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Tack
The Manual
Introduction:
This manual describes the operation of the Tack data analysis
program. The current revision of this program is 3.20. This
software and manual are copyright 1993 through 1989 by George B.
Grant, Somerville, MA 02144.
Compatibilities:
Tack runs on IBM PC compatible computer systems. It operates
entirely in graphics mode. As such, it requires a compatible
graphics display adapter. Tack supports all major display adapters
(Hercules, CGA, EGA, VGA) and has drivers for several other
graphics display adapters including Super VGA. Tack works with a
Microsoft compatible mouse.
Tack is a data analysis program. It can read data files
created by Patchit, Ninja or those written in the pClamp version
5.1 file format.
Starting Up:
Tack runs entirely in graphics (not text) mode. In order for
it to run, a graphics driver for the graphics adapter that is
installed in the computer must be available in the directory in
which the Tack executable file is. These drivers have the file
extension ".bgi". The drivers required for the following screen
types are as follows:
Display Adapter Display Driver
Hercules (Hercules Graphics Adapter) herc.bgi
CGA (Color Graphics Adapter) cga.bgi
EGA (Enhanced Graphics Adapter) egavga.bgi
VGA (Video Graphics Adapter) egavga.bgi
Super VGA svga16m.bgi
(Supports several common SVGA cards and the VESA standard
SVGA interface)
IBM 8514 Graphics Adapter ibm8514.bgi
AT&T 400-Line Graphics Adapter att400.bgi
3270 PC Graphics Adapter pc3270
By default, Tack will automatically try to detect the proper
graphics driver for the computer. If the proper driver is not
found by Tack (in the same directory as Tack) when it is started it
will end with an error message. Otherwise the program will start
and Tack's main screen will appear.
The Screen:
Tack's main screen is divided into three areas. The menu bar
is on the top of the screen, it allows the user to access all of
the Tack's commands. The right-most portion of the menu bar shows
the amount of free conventional (real mode) memory available for
Tack's use. The lower part of the screen shows the status line.
This line displays information about the current status of the
program (which data file, channel and record is currently
selected). The data display area fills the screen between the menu
bar and the status line.
General:
Tack is a data analysis program. It can load multiple data
files. Each file will be loaded into its own "buffer". New
buffers can be created by the copy buffer operation or by the
result of adding, subtracting or averaging existing buffers. A
buffer, like a file, can contain multiple channels of data and
multiple records (a record is equivalent to a Clampex "episode").
Most of Tack's functions work on individual buffers, and these
commonly default to the current buffer. The current buffer is
indicated on the status line at the bottom of the screen. Buffers
are named with the letters of the alphabet and the current buffer
can be changed (when no menus are active) by typing the letter of
that buffer. The current buffer can be changed to the
next/previous buffer by typing the up/down arrow key. Similarly,
the current channel (in the current buffer) can be changed (when no
menus are active) by typing the number of the channel. Note that
channels are numbered from 0 (i.e. 0 is the first channel, 1 is the
second). The current channel can be changed to the next/previous
channel by typing the right/left arrow key. If the buffer only has
one channel of data then you won't be able to switch channels,
obviously. The current record works slightly differently. When
you select it (e.g., by Display:Record) it is both selected and
displayed. The next/previous record can be selected (and
displayed) by typing the plus/minus key.
In many of Tacks' functions, you will need to select a range
of timing within a data record. For these cases you have the
option of numerically selecting the timing (by entering the times
at the prompt) or by cursor selecting the timing. If you choose to
select the timing with cursor selection, then the screen will be
redrawn and the data record will be shown. You can use the mouse
or cursor keys to move the cursor. The home and end keys move the
cursor to the beginning and end of the data trace respectively.
The left and right arrow keys move the cursor to the one data point
to the left and right on the data trace respectively. Holding down
the shift key while typing the left and right arrow keys causes the
cursor to move by the step indicated by the "step" value shown on
the top line of the screen. This step value can be changed by
typing the plus key, which doubles this value (it eventually rolls
over). Holding down the CTRL key while typing the left and right
arrow keys causes the cursor to move by 1/20th of the width of the
displayed data. The cursor can be moved under mouse control by
holding down the left mouse button and moving the mouse to the left
and right. NOTE that if there are more data points in the
displayed data trace than there are points on the screen, then the
cursor (while under mouse control) will not move in increments of
the data points. For the finest control of timing you will need to
use the cursor keys in this case. Typing the "ESC" key allows you
to cancel the timing selection operation. Typing the Enter key, or
the right mouse button accepts the timing for this cursor. During
the cursor selection operation, the value (both real and 12-bit) of
the data and the time will be shown on lower line of the screen.
Help:
On-line help is available throughout Tack. Just type the F1
key and a relevant help message will pop up. The help file
"Tack.hlp" must be in the same directory as Tack and the graphics
driver files.
Accessing the Menus:
The menu bar has a series of pull down menus. A menu (e.g.
"File") can be accessed in a number of ways. 1) A menu can be
pulled down by clicking on the desired menu entry with the mouse.
2) A menu can be pulled down by holding down the ALT key while the
selection letter of the desired menu is typed (the selection letter
is usually the first letter of the word and is shown underlined and
in a different color from the rest of that word (unless the current
graphics display only supports two colors, or the color
configuration has been messed with)). For example, to pull down
the File menu, type ALT-F. 3) A menu can be pulled down by first
activating the menu bar with the F10 or "/" key. The file menu
will drop down, but not be selected. The selection letter of any
of the main menu items can then be typed in order to access that
particular menu.
Certain functions on the individual menus can be accessed
directly, without pulling down the menus, by typing a hot-key (the
hot-keys are shown to the left of a menu entry, on its menu). For
instance, the F8 key will cause Tack to load a data file if pressed
when the menu bar is not activated.
The Menus:
File Menu:
Load File: Selecting this option allows the user to load a new
data file into Tack. If there are data files in the current
directory (files with the extension ".dat"), a selection box will
appear listing the available data files. A data file may be cursor
selected from this box (with the mouse or keyboard) or else the
name of a file may be typed in (do not type the ".dat" extension).
To change directories, type the F2 key, or click the left mouse
button in the upper, directory, window and type the pathname of the
desired directory. The list of data files will be updated for this
new directory.
