tag values are not in the "Tag list" are excluded.

This analysis method can also be used to view raw traces; just set the "Frame list" to select a single frame, and set the "Trace # list" to select the traces you want to see. The traces are shown in numerical order, and any repetitions in the list are ignored.

If your current run is a run of already averaged data, you can still perform this averaging. The total number of sweeps shown takes into account the number of sweeps already averaged into each frame in the run. The "Start of run" and "End of run" parameters have no effect here, since frames of averaged data have no inherent "time of occurrence."

^ top

Analysis: Trace averaging based on cycle phase

A number of bins are set up for each trace in the "Trace # list", evenly dividing the normalized cycles. Each frame in the range to be analysed is added in to the appropriate bin, based on the point in the cycle where the frame was triggered. Deleted frames, and frames whose tag values are not in the "Tag list" are excluded.

^ top

Analysis: Trace averaging based on W.F. level

A number of bins are set up for each trace in the "Trace # list", evenly dividing the range of voltage levels measured from the waveform selected by the "Amplitude W.F. #". Each frame in the range to be analysed is added in to the appropriate bin, based on the waveform level associated with the frame. The parameters "W.F. amplitude delay" and "W.F. amplitude window" indicate a range of points, relative to the point where the frame was triggered, used to obtain a level reading on the waveform.

The range of voltage levels can be restricted to a smaller range, by setting the parameters "Min W.F. amplitude" and "Max W.F. amplitude". Only frames whose associated waveform level readings stay within these bounds will be included in the average. Normally, these two parameters only restrict the range, and do not enlarge it: if the parameters are beyond the range of voltage levels in the waveform, it is the measured range which is divided into bins, not the range defined by the parameters. However, if the "Fixed W.F. level bins" option is enabled, then the two parameters above will always define the range which is divided into bins, even if it exceeds the range of levels in the waveform.

Deleted frames, and frames whose tag values are not in the "Tag list" are excluded. You can also exclude frames that occur during the inactive phase of cycles on the waveform selected by the "Cycle W.F. #", by enabling the "Active cycle phase only" option. This restricts the average to frames that occur between the start and stop times of activity in any cycle. If the "Base cycles on stop time" option is also enabled, then the opposite is true; frames occurring in the inactive phases are included, and frames in the active phases are left out.

^ top

Analysis: Trace averaging based on tag value

A number of bins are set up for each trace in the "Trace # list", corresponding to the tag values in the "Tag list". Each frame in the range to be analysed is added in to the appropriate bin, based on its tag value and where this value appears in the list. Deleted frames, and frames whose tag values are not in the "Tag list" are excluded.

^ top

Analysis: Waveform averaging - spike triggered

A single bin is set up for each waveform in the "W.F. # list". Each action potential in the range to be analysed triggers a "sweep" from each of the above waveforms. The sweeps are added to obtain a single average for each waveform.

The parameter "W.F. avg window" controls the duration of each sweep, and "W.F. avg delay" is a positive, zero or negative offset from the time the sweep is triggered to the time the sweep's window begins.

^ top

Analysis: Waveform averaging based on cycle phase

A number of bins are set up for each waveform in the "W.F. # list", evenly dividing the normalized cycles. For each cycle in the range to be analysed, a "sweep" is triggered at the start of each bin in the cycle, and the sweep is added into its bin. The window and delay are set as they are for spike triggered averages.

^ top

Analysis: W.F. averaging - spikes within cycle

A number of bins are set up for each waveform in the "W.F. # list", evenly dividing the normalized cycles. Each action potential in the range to be analysed triggers a "sweep" from each of the above waveforms. Sweeps are added in to the appropriate bins, based on the point in the cycle where each sweep was triggered. The window and delay are set as they are for spike triggered averages.

^ top

Analysis: W.F. averaging - spike occurrence in cycle

A number of bins are set up for each waveform in the "W.F. # list", corresponding to individual action potentials, or spike occurrences, in the cycles. For example, 10 bins represent the first 10 action potentials in each cycle. A sweep is triggered for each of these action potentials, and added into its corresponding bin. The window and delay are set as they are for spike triggered averages.

