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Typical Application Log Window.
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September 9, 2000
For definitions of terminology used in this document, please see the CESLab Glossary of Terminology.
Some Instruments present a view of Preparation data that is oriented along one of the three axes of 3-D space. Since there are two possible viewing directions along each axis, there are six distinct viewing orientations:
These instruments present an italicized "compass rose" in the upper left corner, indicating the correlation of directions onscreen with those of the Preparation.
Some Instruments present a numeric field labelled "Scale" next to a slider with the labels "Out" and "In" at the endpoints. These control the viewing magnification at which data is displayed in the scrolling subwindow of the Instrument. A value of 1 indicates that the data appears at actual size, 2 that the Preparation appears at twice the actual size, .5 indicates that the display is approximately half-sized, etc..
Note that the exact observed size onscreen is, of course, dependent upon individual monitor characteristics.
Some instruments present a field labelled "Cutaway" and an adjacent slider, the end labels of which vary with the viewing orientation of the Instrument. These sliders control the position of the Instrument viewing plane along the viewing axis.
Some instruments present a checkbox labelled "Show Grid", and an adjacent spacing field. If this box is checked, the Instrument will display the data overlaid onto a background grid. The grid line spacing is computed automatically from the scaling factor, and is not editable by the user.
Some instruments present a checkbox labelled "Black Background". If this box is checked, the scrolling subwindow will display its data on a black background instead of white.
The preference file application variable
DefaultBackgroundsToBlack may be set to True in order to
change the default background color to black.
Certain instruments (e.g. ECG and VCG windows) present a checkbox labelled "Overlay Trials". If this box is checked, the Instrument accumulates data with each trial in a separate trace, and displays the tracings simultaneously, overlaid in different colors. This feature enables the user to easily perform many types of A/B comparisons onscreen, or display entire sets of related trial results.
Unchecking this box causes all but the most recent tracing to be discarded.
Some instruments present a bar to the left of the scrolling subwindow containing placards of different colors, each with an accompanying descriptive legend. These color keys indicate the mapping between the colors used for display of the data and the indicated quantities or entities.
If a "Recalibrate Colors" button is shown, hitting this button will clear all extant entries from the color key, and reconstruct it based solely on the data currently being displayed.
The contents of this file should not be edited by the user.
This script file is editable, and permits the user to customize the behavior of CESLab. See the comments in the file for more information.
SimpleText or any other Macintosh text editor.
Instrument windows can always be closed. If the Bench Window is closed, this closes the Bench, and all associated windows.
Bench Windows cannot be closed if the Bench is active (a Bench Progress window is open for the Bench). The Application Log Window cannot be closed.
The following windows offer the Print command:
If any Bench is busy (a Bench Progress Window is visible), this command is ignored. Each active Bench must be stopped before CESLab can be quit.
Trials are discontinued, returning control to the user or script, when any of the following events occur:
Trials may be conducted even if there are no Instruments open, but this is not particularly useful, since no results would be shown. The most relevant windows for observing the results of trials are:
Note that editing certain Preparation parameters will render the current trial uncontinuable, so that the Start New Trial command will have to be issued.
Since 1 Amp-meter is a much larger amount of current dipole than is generated by biological hearts, the initial and final G&S potentials may seem extremely large in comparison with those associated with normal cardiac cycles.
Note that if a non-zero number of G&S iterations has been selected in the Bench Window, this command may take many minutes to complete, and that this command is uninterruptable.
The Windows Menu contains the following entries:
This command opens a window in which free-form text may be entered, to be associated with the Current Bench. This is intended for use in describing the Bench, its configuration, history, etc..
This command opens a new Decremental Conduction Curve Editor window.
This command opens a new Modulator Effect Editor window.
This command opens a new ECG Viewer.
This command opens a new ElectroWorld Viewer window.
This command opens a new Heart Dipole Scope window.
This command opens a new Heart Dipole Graph window.
Opens a new Interval/Duration Curve Editor window.
Opens a new Interval/Potential Curve Editor window.
This command opens a new VCG Viewer window.
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Typical Application Log Window.
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Note that the Application Log Window is not associated with any particular Bench, so if it is the frontmost window, bench-oriented commands (such as Command-R) are ignored, as will be attempts to open (typically via double-clicking) script files.
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Typical Bench Window.
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Any number of benches may be opened simultaneously (assuming that enough RAM is installed in the host computer, and that the CESLab application's memory partition is set to a sufficiently large value, and that there are not too many other applications running simultaneously), and each Bench can be running a command or script simultaneously.
Note that a Bench can duplicated just by copying the Bench file. This enables the user to conduct complex A/B comparisons in a safe, straightforward manner.
This field displays the exclusion radius to be employed during automatic generation of DSL's. The locations selected by CESLab for regional dipoles are arbitrary, but it is guaranteed that no two DSL's will be permitted to be closer than this distance, and that any given Cell will be associated with the geometrically closest regional dipole.
The generated set of regional dipoles can be observed in the ElectroWorld Viewer window. The Cells assigned to each regional dipole can be seen in Cell Set Viewer or Microscope windows set to the Regional Dipole Cell Display Modality.
The user may edit the contents of this field to change the regional dipole exclusion radius. Note that the number of regional dipoles is inversely correlated to the cube of the Exclusion Radius, and that the time required for generation of SPTC varies linearly with the number of regional dipoles. Exclusion radii outside the range of 1 to 5 centimeters are not recommended.
Note that, for any given Cell layout, the exact locations of the dipole centroids selected by CESLab will differ for each possible DSL Exclusion Radius. Depending on the geometry of the employed polyhedra, this may place a centroid too close to the center of a polyhedron facet, decreasing the accuracy of the SPTC (and thus adversely affecting the ECG, VCG, and BSPM). To make sure that this does not occur, when changing the DSL Exclusion Radius, the user should make sure that the results obtained with the new value do not differ significantly from those obtained with slightly smaller values. Alternately, the distances between each DSL and the closest facet centroid can be directly examined using the menu bar command Report DSL/Facet Proximities.
This field displays the number of iterations of the algorithm of Gelernter and Swihart that will be applied during SPTC generation (see the document CESLab Technical Specifications for more information). The user may edit this field to change the number of iterations, but note that this will render the SPTC out of sync such that they must be recomputed before electrophysiological simulation can occur.