Save File: Selecting this option allows the user to save the
contents of the currently selected buffer to a new data file. You
will be prompted to specify the name of the data file (do not type
the ".dat" extension). If a file of this name already exists, Tack
will warn you and give you the option of overwriting that file or
else of choosing a new filename. You will then be asked if you
wish to keep the original file's time stamp. If you specify that
you want to do that thing, then the file creation date and time
will be set to that of the original file. If you specify not
(don't keep original file time stamp), then the creation date and
time will be set to the current date and time. This option is very
useful if you like to sort your files by date.
Export: Selecting this option allows the user to export data from
Tack in a variety of numerical formats. The export menu has eleven
options:
Buffer: Selecting this item allows the user to specify the buffer
whose data will be exported. The buffer selection box lists the
letter corresponding to the buffer and the name of the file that
was originally loaded into the buffer (unless the buffer contains
the result of a combination (addition, subtraction, etc.) of data
from two or more buffers, in which case the name is "untitled").
Channel: Selecting this item allows the user to select the channel
of data in the specified buffer that will be exported. Only one
channel of data may be exported in a single operation. If you need
to export data on multiple channels, you will need to perform the
export operation separate times, creating multiple files.
Records: Selecting this item allows the user to select which
records of data in the selected buffer, on the selected channel are
to be exported.
Time: Selecting this item allows the user to select the timing of
the data to be exported. The user has the option of cursor
selecting the timing from the data traces or else of entering the
times numerically.
Format: Selecting this item allows the user to specify the export
format for the data. Two formats are available, Ascii and
Asystant+. The Ascii format is a text file containing the data as
numbers separated by a user-specified character (the comma ","
character is typically used). The Asystant+ format writes a binary
data file that can be read by the Asystant+ data analysis program.
X Values: Selecting this item allows the user to select what
values will be written in the data file for the X axis (the
right-most column of data). This option is not available for the
Asystant+ export format. Three X axis options are available:
Time: The time (in milliseconds) of the data point.
Point #: The numerical point (beginning from 0) in the data at
which the point occurs.
None: No value is entered for the X axis.
Y Values: Selecting this item allows the user to select the format
of the values that are to be exported from the data. The normal
format is "Real Values", which causes the values to be the true
value of the data (this takes into account the gain). The other
format is "12 Bit" in which case the values written are the 12-bit
values (-2048 -> 2047) recorded by the data acquisition board.
Sample: Selecting this item allows the user to select whether or
not to undersample the data in the exported file. The data can
either not be undersampled or else undersampled by a factor as much
as 20 (every twentieth data point is written to the data file).
This feature is useful if your exported data files are too large.
Go!: Selecting this item causes the export operation to begin.
You will be prompted for the name of the file to which the data
will be exported. If a file of this name already exists, Tack will
warn you and give you the option of overwriting the file or else of
choosing a new name.
Quit: Selecting this item cancels this operation and the data is
not exported.
DOS Shell: When this is selected the user temporarily exits to DOS
to perform simple commands. In order to allow this, Tack "spawns"
a copy of the DOS command interpreter. Note that Tack is still
loaded in memory so there will be less DOS memory available to
execute a command. Type "EXIT" at the DOS command line ("C:\>") to
return to Tack.
Plot: When this option is selected Tack plots (or prints) data
traces to the currently selected printer/plotter using the
currently displayed data as its guide. If a printer/plotter has
not been selected then Tack will nag you to select one (see
Config:Printer).
If Tack has been configured to print to file, you will be
prompted for the name of the file to write. You will then be
prompted to hit any key to begin printing, you may abort the
process here with the ESC key or the right mouse button.
Otherwise, Tack will print/plot. As mentioned, Tack uses what is
on the screen as its guide for printing. All displayed buffers
will be printed at their current scale factor. If scale bars are
displayed (see Display:Scale Bars), then they will be printed.
Note that Tack will only print once per buffer. That means that if
you have displayed data records from a single buffer more than once
on the screen (for instance using different magnifications) then
only one will be printed/plotted.
About: When this option is selected Tack will display informative
things about itself, these can be selected from the submenu:
Data: Selecting this item causes information to be displayed about
the data stored in one of Tack's buffers. If more than one buffer
is loaded, then you will be prompted for the buffer to display
information about. A menu appears with the following items:
A/D Info: General information about the data and how it was
sampled.
Gain List:: Displays the gains for all of the channels and records
of data in the buffer.
D/A Info: Displays information about the Output waveform used
during data acquisition.
Comments: Displays any comments recorded with the data file.
Quit: Closes the menu.
Memory: Selecting this item causes a box to appear citing
information about the memory available and in use by Tack. There
are three types of memory used by Tack.
Conventional Memory: This is the memory used by all DOS real mode
programs it is limited to a maximum of 640 Kilobytes (KB). Tack
will show you the total amount and the amount available.
XMS Memory: This is memory above the 1 Megabyte boundary that can
be accessed by Tack if an XMS driver (such as Microsoft's
Himem.sys) is loaded. XMS memory allows Tack to store a great deal
of data without filling up the DOS (conventional) memory area. If
XMS is available Tack will store data in it. The handle to and the
amount of XMS memory used by each buffer are shown.
Disk Memory: This shows the total amount and available amount of
disk space on the current disk.
Tack: Selecting this item causes a box to appear citing
information about Tack (it's current revision level), a copyright
notice and information about its author (me!).
Quit Program: Selecting this item allows the user to exit the
program.
Buffer Menu:
Copy Buffer: Selecting this option allows the user to copy the
data in one of Tack's buffers to another buffer. The copy buffer
menu has four entries:
Source Buffer: This is the buffer from which the data is to be
copied. If only one buffer is loaded, then this is automatically
set to that buffer. Otherwise, selecting this item brings up a
selection box from which the user can choose the buffer to copy
from.
Dest Buffer: The buffer to which the data is to be copied.
Selecting this item brings up a selection box from which the user
can select the buffer to copy to. The user can either overwrite
existing data in an already loaded buffer or else copy into a new
buffer.
Go!: Selecting this item causes the buffer to be copied.
Quit: Selecting this item cancels this operation and the buffer is
not copied.