The "Spikes to skip" parameter can be set to indicate how many spikes to ignore at the beginning of each cycle. If it were set to, say, 5, then 10 bins would represent the sixth to the fifteenth actions potentials. If the "Reverse spike occurrences" option is then enabled, the 10 bins would represent the fifteen down to the sixth action potentials from the end of the cycle.

^ top

Analysis: W.F. averaging based on spike interval

A number of bins are set up for each waveform in the "W.F. # list", evenly dividing the range of inter-spike intervals selected by the "Min inter-spike interval" and "Max inter-spike interval" parameters. Each action potential in the range to be analysed triggers a sweep from each of the above waveforms. Each sweep is added in to the appropriate bin, based on the interval from the previous action potential. No sweep is triggered for the first spike in the range to be analysed, since no previous spike exists to permit an interval calculation. If the spike trains for the waveform selected by the "Spike W.F. #" have been properly set, intervals are calculated and sweeps are triggered only for spikes in the same spike train, and no sweep is triggered for the first spike in each train. The window and delay are set as they are for spike triggered averages.

If the "Take interval after spike" option is enabled, the bin for a given sweep is selected based on the interval to the next action potential, rather than the interval from the previous one. No sweep is triggered for the last spike in the range to be analysed, rather than the first, nor for the last spike in each train, when spike trains are set.

^ top

Analysis: W.F. activity start & stop time analysis

The start or stop of activity on the waveform selected by the "Y-axis W.F. #" is plotted with respect to the start or stop of activity on the waveform selected by the "X-axis W.F. #". A point is plotted for each cycle on the waveform selected by the "Cycle W.F. #", and the start or stop times are calculated relative to the start of the cycle in which they occur. If the "Normalization" option is enabled, times are calculated as a percentage of the cycle length.

If the option "Base X on stop time" is enabled, times for the end of activity, rather than for the start of activity, are used for the X coordinates. If the option "Base X on spike trains" is enabled, the start or end of spike trains for this waveform are used for the X coordinates, rather than the usual (duty cycle) activity. The "X-axis cycle offset" is used to effectively time-shift the cycles for the purpose of determining in which cycle a particular burst of activity or spike train falls. This allows more reliable results in borderline cases. For example, if a burst usually starts somewhat after the start of the cycle, but starts a bit early for a few cycles, you can select a negative offset of a few milliseconds so that these few bursts will properly be associated with the cycles in which they occur, even though they start a few milliseconds before the start of their associated cycles. Similarly, a positive offset can be used if a few bursts end slightly after the end of the cycle in which they occur. Note that this offset does not affect the calculation of the coordinate, so it is possible to get negative points plotted. Similar options for the Y-axis waveform exist, and are used in the same way.

If the "Cycle durations on X" option is enabled, the usual X-axis is overridden by the cycle durations. In other words, the graph becomes one of start or stop time of activity in cycle, versus cycle duration.

^ top

Analysis: W.F. activity burst duration vs cycle duration

The duration of activity (duty) on the waveform selected by the "Amplitude W.F. #" is displayed with respect to the duration of cycles on the waveform selected by the "Cycle W.F. #". A point is plotted for each activity burst on the former waveform, which falls into one of the cycles of the latter waveform in the selected range to be analysed. If the option "Base cycle stats. on start" is enabled, the start of activity, rather than the end of activity, is used for the purpose of determining in which cycle a particular burst of activity falls, and where it falls within the cycle.

The "Burst cycle offset" is used to effectively time-shift the cycles for the purpose of determining in which cycle a particular burst of activity falls, much like the cycle offset parameters for the "W.F. activity start & stop time analysis" graph. The "Burst duration type" parameter determines the way in which the burst duration is calculated for each burst of activity. The initial value, 0, means the duration is the time from the start of the burst to the end of it. A 1 means the time from the start of the burst to the start of the next burst. A 2 means the time from the end of the burst to the start of the next, and a 3 means the time from the end of the burst to the end of the next. If the "Relative burst durations" option is set, burst durations are shown as a percentage of the corresponding cycle durations.