With zero iterations specified, generation of the coefficients typically requires less than one minute (unless Surface Potential Mapping is enabled for any polyhedron). The SPTC generated with zero iterations are approximate, but are often accurate enough for the computation of other than final experimental results. Specifying one or more iterations will significantly slow electrode transfer coefficient generation, but will increase their accuracy. For most Preparations, even one G&S iteration will achieve extremely accurate results.
This field displays the conductivity of the region of the torso that contains the dipole source locations. This field may be edited by the user to change the base torso conductivity.
Note that the base torso conductivity should always equal the gross conductivity of the generic torso Tissue Type.
If this box is unchecked, automatic cells will self-activate only once per trial. If checked, automatic cells will trigger periodically throughout the trial, so the trial will never become static.
For full-heart Preparations such as the standard CESLab HHA series adult human heart model, checking this box will cause the SA nodal Cells to trigger periodically, producing a series of simulated cardiac cycles.
This field specifies the duration gradient to be applied to the duration of activation phase 2 dependent upon the vertical offset of the Cell from the bottom of the Preparation (the inferior aspect in the Cell Set's Cartesian space). This is typically used to establish ventricular gradients.
If this box is checked, then if a simulation trial reaches a state where there is no additional electrophysiological activity remains to be simulated (typically requiring the Retrigger Automatic Cells checkbox to be unchecked), the trial is discontinued. Otherwise, the trial will continue until another termination criterion is achieved, or the trial is aborted by the user.
Upon automatic completion of a static trial, the Dipole Generation Checksum for the trial activity will be written to the Bench Log.
If this box is checked, then any Decremental Conduction Curves specified will be used to adjust conduction speeds in accordance with the temporal offset from the last entry into phase 3 RRP at which a given Cell is activated. Else, conduction speeds will be independent of Interactivation Intervals.
If this box is checked, then the durations of phases 2 and 3 will be adjusted in accordance with prevailing interval/duration curves and the last (or default) per-cell Interactivation Interval. Else, interval/duration effects will be ignored.
If this box is checked, then for each activation of any given Cell in a trial, the Action Potential Waveform will be adjusted in accordance with any prevailing interval/potential curve and the last (or default) per-cell Interactivation Interval. Else, no such adjustment will be performed.
The Default Interactivation Interval for this Bench. Generally, this is set in accord with a typical heart rate, e.g. 750 ms.
This slider controls the Dipole Sampling Interval.
Note that the dipole sampling interval effectively filters the generated dipoles over time. If it is lowered too much, the dipole samples may exhibit an unacceptable sample to sample variability (perceived as noise). If it is raised too much, the samples may be too smooth, lacking detail.
If a trial has been started for the Bench, this field will display the simulated temporal offset from the beginning of the trial to the current state of the Preparation. It is updated periodically while a trial is in-progress.
If this box is checked, then the associated temporal interval will be employed as the maximum duration for which electrophysiological simulation will be conducted after a trial is started or continued before control returns to the user or script.
The time segmentation feature may be used in many ways, including:
These checkboxes indicate which subsets of the Preparation exist and are not in need of regeneration before a trial may be initiated. The user may click on any of the unchecked checkboxes to request that the associated part of the Preparation be brought up to sync:
The Cell layout refers to the number, locations, and Subtissue associations of the Cells contained in the Preparation, plus the intercellset junctions. It is rendered out-of-sync by changes to cell sizes, Subtissue geometric parameters, or edits made to the associated Compound Shapes.
Note that the time required to bring the Cell layout into sync varies linearly with the number of Cells that have to be generated, which is, in turn, inversely proportional to the cube of the cell size.
This checkbox indicates whether the current set of regional dipoles is valid. The regional dipoles are rendered out-of-sync by changes to the cell layout, or the DSL exclusion radius.
The SPTC are used to map electrical current dipoles (collected at the regional dipoles during electrophysiological simulation) to potential values at polyhedra facets.
The coefficients are rendered out-of-sync by changes to the regional dipoles, the number of Gelernter and Swihart iterations, or the torso geometry. Note that the time required to bring the coefficients back into sync varies with the number of G&S iterations selected.
The activation parameters consist of the internal data used to propagate activation during trials. They are rendered out-of-sync by changes to Modulator levels, or to Subtissue or Tissue Type electrophysiological parameters.
Note that if activation parameter resyncing is aborted by the user, it renders any current trial uncontinuable.
The entirety of the Preparation is automatically brought up to sync when a new trial is started. Note that this process may require anywhere from a few seconds to many minutes, depending on what parameters have been modified by the user.
If this box is checked, then each Bench Log entry displayed will be prefixed with the date and time at which the message was generated.
This popup menu controls what types of messages are displayed in the Bench Log:
All extant log entries will be displayed.
Only warning and error messages will be displayed.
Only error messages will be displayed.
This button may be used to clear the contents of the Bench Log. Note that all entries will be deleted: errors, warnings, and informational messages.
The scrolling subwindow displays the Bench Log, a record of bench-specific events in chronological order.
Note that the contents of the Bench Log are saved in the Bench file, so that the number of log entries will accumulate until the Clear Log button is hit.
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Typical Bench Progress Window.
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Each Bench Progress Window features a button labelled "Stop". Clicking on this button will stop the current activity in that Bench as soon as possible, returning control to the user. Note that hitting the key combination Command-. (Command-period) is equivalent to hitting the "Stop" button for the Bench Progress Window associated with the Current Bench.
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Typical Tissue Type Window, showing the characteristics of the
simulated ventricular myocardial Subtissue
in the CESLab HHA Series predefined benches.
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If this box is checked, Cells of this Tissue Type are considered to be neuromuscular in nature, in that they are capable of electrophysiological activation. If unchecked, then Cells of this Tissue Type will not be capable of electrophysiological activation. In addition, this characteristic determines which Cells are visible in Cell Set Viewers when the Show Neuromuscular Cells Only box is checked.
This checkbox is not modifiable by the user.
If this box is checked, Subtissue Walls of this Tissue Type will possess fibers oriented according to the inside and outside fiber angles specified for the wall. If unchecked, Subtissue Walls of this Tissue Type will be treated (like all non-walls) as having no distinct orientation to their simulated fibers (i.e. conduction is isotropic).