Delete: Selecting this option allows the user to delete various
things from Tack's memory (not disk). The delete menu has five
entries:
Buffer: Selecting this allows the user to delete the contents of
a single buffer. Select the buffer you wish to delete from the
selection box that appears. Once a buffer is deleted, all buffers
above it are shifted down. So, if you have four buffers loaded
(A-D) and delete buffer B, then you will end up with three buffers
(A-C), where buffer B now contains what was in C previously and
buffer C contains what was in D previously.
All Buffers: Selecting this allows the user to delete all data
that is loaded in Tack. The contents of all buffers are deleted.
Channel: Selecting this allows the user to delete a single channel
of data from the current buffer. If there is only one channel of
data in the current buffer, then the entire buffer will be deleted.
The current buffer is shown on the bottom of the screen on the
status line.
Records: Selecting this allows the user to delete a range of data
records from the current buffer. If you select all of the records
in the buffer, then the entire buffer will be deleted. The current
buffer is shown on the bottom of the screen on the status line. If
the current buffer contains multiple channels of data, then the
selected range of records will be deleted from all channels in the
buffer.
Quit: Selecting this item exits from this menu.
Modify: Selecting this option allows the user to modify various
aspects of data that is loaded in Tack's memory (not disk). The
modify menu has five entries:
Sampling Int: Selecting this allows the user to change the
sampling interval of the data in the current buffer. The value for
the sampling interval entered here must be larger than the existing
sampling interval, and must be an integer multiple of the old
value. Tack will enforce this.
NOTE: It is not good practice to change the sampling interval
of data after it has been recorded. This feature was implemented
as a means of reducing the number of data points for generating
HPGL plots (as some programs to which HPGL data is imported cannot
handle HPGL plots with large numbers of points).
Timing: Selecting this allows the user to change the timing of the
data in the current buffer. The new timing range can be entered
either numerically or graphically (by cursor selecting the timing
in the data trace with the mouse and cursor keys).
Gain: Selecting this item allows the user to change the gain for
the data in the current buffer.
NOTE: The gain of the data is not likely to change after the
data has been recorded. This feature was implemented in order to
allow you to correct for stupid errors.
Data: Selecting this allows the user to change the values of the
data loaded into Tacks' buffers. The modify data menu has five
options:
Buffer: This allows the user to select the buffer whose data will
be modified.
Channel: This allows the user to select the channel of data in the
selected buffer whose data will be modified.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, will be modified.
Operation: This allows the user to select the operation to perform
on the data. Five operators are available, these allow the user to
combine the selected data with a user-specified factor:
* Multiply: This multiplies the selected data by a user-specified
factor. The user will be queried as to whether to scale the gain
of the data accordingly. You would typically answer yes.
/ Divide: This divides the selected data by a user-specified
factor. The user will be queried as to whether to scale the gain
of the data accordingly. You would typically answer yes.
+ Add: This adds to the data a user-specified factor. Note that
in this case, the user-specified factor is 12-bit, i.e., -2048 to
2047.
- Subtract: This subtracts from the selected data a user-specified
factor. Note that in this case, the user-specified factor is
12-bit, i.e., -2048 to 2047.
Separate Recs: This separates (staggers) the data records from
each other by a user-specified factor. Note that in this case, the
user-specified factor is 12-bit, i.e., -2048 to 2047.
Go: Selecting this causes the selected operation to be performed
on the selected data.
Quit: Selecting this closes the menu. The selected operation is
not performed on the selected data.
Quit: Selecting this item exits this menu.
Add: Selecting this option allows the user to add the data in two
of Tacks' buffers together. The resultant data may be stored in
another buffer or overwrite one of the original buffers. Between
the two buffers, channel 0 is added to channel 0, channel 1 is
added to channel 1, etc., and record 1 is added to record 1, record
2 is added to record 2 etc. If the buffers have unequal numbers of
records or channels, then Tack will use the least common
denominator between the two buffers.
NOTE: Tack does not check that the gains for the two buffers
are the same. You should ensure that the data you wish to add
together were recorded at the same gains! Or else you must scale
the data to compensate for the different gains (use
Buffer:Modify:Data).
The add menu has five entries:
X Adder: This is one of the two buffers to add together.
Selecting this brings up a selection box from which the user can
select this buffer.
Y Addend: This is the buffer which is to be added to the adder
buffer (above). Selecting this brings up a selection box from
which the user can select this buffer.
Z = X+Y Dest: This is the buffer to which the result of the
addition operation is to be written. Selecting this brings up a
selection box from which the user can select the destination
buffer. The user can either overwrite existing data in loaded
buffers or else copy the buffer's contents to a new buffer.
Go!: Selecting this causes the buffer addition to occur.
Quit: Selecting this cancels this operation, the buffer addition
does not occur.
Subtract: Selecting this option allows the user to subtract the
data in one of Tacks' buffers from the data in another buffer. The
resultant data may be stored in another buffer or overwrite one of
the original buffers. Between the two buffers, channel 0 is
subtracted from channel 0, channel 1 is subtracted from channel 1,
etc., and record 1 is subtracted from record 1, record 2 is
subtracted from record 2 etc. If the buffers have unequal numbers
of records or channels, then Tack will use the least common
denominator between the two buffers.
NOTE: Tack does not check that the gains for the two buffers
are the same. You should ensure that the data you wish to subtract
were recorded at the same gains! Or else you must scale the data
to compensate for the different gains (use Buffer:Modify:Data).
The subtract menu has five entries:
X Subtractor: This is the buffer from which the subtrahend buffer
is to be subtracted. Selecting this brings up a selection box from
which the user can select this buffer.
Y Subtrahend: This is the buffer which is to be subtracted from
the subtractor buffer (above). Selecting this brings up a
selection box from which the user can select this buffer.
Z = X-Y Dest: This is the buffer to which the result of the
subtraction operation is to be written. Selecting this brings up
a selection box from which the user can select the destination
buffer. The user can either overwrite existing data in loaded
buffers or else copy the buffer's contents to a new buffer.
Go!: Selecting this causes the buffer subtraction to occur.
Quit: Selecting this cancels the operation and the buffer
subtraction does not occur.