If the "Burst positions in cycle" option is enabled, the usual X-axis is overridden by the cycle positions of the activity bursts. In other words, the graph becomes one of burst duration versus position of burst in cycle. Just like any of the other graphs of "something" vs cycle, this graph can be normalized, and the "Cycles on graph" parameter will then take effect.

If the "Flip durations" option is enabled, the usual X and Y axes are transposed, giving you a graph of cycle duration versus burst duration. If the "Flip durations" option and the "Burst positions in cycle" option are both enabled, the graph becomes one of cycle duration versus position of burst in cycle.

When the "Second W.F. bursts" option is enabled, the end of burst durations or train durations are taken from the cycle activity recorded in the waveform parameters of a second waveform, selected by the "Second ampl. W.F. #". Either the start or end of the burst is used, depending on the "Burst duration type" selected. If the "Second W.F. trains" option is also selected, it overrides this one, so the trains are used instead of the cycle activity for the second waveform.

^ top

Analysis: Raw W.F. amplitude vs step cycle

The waveform selected by the "Amplitude W.F. #" is displayed with respect to cycles on the waveform selected by the "Cycle W.F. #". That is, for each cycle on the latter waveform, the corresponding segment of the former waveform is displayed, overlaid by segments corresponding to all other cycles in the range to be analysed. If the cycle related parameters for the displayed waveform have been properly set, statistics will be given for activity on this waveform, relative to the above cycles. The parameters "Min W.F. amplitude" and "Max W.F. amplitude" can restrict the voltage levels allowed in the analysis to a smaller range.

^ top

Analysis: Averaged W.F. amplitude vs step cycle

The waveform selected by the "Amplitude W.F. #" is averaged and displayed with respect to cycles on the waveform selected by the "Cycle W.F. #". That is, the cycles are evenly divided into a number of bins, and for each cycle on the latter waveform, the corresponding segment of the former waveform is split up and the parts are added into their respective bins. An average curve is then calculated and displayed with one point for each bin.

If the cycle related parameters for the displayed waveform have been properly set, statistics will be given for activity on this waveform, relative to the above cycles. The parameters "Min W.F. amplitude" and "Max W.F. amplitude" can restrict the voltage levels allowed in the analysis to a smaller range.

The "Amplitude" reported at the top of this graph is simply the difference between the minimum and the maximum averages calculated, i.e. a peak-to-peak amplitude. On a DC-coupled intracellular recording of a motoneuron, this peak-to-peak amplitude is the locomotor drive potential or L.D.P.

^ top

Analysis: Raw trace amplitude vs frame number

Displacements measured for each frame, on the trace selected by the "Amplitude trace #", are displayed with respect to their frame numbers. The "Frame list" parameter selects the frames to be measured, and the order in which they are presented. The Frame number for each point on the X-axis corresponds to the frames' position in the sequence in which frames are presented. These numbers do not represent actual frame numbers unless frames are displayed in sequence, beginning with frame 1, and no frames are excluded.

The trace amplitude measurements are taken the same way they are for the "Raw trace amplitude vs step cycle" graph. Deleted frames, and frames whose tag values are not in the "Tag list" are excluded.

^ top

Analysis: Raw trace amplitude vs step cycle

Displacements measured for each frame, on the trace selected by the "Amplitude trace #", are displayed with respect to cycles on the waveform selected by the "Cycle W.F. #". That is, for each cycle on the latter waveform, the corresponding frames are examined. For each of these frames, two points are measured on the selected trace, and the difference is shown on the graph, at the position in the cycle where the frame was triggered.