This field contains the temporal delay to be used for conduction of activation from Cells of this Tissue Type to other cell sets. It is typically used to establish the junctional delays to/from Purkinje to myocardial Subtissues.
This checkbox indicates whether the duration of activation phase 2 for Cells of this Tissue Type will be adjusted in accordance with the vertical phase 2 duration gradient specified in the Bench Window. This is typically enabled only for ventricular Tissue Types to establish vertical ventricular gradients.
This field specifies the relative ratio of conduction speeds parallel to the simulated fibers to those perpendicular to them for Cells of this Tissue Type. For Tissue Types without distinct fibrous organization, this should be left at unity.
This field specifies the bulk electrical conductivity of Subtissues of this Tissue Type. This is used to establish conductivity ratios between the inside and outside of polyhedra for computation of SPTC. The base torso conductivity in the Bench Window is used for computation of current dipoles generated during trials.
Note that the conductivity of a Tissue Type is only used by CESLab if the Tissue Type is associated with the interior of an employed polyhedron.
This slider may be used to control the range of potentials shown in the Action Potential Waveform subwindow.
This slider may be used to control the range of temporal values shown in the Action Potential Waveform subwindow.
If this box is checked, then an Action Potential Waveform adjusted for the effects of the current levels of all extant Modulators will be displayed in the scrolling subwindow. This waveform is not editable by the user, as it is computed from the non-adjusted waveform and the prevailing electropharmacology.
Note that if the activation parameters are not in sync (see the Bench Window sync checkboxes), no Modulator Action Potential Waveform will be displayed.
If this box is checked, then the Action Potential Waveform before adjustment for prevailing Modulator levels will be displayed in the scrolling subwindow.
This subwindow displays a graphical representation of the modulated and/or non-adjusted Action Potential Waveforms for Cells of this Tissue Type.
Note that interval/duration and interval/potential effects are computed per-cell during electrophysiological trials, and are not evident in this subwindow. Likewise, phase 2 duration gradients (vertical or intramural) are computed per-cell and are not indicated here. Microscope Windows can be used to examine such per-cell data if desired.
The color key at the left of the subwindow indicates the colors used for the various activation phases:
Boundaries between phases are indicated by square markers, and may moved (within the temporal interval established by the surrounding subphases) but not deleted. Boundaries between piecewise linear subphases are indicated by round dots, and may be deleted or moved.
The user may edit the Action Potential Waveform arbitrarily using the mouse:
Note that the actual duration of phase 2 may be modified for Cells within particular tissues by their per-subtissue phase 2 duration gradients. This is typically used to tune ventricular repolarization gradients for the Preparation.
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Typical Subtissue Window, displaying the characteristics of the simulated
left ventricular myocardial Subtissue
in the CESLab standard HHA series heart models.
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This field displays the name of the Tissue Type associated with this Subtissue.
This field is not editable by the user.
If this box is checked, then Cells of this Subtissue will generate electrical current dipoles during simulation trials, thus contributing to the data observable in ECG Viewers, VCG Viewers, etc.. If unchecked, Cells of this Subtissue will depolarize and repolarize normally during trials, and will conduct excitation to their neighbors appropriately, but will produce no dipole.
If this box is checked, Cells of this Subtissue will be electrophysiologically excitable, such that if neighboring Cells are activated during electrophysiological simulation, Cells of this Subtissue will activate (after a suitable simulated time delay). If this box is unchecked, then Cells of this Subtissue will be electrophysiologically inactive.
The coupling interval to be associated with automatic cells of this Subtissue.
If this box is checked, then Cells of this Subtissue will be electrophysiologically automatic, in that they will depolarize themselves once at the temporal offset into the trial specified by the coupling interval field (unless activated by neighbors at an earlier point in the trial), and then periodically thereafter (if Retrigger Automatic Cells is checked in the Bench Window) according to their modulated automatic period.
These fields specify the modulated and non-adjusted automatic periods at which Cells of this Subtissue will reactivate. The non-adjusted automatic period field is editable by the user; the modulated automatic period actually employed during simulation trials is computed from the non-adjusted automatic period and prevailing electropharmacology, and is not directly editable.
The numerical value in this field serves as a linear scaling factor for conduction speeds of Cells of this Subtissue (see the document CESLab Technical Specifications for more information).
Note that if the conduction speed factor is decreased too much for a given cell size, Cells of that Subtissue will begin to reactivate spontaneously, since by the time activation propagates from Cell A to a neighbor B, Cell A has recovered sufficiently to become reexcited by neighbor B. This can occur in any finite-element propagation model, and is best addressed by decreasing the cell size.
These fields display the conduction speeds for propagation of the activation wavefronts during electrophysiological simulation along the axial and transverse directions with respect to the local fiber orientation (or non-directionally if there is no local fiber orientation).
These values are not directly editable by the user, but may be controlled by the conduction speed factor, the longitudinal/transverse speed ratio specified in the associated Tissue Type, and the phase 0 upstroke slew rate specifed in the association Action Potential Waveform.
This field specifies the threshold potential that must be exceeded by a neighbor for a given Cell of this Subtissue to activate (during phase 3 RRP or phase 4). If this value is too low, Cells of this Subtissue may repeatedly self-activate; if too high, Cells of this Subtissue will not activate, blocking conduction.
Note that changes to excitation threshold in CESLab will not automatically modify conduction speeds, since if cell-to-cell propagation delays were based on activation waveforms, conduction speeds would become dependent on cell size. If changes in conduction speed must be made synchronously with changes in excitation threshold, they may be made by changing the conduction speed factors, or the phase 0 durations via simulated pharmacology.
This field displays the target thickness of the Subtissue Wall. As a special case, a value of zero indicates that the wall should be made as thin as possible (typically one Cell thick). This field may be edited by the user to change the wall thickness for synthetic cell sets, but note that this will desynchronize the cell layout.
These fields display the requested fiber orientation angles for the inside and outside of the wall. Cells at the extreme inside and outside surfaces (respectively) of the wall will acquire these fiber angles. Cells at intermediate locations will acquire fiber angles by interpolation between these extrema in accordance with the Bench Function "MapWallDepthFraction" (see the ESL Scripting Reference Manual for more information).
