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AtomicJ specifications


Unique identifier OMICS_27822
Name AtomicJ
Alternative name JRobust
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Biological technology Agilent Technologies
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.7.3
Stability Stable
Maintained Yes




No version available


  • person_outline Pawel Hermanowicz

Publication for AtomicJ

AtomicJ citations


Nanomechanical Phenotype of Melanoma Cells Depends Solely on the Amount of Endogenous Pigment in the Cells

Int J Mol Sci
PMCID: 5855829
PMID: 29463035
DOI: 10.3390/ijms19020607

[…] ion spring constants of the used cantilevers were routinely determined based on the thermal tune procedure []. Analysis of force curves and reconstruction of force maps from the curves was made using AtomicJ software []. In brief, the collected force–displacement curves were first converted into force–indentation curves and fitted with the Sneddon model. In addition, each force curve was analyzed […]


Three dimensional organotypic matrices from alternative collagen sources as pre clinical models for cell biology

Sci Rep
PMCID: 5715059
PMID: 29203823
DOI: 10.1038/s41598-017-17177-5

[…] ea (separated by 35 μm) using a Peak Force Tapping mode, with an average loading force of 1 nN, prior to calculating Young’s modulus values from force curves by the Hertz spherical indentation model (AtomicJ). Matrix thickness was also calculated for each area by subtracting the z position of the point of contact between the probe and the matrix, and the z position of the glass bottom cell culture […]


E cadherin integrates mechanotransduction and EGFR signaling to control junctional tissue polarization and tight junction positioning

Nat Commun
PMCID: 5665913
PMID: 29093447
DOI: 10.1038/s41467-017-01170-7

[…] cities of cantilever approach and retraction were kept constant at 2 μm s−1 ensuring detection of elastic properties only. All measurements were performed at 37 °C. Data analysis was carried out with AtomicJ using the Hertz model of impact.Further detailed information about skin sample preparation, immunohistochemistry, and protein isolation and immunoblotting can be found in the Supplementary Met […]


Identification of Ras suppressor 1 (RSU 1) as a potential breast cancer metastasis biomarker using a three dimensional in vitro approach

PMCID: 5432341
PMID: 28423706
DOI: 10.18632/oncotarget.16062

[…] d. Force spectroscopy was performed with V-shaped silicon nitride probes (PNP-TR, Nanoword, provided by NanoAndMore). Contact mode images and 8x8 points of force curves were collected and analyzed by AtomicJ [] so as to calculate the sample's Young's modulus using the Hertz model (for collagen a 0.3 Poisson ratio was used).The AFM image processing was performed by using the image analysis software […]


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AtomicJ institution(s)
Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland; Department of Medical Physics and Biophysics, Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Kraków, Poland
AtomicJ funding source(s)
Supported by the Polish Ministry of Science and Higher Education (PB 1395/B/P01/2007/33), the Faculty of Biochemistry, Biophysics, and Biotechnology of the Jagiellonian University is a beneficiary of European Union structural funds (Grant No. POIG.02.01.00-12-064/08, “Molecular biotechnology for health”).

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