Python library for Bruker AFMi Nanoscope files
Package to read data files collected using Bruker, Veeco, and Digital Instruments Atomic Force Microscopes (AFMs) using Nanoscope v5.12 - v10.00 acquisition software. There is also some support for data acquired with the NanoDrive acquisition software.
Supported file types include:
- Image data files
- Ramp data (e.g. force curves without a surface hold segment, SECM data, etc. )
- Force curves with a surface hold segment
- Force Volume data without hold segment
- Force Volume data with surface hold segment (electrical DCUBEs, AFM-nDMA, FFV-CR, etc.)
- PeakForce Capture (PFC) data (collected in PeakForce QNM)
- High Speed Data Capture (HSDC) data
- Script data (RampScripting, AFM-nDMA, SS-PFM, etc.)
- NanoDrive Image data
The package parses the header and provides scaled data in desired units (Volt, Metric, Force). Additionally there is a small subset of other header information available (spring constant, etc.).
Use the pip package manager to install nanoscope.
$ pip install nanoscope
This module requires the following:
- Microsoft Windows 7 - 10 operating system
- Python 2.78 - 3.78 (64bit preferred)
- You can check the version and whether it is 64bit by launching the Python command line interface.
- Microsoft Visual C++ 2015 or 2017 Redistributable (x64 version if using 64bit Python).
- You can check which version(s) are installed by looking in “Control Panel\All Control Panel Items\Programs and Features”.
- If needed, download it from https://visualstudio.microsoft.com/vs/older-downloads/
Note that acquisition channel numbers start with zero, not with one as is the convention in Nanoscope software.
For detailed examples, please refer to the included example code (and associated raw data files). It is contained in the module, but not imported by default.
import nanoscope as ns ns.examples.copy_examples_code() # prompt user to save a copy of the examples code Examples.py help(ns.examples) # get a list of specific examples ns.examples.run_example(2) # run example #2
Examples.py contains the following code for example #2 to read and plot a force curve with hold segment:
import matplotlib.pyplot as plt import nanoscope from nanoscope import files from nanoscope.constants import FORCE, METRIC, VOLTS, PLT_kwargs i_chan = 0 # This will provide Nanoscope channel #1 with files.HoldCurveFile("ForceHold.spm") as file_: channel = file_[i_chan] # get timed data of channel ft_plot, ax_properties = channel.create_force_time_plot(METRIC) plt.plot(ft_plot.x, ft_plot.y) plt.gca().set(**ax_properties) # set axes properties plt.show() hold_plot, ax_properties = channel.create_force_hold_time_plot(METRIC) plt.plot(hold_plot.x, hold_plot.y) plt.gca().set(**ax_properties) # set axes properties plt.show()
Resulting in 2 plots, the first showing the deflection error versus time, the second showing the same data but only for the force hold.
Support for installation issues can be obtained by contacting the Bruker AFM service team at email@example.com. As this package is provided at no charge, it is not feasible to provide support beyond helping with installation issues at this time.
For bug reports and feature requests, please email firstname.lastname@example.org with "BUG" or "FEATURE" in the subject line. Also, please include an example raw Nanoscope data file along with the usual other relevant information.
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