If a particular Cell has a fiber angle of zero, its fiber orientation will be horizontal (with respect to the Cell Set's Cartesian space), and approximately tangent to the wall at the Cell location. Negative fiber angle values denote clockwise rotation of the fibers within the plane tangent to the wall at the Cell location as seen from outside the Preparation, and positive values counter-clockwise rotation. Fiber orientations are approximate, since they are computed on a cell-by-cell basis using the geometry of any neighboring Cells, which varies for each location. For some small number of wall Cells, a distinct fiber orientation cannot be computed (particularly at the extreme bottom of the Preparation in the heart space); such Cells will conduct excitation isotropically, as if fiber orientations were disabled.
To view fiber orientations, the user may open a Cell Set Viewer in Fiber Orientation Cell Display Modality in 2-D or 3-D. Note that if the Has Oriented Fibers box is unchecked for the associated Tissue Type, these fiber angle values are ignored.
This field specifies the intramural phase 2 gradient for the wall. See the document CESLab Technical Specifications for more information.
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Typical Cell Set Viewer, showing an anterior 3-D cutaway view of the myocardia of the CESLab
HHA series heart model, including simulated bypass tracts (normally all deactivated).
Click on image to enlarge. |
Any number of Cell Set Viewers may be open simultaneously for any Cell Set, in the same or differing Cell Display Modalities.
If the user option-clicks the mouse when the cursor is on top of any displayed Cell, a Microscope Window is opened at that location, permitting the user to examine the characteristics of the Cell and surrounding ones in detail.
If this box is checked, then the scrolling subwindow will present a 3-D view of the Cell Set as seen from the cutaway plane, shaded by distance as if the illumination came from the viewer. In particular, if the cutaway offset slider is moved all the way to the left in 3-D mode, all the displayable Cells may be seen.
If this box is not checked, only Cells that intersect the viewing plane will be displayed.
This popup menu permits the user to select the model by which activation within this Cell Set is propagated to neighbors:
Propagation delays for conduction to neighbors will conform to an ellipsoid oriented along the local fiber orientation axis, where the major axis indicates the axial conduction speed, and the minor axis the transverse conduction speed.
This propagation model is currently unsupported.
This field displays the number of neighbors to which any given Cell in this Cell Set may propagate excitation:
Up to eighteen neighbors may be excited: the six Cells that share a cubic face with a given Cell, and the twelve Cells that share a cubic edge with the Cell.
Up to twenty-six neighbors may be excited: the six Cells that share a cubic face with a given Cell, the twelve Cells that share a cubic edge with the Cell, and the eight Cells that share a corner with the the Cell.
In all cases, propagation delays for the transmission of excitation between adjacent Cells are scaled by the Euclidean distance between the centers of the Cells: Cells that share an edge are considered to be separated by the cell size times the square root of two, and those that share corners are considered to be separated by the cell size times the square root of three.
This field is not editable by the user.
This field displays the size of each cubic simulated cell, i.e. the length of any of its edges.
The user may edit this field to change the size of the Cells in the Cell Set, but note this will cause regeneration of the Cell Set, which may take many minutes. Cell sizes outside the range of 0.8 to 3.0 millimeters are not recommended.
Note that the number of Cells is approximately proportional to the cube of the reciprocal of the cell size, and that the bulk of the main memory per Bench required by CESLab is consumed by the Cells.
At any point in time, each Cell Set Viewer is in one of a predefined set of Cell Display Modalities, which determine the meaning of the colors used to represent the Cells.
The set of available modalities is as follows:
In this modality, Cells are displayed in colors keyed by their electrophysiological activation phase (e.g. phase 2). If a trial is in progress, any Cell Set Viewers in the Activation Phase Cell Display Modality will display an animated view of the depolarization and repolarization processes.
In this modality, only Cells instantaneously adjoining the depolarization wavefront during electrophysiological simulation are displayed, and are drawn in colors to distinguish whether the wavefront is advancing towards or retreating from the viewer.
Note that display is not animated in this modality, so trials must be interrupted via Command-. (Command-period) or time segmentation for changes in activation wavefronts to be observed. This modality is typically employed in 3-D, with the cutaway offset slider positioned at the left end.
In the diagrammatic modality, each Cell is displayed in the diagrammatic color specified for its associated Subtissue.
In this modality, Cells are displayed in colors keyed to their last activation time relative to the start of the last simulation trial, showing the temporal progression of the activation wavefront.
No data will exist for display in this modality unless a trial has been initiated.
In this modality, Cells are displayed in colors keyed to their last repolarization time relative to the start of the last simulation trial.
No data will exist for display in this modality unless a trial has been conducted until at least some Cells have repolarized.
In this modality, Cells are displayed in colors keyed to their associated regional dipoles.
No data will exist for display in this modality unless the regional dipoles have been resynced since the Cell Set was generated.
In this modality, Cells are displayed in colors keyed to their fractional depth within the associated Subtissue Wall (if any).
In this modality, Cells with distinct fiber orientations are drawn so as to project the local fiber orientation onto the viewing plane.
No data will exist for display in this modality unless the Activation Parameters have been resynced since the Bench was last opened.
In this modality, Cells are displayed in colors keyed to their phase 2 action duration, as adjusted by any prevailing phase 2 duration gradients.
No data will exist for display in this modality unless the Activation Parameters have been resynced since the Bench was last opened.
In this modality, Cells are displayed in colors keyed to their phase 3 action duration.
No data will exist for display in this modality unless the Activation Parameters have been resynced since the Bench was last opened.
In this modality, Cells are displayed in colors keyed to their absolute refractory period (the total duration of phases 0 through 3 ARP).
No data will exist for display in this modality unless the Activation Parameters have been resynced since the Bench was last opened.
In this modality, Cells are displayed in colors keyed to their phase 2 starting potential.
No data will exist for display in this modality unless the Activation Parameters have been resynced since the Bench was last opened.
In this modality, Cells are displayed in colors keyed to their total action duration.
No data will exist for display in this modality unless the Activation Parameters have been resynced since the Bench was last opened.