Average: Selecting this option allows the user to average the data
in two of Tacks' buffers. The resultant data may be stored in
another buffer or overwrite one of the original buffers. Between
the two buffers, channel 0 is averaged with channel 0, channel 1 is
averaged with channel 1, etc., record 1 is averaged with record 1,
record 2 is averaged with record 2 etc. If the buffers have
unequal numbers of records or channels, then Tack will use the
least common denominator between the two buffers.
NOTE: Tack does not check that the gains for the two buffers
are the same. You should ensure that the data you wish to average
were recorded at the same gains! Or else you must scale the data
to compensate for the different gains (use Buffer:Modify:Data).
The average menu has five entries:
X Buffer 1: This is one of the buffers to average. Only two
buffers may be averaged together. Selecting this item brings up a
selection box from which the user can select this buffer.
Y Buffer 2: This is the other buffer to average. Only two buffers
may be averaged together. Selecting this item brings up a
selection box from which the user can select this buffer.
Z Destination: This is the buffer to which the result of the
averaging operation is to be written. Selecting this item brings
up a selection box from which the user can select the destination
buffer. The user can either overwrite existing data in loaded
buffers or else copy the buffer's contents to a new buffer.
Go!: Selecting this causes the buffers to be averaged.
Quit: Selecting this cancels this operation, the buffers are not
averaged.
Edit Menu:
Normalize: Selecting this option allows the user to subtract
baseline data from data. The normalize menu has six entries:
Buffer: This allows the user to select the buffer whose data will
be normalized.
Channel: This allows the user to select the channel of data in the
selected buffer whose data will be normalized.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, will be normalized.
Timing: This allows the user to select the timing of the baseline
segment of the data. The user may select the baseline timing
either graphically or numerically.
Go!: Selecting this item causes the selected data records to be
normalized.
Quit: Selecting this item cancels this operation, the selected
data records are not normalized.
Leak Subtract: Selecting this option allows the user to subtract
a "leak" current (time-invariant current, that scales linearly with
voltage) from the data. This function is implemented for data
records that represent current. The leak subtract menu has eight
entries:
Buffer: This allows the user to select the buffer whose data will
be leak subtracted.
Channel: This allows the user to select the channel of data in the
selected buffer whose data will be leak subtracted.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, will be leak subtracted.
Input Res: This allows the user to specify the resistance that
will be used to calculate the leak current. The user can enter the
input resistance (in megaohms) or else can choose to calculate the
input resistance from the data. If you choose to calculate the
input resistance, when you select go (see below), you will be
transferred to function that will calculate this (see Measure:Input
Resistance, below).
V (mV): This allows the user to specify the voltage range for the
range of records that you wish to leak subtract. If more than one
record is specified, you will be prompted for a voltage and an
increment. The voltage, should be the voltage for the starting
record, the increment specifies how much the voltage is to be
incremented with each successive record. The starting voltage
should be relative to the holding potential.
Timing: This allows the user to select the range of timing in the
data records that will be leak subtracted. This timing may be
selected either graphically or numerically.
Go!: Selecting this item causes the selected data records to be
leak subtracted.
Quit: Selecting this item cancels this operation, the selected
data records are not leak subtracted.
Average Recs: Selecting this option allows the user to overwrite
a data record in a buffer with the average of a range of data
records from that buffer. The average recs menu has six entries:
Buffer: This allows the user to select the buffer whose data
records will be averaged.
Channel: This allows the user to select the channel of data in the
selected buffer whose data records will be averaged.
Records to Average: This allows the user to select which data
records, on the selected channel, in the selected buffer, will be
averaged.
Overwrite Record: This allows the user to select the data record
that will be overwritten with the average of the records specified
above.
Go!: Selecting this item causes the selected data records to be
averaged.
Quit: Selecting this item cancels this operation, the selected
data records are not averaged.
Scale 'n Sub: Selecting this option allows the user to subtract
from a range of data records a scaled copy of the data in a given
record. The algorithm used is as follows:
record#i = record#i - factor * model_rec,
where
factor = (i - zero_level) / (model_rec - zero_level).
The normalize menu has six entries:
Buffer: This allows the user to select the buffer whose data
records will be scaled and subtracted.
Channel: This allows the user to select the channel of data in the
selected buffer whose data will be scaled and subtracted.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, will have a scaled copy
of the model record (see below) subtracted from them.
Model Rec: This allows the user to specify which data record to
scale and subtract from the other specified records in this buffer.
Zero Level: This allows the user to specify the record at which
the data traces would change sign. This does not have to be an
integer value, you may use a fractional value if needed. This
value is used in calculating the scaling factor (see above).
Go!: Selecting this item causes the scale 'n sub operation to
occur.
Quit: Selecting this item cancels this operation, the scale 'n sub
operation does not occur.
Smooth: Selecting this option allows the user to smooth (low-pass
filter) the data. The smooth menu has eight entries:
Buffer: This allows the user to select the buffer whose data will
be smoothed.
Channel: This allows the user to select the channel of data in the
selected buffer whose data will be smoothed.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, will be smoothed.
Timing: This allows the user to select the range of timing in the
selected data records, over which the data will be smoothed. The
user may select this timing either graphically or numerically.
Smooth By: Selecting this allows the user to select the smoothing
method that will be used. Three smoothing methods are available,
a Gaussian filter, a moving average (rolling window) and a FFT
(fast fourier transform)-based algorithm. The Gaussian Filter
lowpass filters the data with a user-specified -3db cutoff freq.
This uses the algorithm from "Single Channel Recording" ed. B.
Sakmann & E. Neher, Chap 11. The moving average algorithm
successively takes the local average of a number of data points
around some central data point and then replaces the central data
point with the average. The FFT algorithm, performs a FFT on the
data, and then low pass filters it and then reverse FFTs it. This
uses an algorithm from Numerical Recipes in C.
Cutoff Freq/Window Size/Degree: Selecting this allows the user to
specify the parameter that determines the amount of smoothing that
will happen to the data. This menu entry has a different name
depending on what smoothing algorithm is selected. Cutoff freq -
this specifies the -3db cutoff frequency for the Gaussian Filter.
Window Size - this specifies the width of the window over which the
data will be locally averaged for the Moving Average algorithm.
Degree - this specifies the point in frequency space where the
smoothing begins for the FFT algorithm. For the latter two
algorithms, higher values give more smoothing.