The position of these two points in the frame's window are selected by the parameters "Trace amplitude point" and "Trace amplitude ref". The first select the actual point to be sampled, and the second selects the reference measurement location. These two parameters have corresponding "window" parameters, which can be used to select two ranges of points in the frame's window: the program will search for the maximum point, or the minimum point, in each of the two ranges, based on the setting of the "Find max trace amplitude" parameter. If either of the two "window" parameters is set to 0, only one point is used for the corresponding measurement. A line above the graph will indicate which point or range of points was used for each of the two measurements. Regardless of whether the sample level and the reference level are obtained each from a single point, or the minimum or maximum in a range of points, the reference level is subtracted from the sample level to obtain the amplitude reading for the frame.

If the "Trace amplitude ref" option is set to a negative value (e.g. -1p), then the reference level is not measured, and the sample level is taken as an absolute reading.

If the "Average trace ampl. ref." option is enabled, rather than searching for the maximum or minimum point in the "Trace ampl. ref window" for each frame, the program will instead take the average of the points in this range as the reference level.

If the "Trace ampl. integration" option is enabled, rather than searching for the maximum or minimum point in the "Trace ampl. point window" for each frame, the program will instead integrate (sum up) the points in this range. (What are actually summed up are displacements relative to the reference level measured.)

The measurements for all cycles in the range to be analysed are overlaid on the graph. Deleted frames, and frames whose tag values are not in the "Tag list" are excluded.

^ top

Analysis: Averaged trace amplitude vs step cycle

Displacements measured for each frame, on the trace selected by the "Amplitude trace #", are displayed with respect to cycles on the waveform selected by the "Cycle W.F. #". That is, for each cycle on the latter waveform, the corresponding frames are examined. The cycles are divided evenly into a number of bins, and for each of the examined frames, two points are measured on the selected trace, and the difference is added into the appropriate bin for the position in the cycle where the frame was triggered. An average curve is then calculated and displayed with one point for each bin.

The position of these two points in the frame's window are selected by the parameters "Trace amplitude point" and "Trace amplitude ref". The first select the actual point to be sampled, and the second selects the reference measurement location. These two parameters have corresponding "window" parameters, which can be used to select two ranges of points in the frame's window: the program will search for the maximum point, or the minimum point, in each of the two ranges, based on the setting of the "Find max trace amplitude" parameter. If either of the two "window" parameters is set to 0, only one point is used for the corresponding measurement. A line above the graph will indicate which point or range of points was used for each of the two measurements. Regardless of whether the sample level and the reference level are obtained each from a single point, or the minimum or maximum in a range of points, the reference level is subtracted from the sample level to obtain the amplitude reading for the frame.

If the "Trace amplitude ref" option is set to a negative value (e.g. -1p), then the reference level is not measured, and the sample level is taken as an absolute reading.

If the "Average trace ampl. ref." option is enabled, rather than searching for the maximum or minimum point in the "Trace ampl. ref window" for each frame, the program will instead take the average of the points in this range as the reference level.

If the "Trace ampl. integration" option is enabled, rather than searching for the maximum or minimum point in the "Trace ampl. point window" for each frame, the program will instead integrate (sum up) the points in this range. (What are actually summed up are displacements relative to the reference level measured.)

The measurements for all cycles in the range to be analysed are overlaid on the graph. Deleted frames, and frames whose tag values are not in the "Tag list" are excluded.

^ top

Analysis: Raw trace amplitude vs W.F. level

Displacements measured for each frame, on the trace selected by the "Amplitude trace #", are displayed with respect to corresponding level measurements on the waveform selected by the "Amplitude W.F. #". The trace amplitude measurements are taken the same way they are for the "Raw trace amplitude vs step cycle" graph. The waveform amplitude measurements are taken the same way they are for the "Trace averaging based on W.F. level" analysis. The "Fixed W.F. level bins" option has a slightly different effect here, since the range of levels is not divided into bins, but it may affect (increase) the range of levels displayed to the full range defined by the "Min W.F. amplitude" and "Max W.F. amplitude" parameters.

Deleted frames, and frames whose tag values are not in the "Tag list" are excluded. You can also exclude frames that occur during the inactive phase of cycles, or the active phase, in the same way as for the "Trace averaging based on W.F. level" analysis, using the "Active cycle phase only" option.