In this modality, Cells are displayed in colors keyed to the number of interspace (e.g. Purkinje/myocardial) junctions with which they are associated.
In this modality, Cells are displayed in colors in accord with their outward depth.
If this box is checked, then only Cells associated with tissue types that have been designated as neuromuscular will be visible; all other Cells will be considered transparent. If this box is unchecked, then all Cells in the Cell Set will be displayed.
This button causes the Cell Set layout to be brought into sync.
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Typical Microscope Window, showing two simulated SA node foci. The single
Cell
associated with SA Node 1 is selected, so its
characteristics are displayed in detail.
Click on image to enlarge. |
The Microscope Window view orientation is fixed at anterior. It displays five grids, each of which is a seven by seven array of squares. Each grid represents a square 2-D subset of cell space in the X-Y plane. Each grid is associated with a particular value of the Z-coordinate within a contiguous range of five integral values (which vary with the position of the microscope). The grids are displayed in left to right order by increasing Z-coordinate value.
Each entry in this grid contains a particular color, selected as follows:
This field displays the location (in quantized cell space) of the cell slot (which might or might not be occupied by a Cell) around which the microscope view is centered. The center location may be changed using the navigation buttons.
Identical to the Cell Display Modalities of the Cell Set Viewer.
If the user clicks on any displayed Cell, that Cell becomes selected, turning pink to indicate this status. The Microscope Window displays additional information when a Cell is selected:
This field displays the location of the selected Cell (in quantized Cartesian coordinates).
This checkbox indicates whether an electrophysiological activation breakpoint has been set for the selected Cell. Simulation trials are automatically discontinued whenever a breakpointed Cell activates, returning control to the user (who may use the Continue Current Trial command to resume the trial. This box may be checked/unchecked by the user to set/clear such breakpoints. The menu command Clear Activation Breakpoints may be used to clear all extant electrophysiological breakpoints in the Preparation.
This field displays the Decremental Conduction factor computed for the selected Cell after its most recent activation. Values less than unity cause propagation of excitation to neighbors to be linearly slowed accordingly.
This field displays the fractional depth of the selected Cell within the associated Subtissue Wall (if any).
This field displays the scalar interval/duration factor computed for the selected Cell after its most recent activation. Numbers greater than unity imply linearly prolonged phase 2 and phase 3 durations.
This field displays the scalar interval/potential factor computed for the selected Cell after its most recent activation. Values greater than unity indicate linear enhancement of the action potentials with respect to the phase 4 potential.
This field displays the per-cell scalar factor applied to the phase 2 temporal duration in accord with vertical and intramural phase 2 duration gradients in effect.
This field displays the absolute refractory period of the selected Cell (in temporal quanta).
This field displays the last electrophysiological activation time (in units of temporal quanta) of the selected Cell, or zero if the Cell has not been activated since the Bench was last opened.
This field displays the last electrophysiological repolarization time (in units of temporal quanta) of the selected Cell, or zero if the Cell has not repolarized since the Bench was last opened.
This field displays the current per-bench simulation time in units of temporal quanta.
This button adds a tracing for the selected Cell to the current Electrogram Window (opening a new one if none exists).
These fields display the propagation delays (in units of temporal quanta) for conduction of electrophysiological activation from the selected Cell to each of the neighboring Cells. The individual field labels incorporate the prefixes of the axial directions that make up the displacement from the selected Cell to the neighbor, e.g. "FR" indicates the neighbor one linear quantum each forward and rightward from the selected Cell.
Zero values mean that there is no conduction to that neighboring Cell, the Cell Set has not been electrophysiologically resynced since the Bench was opened, or that no neighboring Cell exists in that location.
Note that the propagation delays employed during trial execution may be adjusted by prevailing Decremental Conduction Curves.
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Typical ElectroWorld Viewer window, showing an anterior view of
the outer and inner torso polyhedra, lungs,
Intracavitary Polyhedra,
regional dipole centroids,
and electrode attachment points.
Regional dipole 2 (indicated by the pink dot just to the left of the attachment point of electrode "McFee 1") has been selected, so its characteristics are displayed in the box labelled "Selected Regional Dipole". Click on image to enlarge. |
If checked, the scrolling subwindow will display all employed polyhedra.
If checked, the scrolling subwindow will display regional dipole locations. If the user clicks on a displayed regional dipole, it will become selected.
If this box is checked and a regional dipole is selected, the scrolling subwindow will display the voltage surface swept by the projection of unit test dipoles through the VCG lead system and torso model. The VCG lead system (Frank or McFee) may be selected via the popup menu next to the checkbox.
Note that the VCG image surface results are dependent upon the prevailing heart transformation matrix, torso geometry, and VCG electrode placement.
This field displays the aggregate count of the number of facets on all employed polyhedra.
If this box is checked, red markers will be drawn at each polyhedral facet associated with an electrode, along with the electrode names. An electrode may be repositioned arbitrarily by adjusting the position of the corresponding locus in a Shape Editor window for the torso Compound Shape.
This field shows the number of extant regional dipoles used for electrophysiological simulation. This field may not be edited by the user, as the number of regional dipoles is controlled via the Dipole Source Location exclusion radius specified in the Bench Window.
If a regional dipole is selected, its detailed characteristics are displayed:
This field displays the ID of the selected regional dipole. The user may select an arbitrary regional dipole by entering its ID in this field.
This field displays the number of Cells associated with the selected regional dipole.
This field displays the name of the Subtissue associated with the Cell located at the centroid of the selected regional dipole.
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Typical Polyhedron Editor window, showing the potentials on the surface of the left
ventricular
Intracavitary Polyhedron as
seen from the front in the heart's Cartesian space midway
during ventricular activation. Potential minima are evident at the middle of the
ventricular septum and posterior papillary region, caused by early activation wavefronts
moving away from the cavity.
Click on image to enlarge. |
Similar to the manner in which the Cell Set Viewer Cell Display Modality popup menu controls the color scheme used to display Cells, the Polyhedron Editor Facet Display Modality controls the colors used to depict the visible facets of the polyhedron:
The facets are displayed in the diagrammatic color of the polyhedron.
Facets are displayed in colors keyed to their initial potential during the last execution of the procedure of Gelernter and Swihart.