Go!: Selecting this item causes the selected data records to be
smoothed.
Quit: Selecting this item cancels this operation, the selected
data records are not smoothed.
Display Menu:
Buffer: Selecting this item allows the user to select the current
buffer. If more then one buffer is loaded, a selection box will
appear from which the user can select a buffer. The current buffer
is indicated on the status line at the bottom of the display.
Buffers may also be selected with the up or down cursor keys or by
typing the letter of the buffer (these only work no menu is
currently selected).
Channel: Selecting this item allows the user to select the current
channel of data in the current buffer. The current channel is
shown on the status line on the bottom of the display.
Record: Selecting this item allows the user to select the current
data record in the current buffer on the current channel. The
current record is then displayed on the screen. This differs from
the Display:Buffer and Display:Channel in that in addition to
selecting the record, the data is also displayed on the screen.
The current record is shown on the status line on the bottom of the
display.
Clear Screen: Selecting this option clears the data display area.
All Records: Selecting this option causes all of the records in
the currently selected buffer on the currently selected channel to
be displayed in the data display area. The current record is set
to the last record in the buffer.
Zoom: Selecting this option allows the user to zoom in on (or
reset the zoom of) the currently displayed data records. The zoom
menu has four options.
Dynamic: This allows the user to select the scale factor, offset
factor and range of timing used for zooming in on the data, in a
dynamic fashion. The user marquee-selects the part of the data
traces to zoom in on. All displayed data traces are redrawn to
zoom in on the selected area.
Select the area in the data traces that you want to zoom
in on. Use the mouse or keyboard: Marquee-select a region using
the mouse (click and drag). Once you release the mouse button you
will zoom in. Or: Use the cursor keys to move the box. Hold the
shift key down while using the cursor keys in order to resize the
box. For both of these ops, the amount of box movement for each
keystroke is controlled by the step factor, which can be increased
or decreased using the + and - keys. Hit return when done, or else
cancel with ESC.
Manual: Selecting this allows you to set the scale factor, offset
factor and timing range used for scaling manually. You will select
these values for a single buffer at a time and any displayed data
for this buffer will be redrawn at the new zoom factors. There are
six entries on the manual zoom menu.
Buffer: This allows you to select the buffer whose data records
you will be setting the scale, offset and timing ranges for.
Scale by: This allows you to enter manually the scale factor at
which records are displayed (magnified by). When you enter a value
for this parameter, all displayed records will redraw at this scale
factor.
Offset: This allows you to enter manually the offset factor by
which records are vertically offset when displayed. 0 would cause
no offset, 1.0 would cause the displayed records to move to the top
of the screen, -1.0 to the bottom of the screen etc. If a number is
entered for this parameter, all displayed records will redraw using
this offset factor.
Timing: This allows you to enter manually the range of timing over
which records in the currently selected buffer will be displayed.
Reset: This causes the scale factor, offset factor and timing
range to be reset for the currently selected buffer. All displayed
records for the currently selected buffer are redrawn.
Quit: Selecting this exits this menu.
Reset: This causes the scale factor, offset factor and timing
range to be reset for all displayed data in ALL buffers. All
displayed records are redrawn.
Quit: Selecting this exits this menu.
Scale Bars: This allows the user to display scale bars for your
data. The scale bars are displayed for the data in the currently
selected (and displayed) record, on the selected channel in the
selected buffer. The scale bar menu has five entries.
Height: This allows the user to enter the height, or amplitude of
the scale bar.
Width: Enter the width (in msec) of the scale bar.
Label?: This allows you to select whether or not to label the
scale bars.
Go!: Selecting this draws and allows you to control the placement
of the scale bars. The screen clears and you can move and change
the orientation of the scale bars. Use the cursor keys or mouse to
move the scale bars around the screen. The "+" key changes the
cursor key movement increment. Hitting The space bar rotates the
scale bars. Hit Enter when done, or ESC to cancel.
Quit: Selecting this cancels the operation, the scale bars are not
drawn.
Measure Menu:
Dynamic Scan: Selecting this allows the user to take measurements
from the current record, on the current channel in the current
buffer. Using the cursor, you can measure values and times from
the data. The lower line of the screen indicates the value of the
data at the time where the cursor is. Use the cursor keys or the
mouse to move the cursor (vertical scan bar). For cursor movement,
the + key changes the movement increment. Ctrl-Cursor Keys make
bigger jumps. The Enter key (or right mouse button) drops the 1st
cursor and starts a second cursor. The ESC key aborts the dynamic
scan operation. If two cursors are in place then hitting the F2
key will calculate the mean of the data over the timing range,
hitting the F3 key will calculate the minimum and maximum values of
the data over the timing range, hitting the F4 key will calculate
the area under the curve for the timing range. Hitting the F5 key
fits a line (mx+b) to the data for the timing range.
Values: Selecting this allows you to make a series of measurements
from the data. The measurements can be displayed graphically or
numerically and can be saved to a file. The measure values menu
has ten options.
Type: Selecting this allows you to specify the type of measurement
that will be made from the data. The five measurement types are:
Average Value, Minimum Value, Maximum Value, Point Value, and
Integral Value. Average value calculates the average of the data
over the timing selected, the mean and standard deviation will be
calculated. Minimum and Maximum Value find the minimum and maximum
value, respectively for the data over the timing selected. Point
value calculates the value of the data at a single point in time.
Integral value calculates the integral of the data (area under the
data curve) over the timing selected.
Buffer: This allows the user to select the buffer whose data you
wish to make the measurements of.
Channel: This allows the user to select the channel of data in the
selected buffer whose data you wish to make measurements of.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, you wish to make
measurements of.
X Axis Values: This allows the user to enter the type of values
that will be put on the X axis of the data plot (and which would be
put in the first column of an ASCII data file). The X axis may be
either the record number or voltage. For voltage, the values are
entered as such: the voltage of the first record in the series, and
an increment, which is how much the voltage is incremented with
each successive record.
Baseline Timing: This allows the user to select the range of time
in the data records which is the baseline for measuring the values.
The timing can be selected numerically or by cursor selection. If
you have selected to make measurements relative to the baseline,
the average value of the data over the baseline timing will be
subtracted from the values measured over the data timing.
