SPMCON operating manual

Christopher M. Yip
July 4, 1996

SPMCON manual

SPMCON is a Windows 3.11Å program designed to facilitate the analysis of force curve data acquired on Digital Instruments Inc. NanoscopeÅ SPMs.
SPMCON has the following features:


1. Generation of a composite data file from up to 5 separate force curve
data files.

2. Overlay and offsetting of multiple force curves - either retraction or
approach curves.

3. Conversion of deflection data to force data using a user-supplied
cantilever constant.

4. Browse feature for examining multiple force curves - including the
ability to print the browse files.

5. Generation of an average force curve from a set of separate force curves.

6. Integration of force curve retraction traces.

7. Measurements of lateral offset between approach and retraction traces
for a single force curve.

8. Zoom feature for examining specific regions of the force curves.

9. All measurements i.e. force / energy / offset can be recorded and stored
to a user-supplied filename in ASCII format.

10. Automatic conversion of raw force curve data into absolute tip and
piezo motion. Mouse movement is automatically tracked and updated.


SPMCON was developed to speed up the analysis of force curve data and
augment the capabilities of the Nanoscope system from Digital Instruments.
It was developed as freeware and, as such, has no implied warranties.
Updates will be available from the author or from the University of
Minnesota Department of Chemical Engineering and Materials Science's WWW
site under the following URL:

http://www.cems.umn.edu/research/ward


It should be noted that this program was developed to run under Windows 3.1
or later versions including Windows for Workgroups. It is not a Windows95
compliant software package (as yet) although, if sufficient demand exists,
an updated version will be developed.



DOWNLOADING

To download the program, simply click on the hotlink and SPMCON in
compressed form will be uploaded to your computer. It comes as a .ZIP file
and can be decompressed using PKUNZIP (Check your favourite PC software
sites for this shareware program). Note: At some future date, SPMCON will
be set up as a self-extracting archive file.



INSTALLING SPMCON

After the .ZIP file has been decompressed, simply double-click on the
SETUP.EXE file under the Windows File Manager or run SETUP.EXE from the
Windows Program Manager. This should set up a directory called SPMCON on
your local hard drive and install the requisite files and DLLs on your
computer. A new program group entitled SPMCON containing a program item
called SPMCON will be created.



RUNNING SPMCON

Simply double-click on the SPMCON icon in the SPMCON program group and the
program should launch. You will be presented with two sets of file
directories - one is for your Source files and one is for your Destination
files. You can easily navigate by simply clicking and selecting specific
drives or directories. Use the drop-down to access other disk drives
including network and attached drives

The following sections deal with specific SPMCON operations.



REGISTER CURVE MINIMA

Use this option to overlay the force curves such that the individual force
curve minima, as determined from the retraction curves, are aligned.



FILE CONVERSION

Use this option to generate a composite ASCII file which would contain up
to 5 force curve data sets arranged in columns. This format is suitable for
subsequent plotting in Excel or any other program capable of reading
comma-delimited text files. The file is formatted with a header that lists
the date of file conversion and the original filenames and source
directory. The composite data file is made up of columns of
comma-delimited text in the following order:

Piezo1, Retract1, Extend1, Piezo2, Retract2, Extend2, ....

where # refers to the source file, Piezo#, Retract# and Extend# refer to
the piezo position and tip deflections on retraction and extension,
respectively.  Simply highlight the files you are interested in by clicking and dragging with the left-mouse button to highlight a consecutive series of files. To highlight specific files, click on the desired file with the Ctrl key held
down. Once the files are selected, click on Convert and a new file will be
created. The files that are selected are displayed in the Selected Files
listbox. You can set the filename by clicking on the Destination filename
and entering a new name. The default is SPMCON.dat. Use the Destination
file directory and drive list boxes to specify where you want the data
saved.