No data will be present for display in this modality unless SPTC were resynced (or the Run G&S On Region... menu bar command was issued) since the Bench was opened.
Facets are displayed in colors keyed to their old charge density during the last execution of the procedure of Gelernter and Swihart.
No data will be present for display in this modality unless SPTC were resynced (or the Run G&S On Region... menu bar command was issued) since the Bench was opened.
Facets are displayed in colors keyed to their new charge density during the last execution of the procedure of Gelernter and Swihart.
No data will be present for display in this modality unless SPTC were resynced (or the Run G&S On Region... menu bar command was issued) since the Bench was opened when at least one G&S iteration had been specified in the Bench Window.
Facets are displayed in colors keyed to their total charge density during the last execution of the procedure of Gelernter and Swihart.
No data will be present for display in this modality unless SPTC were resynced (or the Run G&S On Region... menu bar command was issued) since the Bench was opened.
Facets are displayed in colors keyed to their final potential computed during the last execution of the procedure of Gelernter and Swihart.
No data will be present for display in this modality unless SPTC were resynced (or the Run G&S On Region... menu bar command was issued) since the Bench was opened. Data will only exist for facets associated with an electrode unless SPM is enabled for the polyhedron.
Facets are displayed in colors keyed to surface potentials computed during electrophysiological simulation. This facet display modality is the only one for which animated results are displayed during simulation trial execution.
Note that surface potentials will only be displayed for facets associated with electrodes unless Surface Potential Mapping is enabled for the polyhedron.
If a numerical Facet Display Modality has been selected, the Range Sensitivity slider may be used to control the color key range. Any facets whose values exceed the extrema of the color keys are displayed in gray.
Hitting the "Recalibrate" button immediately adjusts the range sensitivity slider so as to render all the displayed data within color key's range. If the checkbox labelled "Auto" is checked, such recalibration will be performed automatically whenever the numeric values are out of range. However, note that the range sensitivity is never automatically decreased.
If checked, this polyhedron will be employed in the computation of SPTC for simulation trials. Else, the polyhedron is ignored.
In particular, for the standard CESLab THA adult human torso model, there are only two recommended configurations:
Note that modification of this checkbox will desynchronize the SPTC.
This field displays the maximum facet size, used when generating the polyhedron.
This contents of this field may edited by the user, but note that this will desync the SPTC. The number of facets generated for a given polyhedron is proportional to the square of the inverse of the maximum facet size. Note also that the computational resources (time and memory) required to resync the Surface Potential Transfer Coefficients is proportional to the square of the number of extant polyhedral facets.
If checked, then Surface Potential Mapping will be enabled for this polyhedron, so that animated surface potentials may be displayed during trial execution.
Usually the outermost employed torso polyhedron is selected for this feature ( "Single Torso Polyhedron" or "Outer Torso Polyhedron"), but it is possible to enable Surface Potential Mapping for any polyhedron (e.g. the lungs or Intracavitary Polyhedra) and observe potential data during simulation trials.
Note that checking this box will increase the time required for recomputation of SPTC.
This field displays the number of facets comprising this polyhedron. This field is not editable by the user; the number of facets is controlled indirectly via the maximum facet size.
This field displays the aggregate surface area of all facets of this polyhedron. This field is not editable by the user.
Requests that the polyhedron geometry be brought up to sync.
Hitting this button will cause a red marker dot to be drawn at the center of each facet that has one or more names (associated electrodes), with an adjacent label listing the names.
This field displays the number of dipole samples that will take place between each refresh of the polyhedron display during electrophysiological simulation in Surface Potential facet display modality.
This field is used primarily to tune the speed of surface potential display animation. If it is set to 1, then the polyhedron will be redrawn for each dipole sample. If set to a high enough value, the polyhedron will only be redrawn when the trial is discontinued.
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Typical Shape Editor window, showing a superior cutaway view of the middle of the heart.
The gap between the ventricular endocardium and the intracavitary regions exists to make
sure that the regional dipole centroids
are sufficiently far from the
Intracavitary Polyhedral
facets to compute accurate SPTC.
Click on image to enlarge. |
Each Compound Shape consists of a set of simple shapes, which are are bounded by lines known as Fences that may be edited to change the outlines of the shapes. Singular Fences (ones that exist only as a single point, not a line proper) are critical to shape editing as they serve as the top/bottom of shapes (as well as positioning curves and loci), but are only shown if the Show Singularity Labels box is checked.
A given slice is either editable or uneditable. Uneditable slices are constructed automatically by CESLab from the surrounding editable slices. Editable slices consume more computational resources, so are recommended only for altitudes whose precise geometry is critical.
On uneditable slices, all fences are uneditable. On editable slices, each Fence is either be editable or uneditable. Uneditable fences have their geometry constructed from the surrounding editable fences. Editable fences are distinguished by dots called FencePosts that separate each line segment that makes up the fence. They consume more computational resources, and so are recommended only in places where the precise geometry is critical.
When an editable slice is being displayed, non-singular fences may be selected by clicking on them. Singular fences may be selected by clicking on their associated labels (shown only if the Show Singularity Labels box is checked).
The user is free to adjust the geometry of editable fences arbitrarily, and can even adjust a given fence so that it crosses another. This is generally made obvious by inconsistencies in the color coding of the simple shapes. Such fence crossings should be avoided, since they will produce errors in the polyhedra and/or cell sets generated from the erroneous Compound Shapes.
In some unusual cases, major changes in geometry between adjacent editable slices or fences may result in fences crossing on intervening uneditable slices. To fix such cases, the user should identify the pair corresponding editable fences above and below the pathological zone, make the fence editable approximately midway between the two altitudes (making a slice editable if necessary), and adjust its geometry as necessary.
If this box is checked, the scrolling subwindow will annotate fenceposts associated with singularities with the names of the associated entities. The names will be followed by the letter codes U and/or D if the entity also exists upwards and/or downwards.
If this box is checked, then a color key will be displayed in the left part of the scrolling subwindow, indicating the colors associated with the displayed shapes.
These buttons may be used to move upwards or downwards to the closest editable slice in the indicated direction.
If an editable slice is being displayed that contains no editable Fences (or singularities that are not associated both upwards and downwards), this button will be labelled Make Slice Uneditable , and may be used to make the slice uneditable. If an uneditable slice is being displayed, this button will be labelled Make Slice Editable , and may be used to make the slice editable.