Data Timing: This allows the user to select the range of time in
the data records within which the values will be measured. The
timing can be selected numerically or by cursor selection. Note
that if you are measuring at a single point in time, this will be
only a single time point.
Measurements: This allows the user to specify whether the
measurements that you make should be the actual values of the data
or relative to a baseline measurement.
Go!: Selecting this causes the measurement operation to proceed.
If you have chosen to graphically select any of the timing, the
screen will clear and allow you to do this. After the timings have
all been selected, the measurements will be plotted on the screen
and you have several options. Hit any key to bring up the menus.
File Data: This allows the user to put the numerical measurements
into an ASCII (text) file for use in other programs.
View Data: This allows the user to view the numerical data.
Review Plot: Selecting this clears away the menus so that you can
see the plot unobstructed.
Quit: Selecting this leaves this menu.
Quit: Selecting this leaves the measure values menu.
Mean/Variance: Selecting this allows you to make a mean/variance
plot from your data. The variance of the data will be plotted vs
the mean. This is useful for estimating single channel
conductances from whole-cell currents. The mean/variance plot can
be displayed graphically or numerically and can be saved to a file.
The measure mean/variance menu has seven options.
Buffer: This allows the user to select the buffer whose data you
wish to make the mean/variance analysis from.
Channel: This allows the user to select the channel of data in the
selected buffer whose data you wish to make the mean/variance
analysis from.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, you wish to make the
mean/variance analysis from.
Data Timing: This allows the user to select the range of time in
the data records over which the mean and variance will be measured.
The timing can be selected numerically or by cursor selection.
Subdivisions: This allows the user to subdivide the timing
specified by Data Timing (above) into multiple, equally sized
subdivisions. This allows you to generate multiple mean/variance
data points from each record.
Go!: Selecting this causes the mean/variance measurements to
proceed. If you have chosen to graphically select any of the
timing, the screen will clear and allow you to do this. After the
timings have all been selected, the mean/variance plot will appear
on the screen and you have several options. Hit any key to bring
up the menus.
File Data: This allows the user to put the mean and variance
measurements into an ASCII (text) file for use in other programs.
View Data: This allows the user to view the numerical data.
Review Plot: Selecting this clears away the menus so that you can
see the plot unobstructed.
Quit: Selecting this leaves this menu.
Quit: Selecting this leaves the measure mean/variance menu.
Histogram: Selecting this allows you to make a histogram from your
data. The frequency of occurrence of data values within the
specified bin width will be plotted. The histogram can be
displayed graphically or numerically and the data can be saved to
a file. The histogram menu has nine options.
Buffer: This allows the user to select the buffer whose data you
wish to make the histogram from.
Channel: This allows the user to select the channel of data in the
selected buffer whose data you wish to make the histogram from.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, you wish to make the
histogram from.
Timing: This allows the user to select the range of time in the
data records over which the histogram will be measured. The timing
can be selected numerically or by cursor selection.
Histogram Range: This allows the user to select the range of
values within the data records, over which the histogram will be
calculated.
Width of Bin: This allows the user to select the size of the bin
used in calculating the histogram. The number and width of the
bins are interrelated with the histogram range.
Number of Bins: This allows the user to select the number of bins
used for the histogram. The number and width of the bins are
interrelated with the histogram range.
Go!: Selecting this causes the histogram calculation to proceed.
If you have chosen to graphically select the timing, the screen
will clear and allow you to do this. After the timing has been
selected, the histogram plot will appear on the screen and you have
several options. Hit any key to bring up the menus.
File Data: This allows the user to put the histogram measurements
into an ASCII (text) file for use in other programs.
View Data: This allows the user to view the histogram data in a
numerical format.
Review Plot: Selecting this clears away the menus so that you can
see the histogram plot unobstructed.
Quit: Selecting this leaves this menu.
Quit: Selecting this leaves the measure histogram menu.
Power Spectrum: Selecting this allows the user to generate a power
spectrum from data. The power spectrum can be displayed
graphically or numerically and the data can be saved to a file.
The power spectrum menu has nine options.
Buffer: This allows the user to select the buffer whose data you
wish to make the power spectrum from.
Channel: This allows the user to select the channel of data in the
selected buffer whose data you wish to make the power spectrum
from.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, you wish to make the
power spectrum from.
Timing: This allows the user to select the range of time in the
data records over which the power spectrum will be measured. The
timing can be selected numerically or by cursor selection.
Number of Poles: This allows the user to select the number of
poles (or order) for the power spectrum. This determines the
sharpness of the spectral features you can measure in the spectrum.
In practice you wants to limit the order to a few times the number
of sharp spectral features that you want to fit. Limiting it in
this fashion will smooth the spectrum somewhat, but this is often
desirable. Try values of 10-50 for 1000 to 10000 data points.
Note that the algorithm used can be quirky for large numbers of
poles and will suggest spurious peaks in the spectrum, or might
find multiple peaks for a single true spectral peak. So try to use
the smallest values.
Frequency Range: This allows the user to select the frequency
range over which the power spectrum will be calculated. Note that
the maximum frequency for which you can calculate the power
spectrum is limited to one half the sampling frequency. The
frequency range and interval are interrelated and limited to 16383
data points.
Freq Interval: This allows the user to select the frequency
interval for the power spectrum. The frequency interval and range
are interrelated and limited to 16383 data points.
Go!: Selecting this cause the power spectrum calculation to
proceed. If you have chosen to graphically select the timing, the
screen will clear and allow you to do this. After the timing has
been selected, the power spectrum will be calculated and plotted on
the screen, you then have several options. Hit any key to bring up
the menus.
File Data: This allows the user to put the power spectrum
measurements into an ASCII (text) file for use in other programs.
View Data: This allows the user to view the power spectrum data in
a numerical format.
View Coefficients: This allows the user to view the coefficients
used in generating the power spectrum. This probably isn't very
useful to you.
Review Plot: Selecting this clears away the menus so that you can
see the power spectrum plot unobstructed.
Quit: Selecting this leaves this menu.
Quit: Selecting this leaves the measure power spectrum menu.
Input Resistance: Selecting this allows the user to calculate the
input resistance for data recorded under voltage-clamp. The input
resistance is best calculated from data that has no
voltage-activated currents. The input resistance menu has eight
entries:
Buffer: This allows the user to select the buffer whose data you
wish to calculate the input resistance from.