BROWSING

To browse force curves, simply click on the Browse button. A new window is
created displaying the first 6 files from the file listing. Note: you can
reset the starting filename by simply clicking on a filename to select it
as the starting filename and then clicking on Browse. Both the retraction
and extension curves are displayed for each force curve. The dotted lines
represent the setpoint from the original force curve data while the solid
lines represent the neutral tip position, as determined from the
off-surface portion of the retraction curve. The filenames are displayed
above each force curve. You can use the arrow bottons (<= / =>) to scroll
up and down through the previous / next set of 6 force curve files.
Clicking on the Print All button will output the force curves in the Browse
format to your local printer. To print selected force curves, simply click
on the check box under the force curve to select it and then click on Print
Selected. To annotate the force curve browse printout, double-click on the
comment box in the lower right hand corner. A new pop-up window will
appear. You can enter a comment string here that will be displayed and
printed out with the Browse files. Click on O.K. to return to the main
SPMCON screen.



FORCE CURVE OVERLAY

To overlay force curves, simply select the files that you are interested in
and then click on Overlay. You can use the Overlay Graph option buttons
to select whether you want to overlay the retraction or extension curves.
Use the Register Curve Minima option to enable or disable this option.
There is no limit to the number of curves that may be overlaid; however,
for clarity, it would be best to overlay at most 5 curves. Note: An error
message may appear if there is a problem with the force curve scaling or an
attempt is made to create a force curve plot from an image file. This also
may occur if the force curves are highly irregular and attempts are made to
overlay the curves. A new window is displayed showing the overlaid force curves. Provided the force curves were acquired with the same setpoint, a dotted line denoting this position is displayed. A solid line defines the average off-surface neutral tip position.

Features:
1. As the mouse moves through the graph window, the piezo and tip position
in nm are continuously updated in the upper right hand corner of the
window.
2. The displayed force curves are listed in a list box located on the
bottom of the window. Click on a filename to highlight that specific curve.
3. Clicking on the Average button will generate a curve that represents the
average of the displayed force curves. It also is added to the list of
displayed files. Click on the Average button again to hide the average
force curve.
4. Click on the Offset button to vertically offset the displayed force
curves. The button name will change to Overlay. Click on Overlay to
reoverlay the force curves.
5. Double-clicking on the Comment box located at the top of the window will
bring up a comment box.
6. Click on Print to print the overlaid force curves (either as overlaid or
as offset) to your local printer. The printout will include a file listing
and the comment line (See 5).
7. The lower left hand corner contains a status bar that indicates what
mouse options are enabled.
8. Clicking on the Force units option button will bring up a window asking
for the cantilever spring constant.

A number of the advanced options in SPMCON are controlled by the mouse.
Clicking with the right mouse button on the graph window will bring up a
pop-up menu. Depending on your current mouse status (see status line),
certain options will be active while others will be dimmed.

Cursor: This is the default mouse mode where the mouse pointer motion is
tracked and displayed in the Piezo Position and Tip Deflection boxes.

Line: In this mode, clicking the left mouse button and dragging the mouse
around will "rubber-band" a line extending from the initial mouse position
to the current position. The relative tip deflection and piezo travel are
displayed as is the tip / piezo ratio (or slope). If the Force units
option is enabled, the tip deflection is displayed in nN.

Box: In this mode, you can "rubber-band" a box on a specific region of the
force curves and then click on the Zoom button that will become active in
the lower left hand corner of the window. Note that this button is normally
inactive unless the Box option is enabled. Clicking on Full will restore
the original display.

Linear: When this is enabled, the line you draw simply measures vertical
and horizontal displacements.

Relative Offset: This option is enabled when a single complete force curve
is displayed. A horizontal line is displayed and, by clicking and
dragging with the left mouse button depressed, the relative piezo distance
between the extension and retraction curves can be measured.

Integrate: When this is enabled, you can measure the area between the
force curve and a user-specified baseline.

Endpoint Adjust: This option is enabled when Integrate is chosen and allows
you to select the endpoints for your force curve integration.

Baseline Adjust: When enabled, you can drag a baseline up and down to match
the specific regions of the force curve that you are interested in.

