AtomicJ: An open source software for analysis of force curves

Hermanowicz, Paweł; Sarna, Michał; Burda, Květoslava; Gabryś, Halina

doi:10.1063/1.4881683

Cited by 202 publications

(150 citation statements)

References 37 publications

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“…The stiffness of the cell was deduced from the linear slope of this curve (~400 nm). Analyses were carried out using Atomic J Software version 1.6.0 [22], to determine Young’s modulus values.…”

Section: Methodsmentioning

confidence: 99%

The cytotoxic effect of TiF4 and NaF on fibroblasts is influenced by the experimental model, fluoride concentration and exposure time

et al. 2017

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ObjectiveTitanium tetrafluoride (TiF4) has shown promising effect in preventing tooth lesions. Therefore, we compared the cytotoxicity of TiF4 with sodium fluoride (NaF) (already applied in Dentistry) considering different fluoride concentrations, pH values and experimental models.Materials and methodsStep 1) NIH/3T3 fibroblasts were exposed to mediums containing NaF or TiF4 (from 0.15 to 2.45% F), both at native and adjusted pH, for 6 h. Step 2) NIH/3T3 were exposed to NaF or TiF4 varnishes with 0.95, 1.95 or 2.45% F (native pH), for 6, 12 or 24 h. We applied MTT (1st and 2nd steps) and Hoescht/PI stain (2nd step) assays. Step 3) NIH/3T3 were exposed to NaF or TiF4 varnish (2.45% F), at native pH, for 6 or 12 h. The cell stiffness was measured by atomic force microscopy (AFM).ResultsStep 1) All cells exposed to NaF or TiF4 mediums died, regardless of the F concentration and pH. Step 2) Both varnishes, at 1.90 and 2.45% F, reduced cell viability by similar extents (33–86% at 6 h, 35–93% at 12 h, and 87–98% at 24 h) compared with control, regardless of the type of fluoride. Varnishes with 0.95% F did not differ from control. Step 3) TiF4 and NaF reduced cell stiffness to a similar extent, but only TiF4 differed from control at 6 h.ConclusionsBased on the results of the 3 experimental steps, we conclude that TiF4 and NaF have similar cytotoxicity. The cytotoxicity was dependent on F concentration and exposure time. This result gives support for testing the effect of TiF4 varnish in vivo.

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Section: Methodsmentioning

confidence: 99%

The cytotoxic effect of TiF4 and NaF on fibroblasts is influenced by the experimental model, fluoride concentration and exposure time

et al. 2017

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“…Other free alternative applications are available in Java language, for example, WSXM 49 and Gwyddion 50 focused on imaging or OpenFovea 51 and AtomicJ 52 for FCs and mechanical analysis. The suite is written in Matlab language using event/object programming to provide an alternative tool for basic and advanced analysis.…”

Section: Methodsmentioning

confidence: 99%

Atomic force microscopy methodology and AFMech Suite software for nanomechanics on heterogeneous soft materials

et al. 2018

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Atomic force microscopy has proven to be a valuable technique to characterize the mechanical and morphological properties of heterogeneous soft materials such as biological specimens in liquid environment. Here we propose a 3-step method in order to investigate biological specimens where heterogeneity hinder a quantitative characterization: (1) precise AFM calibration, (2) nano-indentation in force volume mode, (3) array of finite element simulations built from AFM indentation events. We combine simulations to determine internal geometries, multi-layer material properties, and interfacial friction. In order to easily perform this analysis from raw AFM data to simulation comparison, we propose a standalone software, AFMech Suite comprising five interacting interfaces for simultaneous calibration, morphology, adhesion, mechanical, and simulation analysis. We test the methodology on soft hydrogels with hard spherical inclusions, as a soft-matter model system. Finally, we apply the method on E. coli bacteria supported on soft/hard hydrogels to prove usefulness in biological field.

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“…A number of different strategies have been proposed to identify the CP. The simplest approach is based on a sequential inspection of the force curve, where each point of the curve is assessed as potential CP (Hermanowicz et al, ; Shoelson et al, ). For each CP candidate, the Z p versus d curve is converted to δ versus F and then fitted with the chosen contact mechanics model, to obtain an estimate for r 2 or RMSE.…”

Section: Acquisition Of Force Curves and Data Processingmentioning

confidence: 99%

“…Once data acquisition is finalized, the user may choose to use online built-in methods to obtain mechanical information of the sample, or export the data and analyse it offline using commercial, open-source (Hermanowicz, Sarna, Burda, & Gabrys, 2014;Roduit et al, 2012) or custom-built analysis routines (Benitez, Moreno-Flores, Bolos, & Toca-Herrera, 2013;Gavara, 2016). Irrespective of the approach chosen, there are some common data analysis steps that all those routines will perform, and they will be described in the following sections.…”

Section: Acquisition Of Force Curvesmentioning

confidence: 99%

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A beginner's guide to atomic force microscopy probing for cell mechanics

Gavara

2016

Microscopy Res & Technique

156

136

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Atomic Force microscopy (AFM) is becoming a prevalent tool in cell biology and biomedical studies, especially those focusing on the mechanical properties of cells and tissues. The newest generation of bio‐AFMs combine ease of use and seamless integration with live‐cell epifluorescence or more advanced optical microscopies. As a unique feature with respect to other bionanotools, AFM provides nanometer‐resolution maps for cell topography, stiffness, viscoelasticity, and adhesion, often overlaid with matching optical images of the probed cells. This review is intended for those about to embark in the use of bio‐AFMs, and aims to assist them in designing an experiment to measure the mechanical properties of adherent cells. In addition to describing the main steps in a typical cell mechanics protocol and explaining how data is analysed, this review will also discuss some of the relevant contact mechanics models available and how they have been used to characterize specific features of cellular and biological samples. Microsc. Res. Tech. 80:75–84, 2017. © 2016 Wiley Periodicals, Inc.

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AtomicJ: An open source software for analysis of force curves

Cited by 202 publications

References 37 publications

The cytotoxic effect of TiF4 and NaF on fibroblasts is influenced by the experimental model, fluoride concentration and exposure time

The cytotoxic effect of TiF4 and NaF on fibroblasts is influenced by the experimental model, fluoride concentration and exposure time

Atomic force microscopy methodology and AFMech Suite software for nanomechanics on heterogeneous soft materials

A beginner's guide to atomic force microscopy probing for cell mechanics

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