If an editable slice is being displayed, this button may be used to change its altitude, but only within the (exclusive) bounds of the next higher and lower editable slices.
If a singularity has been selected on an editable slice that is not associated both upwards and downwards, one or both of these buttons will be enabled and may be hit to cause the associated entity (shape, curve, or locus) be extended in size (or moved in the case of loci) to the next editable slice in the associated vertical direction.
If a border singularity has been selected, this button expands the singularity into a non-singular fence. This operation is typically used in extending shapes vertically.
If a non-singular fence has been selected, this button requests that the fence be contracted into a singularity. This operation is typically used in reducing the vertical extent of shapes.
This button brings up a dialog box, permitting the user to specify offsets along each Cartesian axis to translate (move) the entire Compound Shape as desired.
This button brings up a dialog box, permitting the user to rescale the Compound Shape along any/all of the Cartesian axes. Scaling factors greater than 1 will linearly enlarge the entire Compound Shape, those less than 1 shrink it.
This button causes the Compound Shape to be written to disk as an ESL script file. If the user double-clicks on such a Compound Shape script file, the Compound Shape is imported into the Current Bench, replacing any existing Compound Shape of the same name.
This feature may be used to save sets of modified geometries for any given Bench, or to copy new geometry to other benches or users.
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Typical Matrix Editor window, showing the rotations used to position the heart within the torso
in an anterior 3-D presentation. In the heart's Cartesian space, the green vector is
directed downward, the blue backward, and the red leftward.
Click on image to enlarge. |
The scrolling subwindow displays a figure composed of three line segments, each of equal length, representing the three axial basis vectors as rotated by the matrix. Translations and rescalings of the matrix are not shown.
Note that, in CESLab, matrices accumulate rescalings, rotations, and translations separately, in that order. This makes it easy, for example, to change the rotation of a Preparation without previous translations causing rotated re-translations.
This button resets the matrix to an identity matrix.
This button brings up a dialog box, permitting the user to enter axial factors for rescaling of the matrix.
These buttons bring up dialog boxes, permitting the user to enter angles for rotation about the associated axes. Positive values cause counter-clockwise rotation as seen from the origin looking along the given axial basis vector.
Rotations are applied to the matrix
These buttons bring up dialog boxes, permitting the user to enter values for translation of the matrix along the associated axes.
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Typical Heart Dipole Graph window, comparing the dipole output of the right and left ventricles
during a simulated normal cardiac cycle.
Click on image to enlarge. |
The Heart Dipole Graph presents its data in left-to-right time sequence, much like an ECG. The axial components of the total heart dipole are presented in separate traces, along with the magnitude of the instantaneous dipole.
The output displayed in the Heart Dipole Graph is qualitatively similar to that of an axial ECG, though the torso model plays no role in generating the tracings.
This button may be used to clear the contents of the scrolling subwindow.
This field specifies the deflection of the tracings in units of electrical current dipole per box.
This field may be edited by the user to enlarge/shrink the tracings vertically.
This field specifies the simulated paper speed of the lead tracings. This field may be edited by the user to enlarge/shrink the tracings horizontally.
This popup menu indicates whether the dipole will be displayed as it exists in the Cartesian space of the heart or that of the torso.
This feature is useful for correlating depolarization sequencing observed in Cell Set Viewers with generated dipoles during tuning of simulation parameters.
If this box is checked, then the window is frozen.
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Typical Heart Dipole Scope window, comparing the dipole output of heart
with differing Posterior Papillary cable conduction speeds
during a simulated cardiac cycle, as seen from the left.
Click on image to enlarge. |
The output displayed in the Heart Dipole Scope is qualitatively similar to that of the VCG Viewer, though the torso model plays no role in generating the displayed data.
The contents of the scrolling subwindow of the Heart Dipole Scope are automatically cleared at the start of each trial (unless trace overlaying has been requested). This button may be used to clear the contents at any time.
For example, this button is may be used to view the dipole produced by ventricular depolarization without the overlaid atrial dipole, or to view the ventricular repolarization dipole without the depolarization being overlaid.
This field specifies the deflection of the heart dipole tracings in units of electrical current dipole per box.
This field may be edited by the user to enlarge/shrink the tracings without effecting the grid display.
If this box is checked, then the window is frozen.
This popup menu indicates whether the dipole will be displayed as seen in heart space or in torso space. In torso space, the tracings will appear similar to a conventional VCG tracing.
This feature is useful for correlating depolarization sequencing observed in Cell Set Viewers with generated dipoles during tuning of simulation parameters.
If this box is checked, small dots will be drawn periodically (as specified by the associated time interval field) as tracings are accumulated to mark the positions of the heart dipole vector at the indicated time intervals.
The time interval field is editable, and may be changed by the user. In particular, it may be used to identify the point in the tracing associated with any time of interest, e.g. 200 ms into the cardiac cycle.
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Typical VCG window, comparing the tracings produced as the conduction speed of the
right bundle branch is varied (as seen from the left).
Click on image to enlarge. |
The contents of the scrolling subwindow of the VCG Viewer are automatically cleared at the start of each trial. However, this button may be used to clear the contents at any other point.
For example, this button may be used to view the VCG produced by ventricular depolarization without the overlaid atrial tracing, or to view the ventricular repolarization tracing without the depolarization.
This field specifies the instantaneous deflection of the VCG tracings in units of potential per box.
If this box is checked, then the window is frozen.
This popup menu can be set to the following values to select the VCG lead system to be employed:
Note that the output produced is dependent on the heart geometry, the torso geometry, and the VCG lead placement.
If this box is checked, small dots will be drawn periodically throughout simulation trials to mark the positions of the VCG tracing at fixed time intervals.
The time interval field is editable, and may be changed by the user. In particular, it may be used to identify the point in the tracing associated with any time of interest, e.g. 200 ms into the cardiac cycle.
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Typical ECG window, showing the frontal leads generated by a simulated
normal cardiac cycle.
Click on image to enlarge. |
This button clears any extant tracings in the scrolling subwindow.
This field specifies the lead deflection in units of potential per box. This field may be edited by the user to enlarge/shrink the tracings vertically.