Channel: This allows the user to select the channel of data in the
selected buffer whose data you wish to calculate the input
resistance from.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, whose data you wish to
calculate the input resistance from.
V (mV): This allows the user to specify the voltage range for the
range of records that you wish to calculate the input resistance
from. If more than one record is specified, you will be prompted
for a voltage and an increment. The voltage, should be the voltage
for the starting record, the increment specifies how much the
voltage is to be incremented with each successive record. The
starting voltage should be relative to the holding potential.
Baseline Timing: This allows the user to select the range of
timing in the data records that is the baseline for calculating the
input resistance. The baseline timing may be selected either
graphically or numerically.
Data Timing: This allows the user to select the range of timing in
the data records over which the input resistance will be
calculated. This timing may be selected either graphically or
numerically.
Go!: Selecting this item causes the input resistance to be
calculated and displayed in megaohms. If you have chosen to
graphically select the timing(s), the screen will first clear and
allow you to do this.
Quit: Selecting this item cancels this operation, the input
resistance is not calculated.
Cell Capacitance: Selecting this allows the user to calculate the
cell capacitance for data recorded under voltage-clamp. The
capacitance is measured by calculating the area under a
voltage-clamp current transient. Data should be leak subtracted
first, no voltage-activated currents should be active in the data.
The cell capacitance menu has eight entries:
Buffer: This allows the user to select the buffer whose data you
wish to calculate the cell capacitance from.
Channel: This allows the user to select the channel of data in the
selected buffer whose data you wish to calculate the cell
capacitance from.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, whose data you wish to
calculate the cell capacitance from.
V (mV): This allows the user to specify the voltage range for the
range of records that you wish to calculate the cell capacitance
from. If more than one record is specified, you will be prompted
for a voltage and an increment. The voltage, should be the voltage
for the starting record, the increment specifies how much the
voltage is to be incremented with each successive record. The
starting voltage should be relative to the holding potential.
Baseline Timing: This allows the user to select the range of
timing in the data records that is the baseline for calculating the
cell capacitance. The baseline timing may be selected either
graphically or numerically.
Data Timing: This allows the user to select the range of timing in
the data records over which the cell capacitance will be
calculated. This timing should encompass the full width of the
capacitive transient. The data timing may be selected either
graphically or numerically.
Go!: Selecting this item causes the cell capacitance to be
calculated and displayed in picofarads. If you have chosen to
graphically select the timing(s), the screen will first clear and
allow you to do this.
Quit: Selecting this item cancels this operation, the cell
capacitance is not calculated.
Series Resistance: Selecting this allows the user to calculate the
series resistance for data recorded under voltage-clamp. The
series resistance is measured by calculating the height of a
voltage-clamp transient. Data should be leak-subtracted first.
Note that this method is not the best method to calculate Rs, and
will give an underestimate. The series resistance menu has eight
entries:
Buffer: This allows the user to select the buffer whose data you
wish to calculate the series resistance from.
Channel: This allows the user to select the channel of data in the
selected buffer whose data you wish to calculate the series
resistance from.
Records: This allows the user to select which data records, on the
selected channel, in the selected buffer, whose data you wish to
calculate the series resistance from.
V (mV): This allows the user to specify the voltage range for the
range of records that you wish to calculate the series resistance
from. If more than one record is specified, you will be prompted
for a voltage and an increment. The voltage, should be the voltage
for the starting record, the increment specifies how much the
voltage is to be incremented with each successive record. The
starting voltage should be relative to the holding potential.
Baseline Timing: This allows the user to select the range of
timing in the data records that is the baseline for calculating the
series resistance. The baseline timing may be selected either
graphically or numerically.
Data Timing: This allows the user to select the range of timing in
the data records over which the series resistance will be
calculated. This timing may be selected either graphically or
numerically.
Go!: Selecting this item causes the series resistance to be
calculated and displayed in megaohms. If you have chosen to
graphically select the timing(s), the screen will first clear and
allow you to do this.
Quit: Selecting this item cancels this operation, the series
resistance is not calculated.
Config Menu:
Graphics Display: Selecting this option allows the user to specify
the type of graphics display installed and the display resolution
that Tack should use. Normally, the graphics autodetect setting
should be used. For a given display type to be used, the requisite
display driver file (they have the extension ".bgi") MUST be
present in the same directory as Tack.
Display Type: Selecting this option allows the user to select a
graphics display type. Twelve settings are available.
Note: If your computer does not support the display type that you
have selected, you may well crash the program when you try to
switch display types.
Resolution: Selecting this option allows the user to select a
display resolution for the selected display type. Note that some
display types have only one available resolution.
Note: If your computer's display adapter does not support the
resolution that you have selected, you may well crash the program
when you try to switch display resolutions.
Okay: Selecting this option causes any changes that have been made
to the graphics display type and resolution to go into effect.
Cancel: Selecting this option causes any changes that have been
made to the graphics display type and resolution to be cancelled.
Colors: When this option is selected a color demonstration window
appears and a menu appears from which the user can select the
colors of the various components of the Tack screen. The various
components are the menu bar, status line, popup boxes and data
window. For menus, the user can control the background, text,
frame and select letter colors. For the status line, the user can
control the background and text colors. For popup boxes, the user
can control the background, text and frame colors. For the data
window, the user can control the background, frame and axis colors
as well as the colors for the data in up to eight buffers.
Menus:
Status Line:
Popup Boxes:
Data Window:
When the user selects one of these menu options, another menu
appears from which the user can select the color for the elements
of the windows (i.e. frame color of popup window). Clicking on an
element will select the next available color for that element, this
will be shown in the color demonstration window. Typing the select
letter of that element will do the same. Holding the SHIFT key
down while typing the select letter of that element will select the
previous color for that element. Select Okay when you are done
setting the colors.
Use Defaults: When this option is selected, the colors of all of
the elements of the Tack display revert to their default settings.
Okay: Selecting this option causes any changes that have been made
to the color scheme to go into effect.
Cancel: Selecting this option causes any changes that have been
made to the color scheme to be cancelled.
