Please see the image key for the explanation of the input variables. Note that all variables must be entered following an absolute sign convention, not the one shown in the key, for example one of the thetas should be a negative number and entered as such.
friction_v_load_new_stripped.m
inputs key

These programs, which are based on the Carpick Lab Toolbox, are used to extract the data from a NanoScope data file.

The scaled results are placed in the matrix data, an N x M x L matrix, where N is the number of lines, M is the number of points per line (N = M in most cases), and L is the number of simultaneous data channels recorded.  The assumption is that the first data channel is topgraphy and all the other channels are not topography.  The data output is nm for the first channel and V for all subsequent channels.  It has been tested on data files with only one channel (topography) three channels (topography and LFM forward and back), and four channels (topography, peak force error, inphase and quadrature).

usage: data = open_di(file_name)
To use open_di.m, you need get_num.m (included here) and di_header_find.m (in the Carpick Lab Toolbox).

Original Version:  Jennifer R. Hampton  2/16/09
7/13/10: adapted for NanoScope v 8.1 data files

Changes in v2:
1) Searching the header for scale_data2 now looks for the string ‘\@2:Z scale: V’
2) The output matrix, data, is preallocated before the final loop.

open_di.m

The file open_di.m is based on get_image_data.m from the Carpick Lab Toolbox, but with updated scaling, as described in the comments of the file. The heart of the code (reading data and placing it in the output matrix) is the same as in get_image_data.m.

get_num.m

The file get_num.m is a rewritten version of extract_num.m from the Carpick Lab Toolbox. The change was necessary to make sure that the correct number from each header line was extracted.

open_di_information.txt

The file open_di_information.txt contains the information described above and additional information about the scaling from hardware to physical units.

Download the free software by clicking here

Dr. Frederick Sachs

SUNY Distinguished Professor

Center for Single Molecule Biophysics

Physiology and Biophysical Sciences

301 Cary Hall, SUNY

Buffalo, NY 14214

Voice Mail (716) 829-3289 x105

FAX (716) 829-2569

Email: sachs@buffalo.edu

www.sachslab.buffalo.edu

These programs, which are based on the Carpick Lab Toolbox, are used to extract the data from a NanoScope data file.

The scaled results are placed in the matrix data, an N x M x L matrix, where N is the number of lines, M is the number of points per line (N = M in most cases), and L is the number of simultaneous data channels recorded. The assumption is that the first data channel is topgraphy and all the other channels are not topography. The data output is nm for the first channel and V for all subsequent channels. It has been tested on data files with only one channel (topography) and data files with three channels (topography and LFM forward and back).

usage: data = open_di(file_name)

To use open_di.m, you need get_num.m (included here) and di_header_find.m (in the Carpick Lab Toolbox).

open_di_v1.m

The file open_di.m (v1) is based on get_image_data.m from the Carpick Lab Toolbox, but with updated scaling, as described in the comments of the file. The heart of the code (reading data and placing it in the output matrix) is the same as in get_image_data.m.

get_num.m

The file get_num.m is a rewritten version of extract_num.m from the Carpick Lab Toolbox. The change was necessary to make sure that the correct number from each header line was extracted.

open_di_information_v1.txt

The file open_di_information.txt (v1) contains the information described above and additional information about the scaling from hardware to physical units.

STM researchers spend substantial time deciphering STM images. The software, which provides 3-D color imaging of research findings, has the potential to save time and money for people researching novel properties on the nanoscale with STM.

Nt_STM calculates the electrical current through any given nanometrical system (microscope tip + sample + surface) and reproduces the results of a real STM. It gives current or topographic mode results as well as I(v) or I(z) curves, just like in the STM experiment.

The nanometrical system is represented by the Extended Hückel Theory (EHT). More precise theoretical chemistry programs can be integrated to ”Nt_STM” for specific simulations. The program involves drawing your system, designing your surface and tip, adjusting your EHT quantum parameters, then launching the simulation and comparing the simulated results with that of your STM.

An AFM simulation package is in the works.

To download the software, click here: http://www.liv.ac.uk/~sdb/ImageSXM/

(1) AFM Model. Set gain, scan speed, and sample height to visualize a the response of a beam-deflection AFM.

Courtesy of Dr. Joseph Griffith

(2) Driven Oscillator. Control frequency and damping of a driven oscillator and view the resulting quality factor and visualize plots of both the driving and resulting frequencies. Great to gain understanding of a Dynamic AFM cantilever!

Courtesy of Dr. Joseph Griffith

(3) Probe Simulator. Simulate the effects of AFM probe size and shape, as well as feature size. Watch how the AFM tip interacts and view the recorded data.

Click here to download.

Click here to download.

• get_image_data.m
• di_header_find.m
• di_versio.m
• extract_num.m
• nano3read.m (original source code for get_image_data)
• getparameter.m (orig. code for di_header_find and extract_num)

Calculating Friction vs Load (UPDATED DEC. 2010) The most important script to analyze your FvL data is ‘friction_v_load_new.’ To process large batches of data, use ‘batch_process’ (see the manual). File ‘latcal’ is a Mathcad file that uses the output of the Lateral Calibration function of ‘friction_v_load’ to find the ratio between normal and lateral calibration factors.

• friction_v_load_new (Matlab file – save this file, then change the “.txt” extension to “.m” to use in Matlab) UPDATED DEC., 2010
• batch_process.m (Matlab file)
• latcal.mcd (MathCad file)

Measuring Pull-Off Forces (UPDATED JULY, 2010) The following files are applicable to force-distance data files only. The output of ‘getfd’ is the pull-off force in volts and the slope of the contact region of a force curve (normal signal deflection sensitivity in volts per nm).

batchfd_new.m is the actual code that you run. This one allows you to run the analysis on a series of force-distance curves. It uses either getfd_new.m or getfd_new_oldNanoscope.m to do the analysis (you can change this on line #48 in batchfd_new.m).

If you are using a newer version of Nanoscope (v6.x), use getfd_new, and if you are using an older version, use the getfd_new_oldNanoscope one. To use batchfd_new.m as-is, all the base names of the files need to be the same, and the file extensions should be consecutive (e.g., forcecurve.000,  forcecurve.001,  forcecurve.002 …). So you will first pick the first file, and then you will tell the program what the extension is on the last file in the sequence. When you run the code, it will show you each force-distance curve, and it will put some markers on the plots. The green and blue markers indicate the range over which the in-contact slope is calculated (V/nm). The red marker indicates the pull-off point. The black marker indicates what the out-of-contact voltage is, and it’s positioned directly above the pull-off point. The code will then display the average pull-off deflection (nm) and its standard deviation. A file is saved that contains the slope (V/nm), pull-off voltage (V), pull-off deflection (nm), and max deflection (nm). If you use Kaleidagraph, you can drag this file into Kaleidagraph (using Space as the delimiter, skipping 0 lines, and reading the titles).

• getfd_new.m
• getfd_new_oldNanoscope.m
• batchfd_new.m

For your convenience, all Matlab and Mathcad files are zipped here: SWfiles (note: this ZIP file does not include the new versions of getfd and batchfd. Upload those directly above. Sorry for the inconvenience.)