Recording Measurements:
Pressing F2 will capture any measurements that have been taken. What
exactly is captured will depend on the current status of the measurements.
For example, in Line/Linear mode, the tip deflection, as measured by a
user-drawn line, will be captured. If the Distance units option is enabled,
the value is in nm. If the Force units option is enabled, the value is in
nN.
Press F3 to bring up the Measurements window that will display all your
logged measurements as well as a file directory listing. You can delete all
the measurements, your last measurements as well as save your data to a
specific file. Click on O.K. to close this window. The data is saved in
ASCII format for easy manipulation. Note that when you return to the main
SPMCON window, all measurements will be cleared - although you will be
warned if there are measurements which have been taken but not saved.

Procedures:

1. Measuring Pull-Off Forces.
- from the main SPMCON screen, select the files you are interested in.
- click on the Enabled option button for Register Curve Minima
- click on the Retraction option button for the Overlay Graph
- click on Overlay
- select the Force units option and enter the cantilever spring constant (N/m)
- click the right mouse button and choose the Box option. Rubber band a box
to outline the region of interest and then click Zoom to enlarge the field
of view.
- the status line should read Line Mode / Linear. This means that you can
now click and "rubber-band" a line to measure the pull-off forces. Note
that the tip deflection and piezo motion are tracked separately.
- press the F2 key to register the measurement.
- use the F3 key to view your stored measurements and to save them to disk.
You also can use this option to delete your last measurement or all
existing measurements.

2. Integrating Force Curves.
- from the main SPMCON screen, select the files you are interested in.
- click on the Enabled option button for Register Curve Minima
- click on the Retraction option button for the Overlay Graph
- click on Overlay
- select the Force units option and enter the cantilever spring constant (N/m)
- click the right mouse button and choose the Box option. Rubber band a box
to outline the region of interest and then click Zoom to enlarge the field
of view.
- the status line should read Line Mode / Linear.
- click on the right mouse button to bring up the mouse option menu and select Integrate
- click on the filename of the curve that you would like to measure. The
selected file will be highlighted.
- click and hold the left mouse button down while moving it around the
force curve will move an arrow denoting the leftmost integration boundary.
When you release the left mouse button, the arrow will stop and a
horizontal line will be drawn denoting the baseline for the integration.
Click and hold the left mouse button down to locate the rightmost
integration boundary. As the second arrow is dragged around, note that the
area defined by the two arrows, the force curve and the baseline is
continuously updated as are the positions associated with the individual
arrows. Release the mouse button to locate the rightmost integration
boundary.
- press F2 to register the area and boundary coordinates for the integration.
- you can move the baseline (which is automatically set at the vertical
position denoted by the leftmost arrow) by clicking on the right mouse
button and selecting Baseline Adjust. Click and drag the baseline to reset
the integration limits. Note again how the integration measurement is
automatically updated as you move the baseline.
- press the F2 key to register the measurement.
- use the F3 key to view your stored measurements and to save them to disk.
You also can use this option to delete your last measurement or all
existing measurements.
- to move the left arrow, simply click the right mouse button, select
Baseline Adjust, click the right mouse button again and select Endpoint
Adjust. You can now move the left arrow around and the baseline will again
be automatically tagged to the position of the leftmost arrow.

3. Converting Files
- from the main SPMCON screen, select the files you are interested in.
- enable the various options, as necessary.
- specify destination filename and path.
- click on Convert.

Possible Problems:
- Should extraneous lines / boxes etc,...be displayed on the overlay
window, this likely is due to an error in the mouse settings. Click on Full
or Offset to refresh the window.

Features to be implemented:
1. Scale bars are to be included in the Browse window and the Browse
printout for easy data comparison.
2. Direct selection of the sample files from the Browse window.
3. Error trapping to be implemented to trap non-force curve files (i.e.
image files) and prevent errors in displaying data files.
4. More robust printing - miscellaneous errors regarding printing outside
of graph window.
5. Conversion to Windows95 format and transition to traditional Windows
look and feel.
6. Possible development of Macintosh based version.




Questions / comments / suggestions / bug reports

Chris Yip
Eli Lilly and Company
Lilly Corporate Center
DC 1523
Indianapolis, IN 46285
(317) 277-1523
(317) 277-0833 (fax)
YIP_CHRISTOPHER_M@lilly.com
yipx0001@gold.tc.umn.edu