Font: Selecting this option allows the user to specify the font
that will be used by Tack. For all but the default font, the
requisite font file (they have the extension ".chr") MUST be
present in the same directory as Tack. An example of some text
written in the selected font is displayed.
Font: Selecting this option allows the user to select the font
family that will be used by Tack. Eleven font families are
available. The default font is a bit-mapped font, the others are
stroked (outline) fonts.
Height: Selecting this option allows the user to set the height of
the font that will be used by Tack. If the selected font family is
the default, bit-mapped font, the height and the width must be the
same.
Width: Selecting this option allows the user to set the width of
the font that will be used by Tack. If the selected font family is
the default, bit-mapped font, the height and the width must be the
same.
Okay: Selecting this option causes any changes that have been made
to the font to go into effect.
Cancel: Selecting this option causes any changes that have been
made to the font to be cancelled.
Printer: Selecting this option allows the user to specify the type
of printer that Tack will use and its configuration.
Printer: Selecting this option allows the user to specify the type
of printer that is installed. Six printer options are available:
None: No printer is attached.
Apple Imagewriter II: This printer configuration will also work
with a C-Itoh 8510.
IBM Proprinter: This printer configuration will also work with
many other Epson compatible printers.
HP Laserjet 2: This printer configuration will also work with many
other PCL-4 compatible printers.
HP Plotter (HPGL): This printer configuration will also work with
many other HPGL compatible printers. It is useful to select this
mode and print to a file in order to export data traces for use in
other programs.
HP Laserjet 3: This printer configuration uses the HPGL mode of
PCL-5. BUT, unless your printer has a bunch of memory it may not
work. Use Laserjet Series II mode in that case.
Destination: Selecting this option tells Tack where to find your
printer. The destination can be to file, or the selected parallel
or serial port. If the destination is file, then whenever you
print, the print job will go to a file in the format used by the
selected printer. Printing to file is useful for exporting data
traces in a graphical format, using HPGL files. If the destination
is a serial port, the menu that appears will allow you to configure
Tack to use the same serial port configuration as the serial
printer you have attached.
Orientation: Selecting this option allows the user to set the
orientation for the print job, landscape (wide) or portrait
(narrow).
Settings: Selecting this option allows the user to controls
settings for specific printers. For dot matrix printers, this
allows you to set whether the print will be bold (two passes) or
normal. For Laserjet printers, this allows you to set the print
resolution in dots per inch (dpi).
Okay: Selecting this option causes any changes that have been made
to the printer configuration to be saved.
Cancel: Selecting this option causes any changes that have been
made to the printer configuration to be cancelled.
Display Options: Selecting this option allows the user to control
aspects of how data is displayed on the screen.
Show all pts in record: If this is enabled then Tack will display
all of the data points for a given record on the screen. That is,
if there are more data points in a record than there are pixels on
the screen horizontally then Tack will show multiple Y points for
each X point. If this is disabled then Tack will only display one
Y point for each X point. Disabling this feature causes the
display to draw faster.
Connect the points: If this is enabled then Tack will connect the
data points on the screen with lines. This causes the display of
data to look nicer, but significantly slows the display of data.
Grid and Axes: Selecting this option allows the user to configure
how the grid and axes in the data window(s) are displayed. There
are five items on this menu:
X Axis: Selecting this option allows the user to specify where X
axes are to be placed in each data window. The user can select a
variety of X axes varying from none to three, appearing at the
top, middle and bottom of each window.
Y Axis: Selecting this option allows the user to specify where Y
axes are to be placed in each data window. The user can select a
variety of Y axes varying from none to three, appearing at the
left, middle and right of each window.
Grid: Selecting this option allows the user to specify the
appearance of the grid in the data window(s). The grid can be
horizontal, vertical, both horizontal & vertical or neither. The
spacing of the grid is determined by the number of divisions (see
next item).
Division: Selecting this option allows the user to specify the
number of divisions for both the X and Y axes. The number of
divisions determines where the ticks are placed on the X and Y axes
and the spacing of the grid.
Line Style: Selecting this option allows the user to specify the
line style for the grid. The line style is specified by a
hexadecimal number (0 -> FFFF) which specifies how the line is
displayed. FFFF corresponds to a solid line, while 0 corresponds
to no line. A value of 0F0F would make a dashed line, while 1
would make a faintly dotted line.
Okay: Selecting this option exits the display options menu.
Other Options: Selecting this option allows the user to control
several very important aspects of Tack's operation. These are
described below:
XMS: Enabling this feature allows Tack to use memory accessed via
the XMS specification in order to store data acquired before
writing it to disk. XMS memory is memory above the 1 MB boundary
on PC-AT class computers (80286 and above class microprocessors).
This memory can only be accessed if you have installed the XMS
driver HIMEM.SYS (supplied free of charge by Microsoft), or a
compatible XMS driver (e.g. Desqview's QEMM memory manager) in your
config.sys file. The use of XMS allows Tack to store data above
the conventional memory area, which allows more room for Tack to
work. This feature need not be disabled unless you suspect a
problem or else have other needs.
Sounds: Selecting this toggles the state of sound generation by
Tack. If sounds are disabled, then Tack will make no noise.
Okay: Selecting this causes any changes that have been made to the
items on this menu to be saved.
Cancel: Selecting this causes any changes that have been made to
the items on this menu to be discarded.
Write Config File: Selecting this option causes the current
configuration data to be written to the Tack.cfg configuration
file. Only the items that are on controlled by config menu are
stored in this file. These are:
- Graphics display adapter & resolution
- Colors
- Font
- Printer
- Sounds
- Display Settings (Show All Pts, Connect the Pts, Grid)
- XMS Usage
Conclusion
I hope that you understand all of the features that I have
described here and that Tack serves you well. I would appreciate
your comments on the program and manual. I always want to know
about bugs in my program and will endeavor to fix them as speedily
as is possible. I am not responsible for any loss of data or
damage caused by this program. I also would value your suggestions
for new features and ways to improve this program. I can be
reached at the following addresses:
George B. Grant (617) 625-2419 (Home Phone)
38 Banks St. #2 (617) 495-2599 (Work Phone)
Somerville, MA 02144
ggrant@husc.harvard.edu (e-mail, over the internet)
or
george@mander.berkeley.edu
72722,3152 (Compuserve address)