This field specifies the simulated paper speed of the tracings. This field may be edited by the user to enlarge/shrink the tracings horizontally.
If this box is checked, then the window is frozen.
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Typical Electrogram Viewer window, showing the unipolar traces generated by
the AV node (upper tracing) and a particular
Cell (lower tracing) in the ventricular septum
during a simulated normal cardiac cycle.
Click on image to enlarge. |
The Electrogram Viewer window is opened automatically when the Open Electrogram button of the Microscope Window is used to add a new trace.
Each trace in the scrolling subwindow is labelled with the quantized Cartesian coordinates of the associated Cell. Each tracing is temporally aligned with the start of the associated trial, so the temporal offsets at which Cells activate may be easily observed.
This field displays the potential per box used for displayed tracings. Its value is controlled by the associated slider.
This field displays the simulated paper speed at which the tracings are accumulated over simulated time, and is controlled by the associated slider.
This button removes all extant Cells from the window.
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Typical Bench Script Window.
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If a Bench Script is named "Bench Initialization Script", it is executed automatically every time the Bench is opened.
Hitting this button will cause CESLab to begin executing the script. The Bench Progress Window will be displayed while the script is being executed, indicating its progress and giving the user the ability to abort script execution.
Script execution continues until aborted by the user, the script terminates normally, or an error is encountered.
New Bench Scripts may be created via the New Bench Script menu bar command.
This button will delete the Bench Script from the Bench. No user confirmation is requested, and the operation cannot be undone.
This field displays the name of the Bench Script, and may be edited by the user.
The bottom of the Bench Script window contains a text box in which the contents of the Bench Script may be read/edited.
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Typical Modulator Window, associated with a modelled Class IA antidysrhythmic agent.
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This field displays the name of the Modulator, and may be edited by the user.
This button causes the Modulator to be deleted from the Bench without requesting confirmation from the user.
This button will write a summary to the Bench Log listing the Modulator Effect Modalities in which this Modulator is currently configured to operate, as well as an indication of whether non-tissue type-specific or tissue type-specific effects are defined.
This field specifies the current level (e.g. concentration) of this Modulator.
The scrolling subwindow at the bottom of the Modulator Window contains free-form comments to be associated with the Modulator, and may be edited by the user as desired.
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Typical Decremental Conduction Curve Editor window.
Click on image to enlarge. |
Any number of Decremental Conduction Curve Editor windows may be open simultaneously, displaying overlaid tracings as requested. This makes A/B comparison of different curves easier.
This slider controls the temporal interval across which Decremental Conduction curves are edited/displayed in the scrolling subwindow.
This button brings up a dialog box for adding a new trace to the scrolling subwindow. The trace may be non-tissue type-specific, or specific to any of the extant Tissue Types.
This slider controls the range of the numeric conduction speed rescale factors displayed in the scrolling subwindow.
This command removes all extant tracings from the scrolling subwindow. Note that this does not actually remove the Decremental Conduction Curves from the Preparation.
This button will write messages to the Bench Log summarizing the Decremental Conduction Curves currently defined for the Bench, both non-tissue type-specific and tissue type-specific.
The scrolling subwindow displays each tracing that was added via the Add Trace button for this window. If a dotted line is displayed at speed factor 1 beginning at relative refractory period offset zero and extending to the right, it denotes that no such Decremental Conduction Curve yet exists.
The displayed curves may be edited via the following mouse actions:
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Typical Modulator Effect Editor window, showing the curves defined for various
Modulator Effect Modalities
at various serum levels of a simulation of a Class IA drug.
Click on image to enlarge. |
This slider controls the level range across which Modulator Effect curves are edited/displayed in the scrolling subwindow.
This button brings up a dialog box for adding a new trace to the scrolling subwindow. Each trace has exactly one associated Modulator, and exactly one Modulator Effect Modality. The trace may be non-tissue type-specific, or specific to any of the extant Tissue Types.
This slider controls the range of the numeric Modulator Effect rescale factors displayed in the scrolling subwindow.
This command removes all extant tracings from the scrolling subwindow. Note that this does not actually remove the Modulator Effect curves from the Preparation.
The scrolling subwindow displays each tracing that was added via the Add Trace button for this window. If a horizontal dotted line is displayed at rescale factor 1 beginning at serum level zero and extending to the right, it denotes that no such Modulator Effect curve yet exists.
If any Modulator Effect trace is associated with a Modulator for which the serum level is currently non-zero, a dotted vertical line of the same color as the trace will be drawn indicating the current level.
The displayed curves may be edited via the following mouse actions:
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Typical Interval/Duration Curve Editor window.
Click on image to enlarge. |
This slider controls the Interactivation Interval range across which interval/duration curves are edited/displayed in the scrolling subwindow.
This button brings up a dialog box for adding a new trace to the scrolling subwindow. The trace may be non-tissue type-specific, or specific to any of the extant Tissue Types.
This slider controls the range of the numeric phase 2/3 duration rescale factors displayed in the scrolling subwindow.
This command removes all extant tracings from the scrolling subwindow. Note that this does not actually remove the interval/duration curves from the Preparation.
The scrolling subwindow displays each tracing that was added via the Add Trace button for this window. If a dotted line is displayed at duration factor 1 beginning at Interactivation Interval zero and extending to the right, it denotes that no such interval/duration curve yet exists.
The displayed curves may be edited via the following mouse actions:
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Typical Interval/Potential Curve Editor window.
Click on image to enlarge. |
This slider controls the Interactivation Interval range across which interval/potential curves are edited/displayed in the scrolling subwindow.
This button brings up a dialog box for adding a new trace to the scrolling subwindow. The trace may be non-tissue type-specific, or specific to any of the extant Tissue Types.
This slider controls the range of the numeric potential rescale factors displayed in the scrolling subwindow.
This command removes all extant tracings from the scrolling subwindow. Note that this does not actually remove the interval/duration curves from the Preparation.
The scrolling subwindow displays each tracing that was added via the Add Trace button for this window. If a dotted line is displayed at duration factor 1 beginning at Interactivation Interval zero and extending to the right, it denotes that no such interval/potential curve yet exists.
The displayed curves may be edited via the following mouse actions: