We strongly recommend that you start using our new data analysis software, softmech [https://github.com/CellMechLab/softmech], which is much more flexible and robust.
Nanoindentation experiments data analysis.
This user friendly graphical user interface (GUI) allows to bulk analyze nanoindentation force-distance curves of soft materials (for example hydrogels and cells) in order to get mechanical properties (Young's modulus) based on:
- The Hertz model;
- The Oliver-Pharr model, to obtain a point-wise calculation of the Young's modulus, namely the elasticity spectra (ES). By fitting the ES with a bilayer model, cell's mechanical properties (cortex's modulus and thickness, cell's 'bulk' modulus) can be estimated. This method is described in our recent paper: https://doi.org/10.1186/s12951-020-00706-2.
Right now, the software only supports analysis of data obtained through a spherical indenter. For more advanced analyses, we developed a new moduluar GUI that can be found here: https://github.com/CellMechLab/softmech. However the project is still lacking documentation. For more questions, feel free to email massimo.vassalli@glasgow.ac.uk or g.ciccone.1@research.gla.ac.uk.
A step-by-step guide and video tutorials on how to use the software is avilable in our recent paper:
- Ciccone, G., Azevedo Gonzalez Oliva, M., Antonovaite, N., Lüchtefeld, I., Salmeron-Sanchez, M. and Vassalli, M., 2021. Experimental and data analysis workflow for soft matter nanoindentation. Journal of Visualized Experiments (10.3791/63401 ).
Data is now uploaded in a standard internal format (.json) after being screened in a newly designed GUI (NanoPrepare: https://github.com/CellMechLab/NanoPrepare). The new GUI allows for cleaning of the dataset and exporting the cleaned dataset in .json, which is then uploaded in this GUI for analysis. Therefore, in order to use this GUI, NanoPrepare should be first downloaded.
Internal format (.json). Conversion from manufacturers' format to .json is done in NanoPrepare. Right now, the following manufacturers' formats are supported: Optics 11 .txt files (both old and new versions are supported), NanoSurf .txt files and other standard AFM formats provided through the afmformats library.
No installer is currently provided. In order use the GUI, a Python 3 environment with the following packages is required: PyQt5, NumPy, SciPy, PyQtGraph.
In order to access the GUI, run the nano file from the command line:
python nano.py If you use this software in your publication and research, please cite the following papers:
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Ciccone, G., Azevedo Gonzalez Oliva, M., Antonovaite, N., Lüchtefeld, I., Salmeron-Sanchez, M. and Vassalli, M., 2021. Experimental and data analysis workflow for soft matter nanoindentation. Journal of Visualized Experiments (10.3791/63401 ).
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Lüchtefeld, I., Bartolozzi, A., Mejía Morales, J., Dobre, O., Basso, M., Zambelli, T. and Vassalli, M., 2020. Elasticity spectra as a tool to investigate actin cortex mechanics. Journal of nanobiotechnology, 18(1), pp.1-11 (doi.org/10.1186/s12951-020-00706-2).
