scholarly journals Easy-DHPSF open-source software for three-dimensional localization of single molecules with precision beyond the optical diffraction limit

2013 ◽  
Author(s):  
Matthew Lew ◽  
Matthew D. Lew* ◽  
Alexander R. S. von Diezmann* ◽  
W. E. Moerner
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Single Molecules ◽  
Three Dimensional ◽  
Diffraction Limit ◽  
Optical Diffraction

scholarly journals PhytoSFDM version 1.0.0: Phytoplankton Size and Functional Diversity Model

2016 ◽  
Vol 9 (11) ◽  
pp. 4071-4085 ◽  
Author(s):  
Esteban Acevedo-Trejos ◽  
Gunnar Brandt ◽  
S. Lan Smith ◽  
Agostino Merico
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Marine Ecosystem ◽  
Three Dimensional ◽  
Functional Trait ◽  
Global Ocean ◽  
Total Biomass ◽  
Spatially Resolved ◽  
Phytoplankton Communities ◽  
Natural Complexity

Abstract. Biodiversity is one of the key mechanisms that facilitate the adaptive response of planktonic communities to a fluctuating environment. How to allow for such a flexible response in marine ecosystem models is, however, not entirely clear. One particular way is to resolve the natural complexity of phytoplankton communities by explicitly incorporating a large number of species or plankton functional types. Alternatively, models of aggregate community properties focus on macroecological quantities such as total biomass, mean trait, and trait variance (or functional trait diversity), thus reducing the observed natural complexity to a few mathematical expressions. We developed the PhytoSFDM modelling tool, which can resolve species discretely and can capture aggregate community properties. The tool also provides a set of methods for treating diversity under realistic oceanographic settings. This model is coded in Python and is distributed as open-source software. PhytoSFDM is implemented in a zero-dimensional physical scheme and can be applied to any location of the global ocean. We show that aggregate community models reduce computational complexity while preserving relevant macroecological features of phytoplankton communities. Compared to species-explicit models, aggregate models are more manageable in terms of number of equations and have faster computational times. Further developments of this tool should address the caveats associated with the assumptions of aggregate community models and about implementations into spatially resolved physical settings (one-dimensional and three-dimensional). With PhytoSFDM we embrace the idea of promoting open-source software and encourage scientists to build on this modelling tool to further improve our understanding of the role that biodiversity plays in shaping marine ecosystems.

scholarly journals In-House, Open-Source 3D-Software-Based, CAD/CAM-Planned Mandibular Reconstructions in 20 Consecutive Free Fibula Flap Cases: An Explorative Cross-Sectional Study With Three-Dimensional Performance Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Lucas M. Ritschl ◽  
Paul Kilbertus ◽  
Florian D. Grill ◽  
Matthias Schwarz ◽  
Jochen Weitz ◽  
...  
Keyword(s):  
Open Source ◽  
Dimensional Analysis ◽  
Open Source Software ◽  
Three Dimensional ◽  
Cross Sectional Study ◽  
Sectional Study ◽  
Free Fibula Flap ◽  
Cross Sectional ◽  
Cad Cam ◽  
Free Fibula

BackgroundMandibular reconstruction is conventionally performed freehand, CAD/CAM-assisted, or by using partially adjustable resection aids. CAD/CAM-assisted reconstructions are usually done in cooperation with osteosynthesis manufacturers, which entails additional costs and longer lead time. The purpose of this study is to analyze an in-house, open-source software-based solution for virtual planning.Methods and MaterialsAll consecutive cases between January 2019 and April 2021 that underwent in-house, software-based (Blender) mandibular reconstruction with a free fibula flap (FFF) were included in this cross-sectional study. The pre- and postoperative Digital Imaging and Com munications in Medicine (DICOM) data were converted to standard tessellation language (STL) files. In addition to documenting general information (sex, age, indication for surgery, extent of resection, number of segments, duration of surgery, and ischemia time), conventional measurements and three-dimensional analysis methods (root mean square error [RMSE], mean surface distance [MSD], and Hausdorff distance [HD]) were used.ResultsTwenty consecutive cases were enrolled. Three-dimensional analysis of preoperative and virtually planned neomandibula models was associated with a median RMSE of 1.4 (0.4–7.2), MSD of 0.3 (-0.1–2.9), and HD of 0.7 (0.1–3.1). Three-dimensional comparison of preoperative and postoperative models showed a median RMSE of 2.2 (1.5–11.1), MSD of 0.5 (-0.6–6.1), and HD of 1.5 (1.1–6.5) and the differences were significantly different for RMSE (p < 0.001) and HD (p < 0.001). The difference was not significantly different for MSD (p = 0.554). Three-dimensional analysis of virtual and postoperative models had a median RMSE of 2.3 (1.3–10.7), MSD of -0.1 (-1.0–5.6), and HD of 1.7 (0.1–5.9).ConclusionsOpen-source software-based in-house planning is a feasible, inexpensive, and fast method that enables accurate reconstructions. Additionally, it is excellent for teaching purposes.

scholarly journals Software-Based Three-Dimensional Deconvolution Microscopy of Cytoskeletal Proteins in Cultured Fibroblast Using Open-Source Software and Open Hardware

2019 ◽  
Vol 5 (12) ◽  
pp. 88
Author(s):  
Kazuo Katoh
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Laser Scanning ◽  
Low Cost ◽  
Three Dimensional ◽  
Cytoskeletal Proteins ◽  
Laser Scanning Microscopy ◽  
Confocal Laser ◽  
Actual Measurement ◽  
Open Hardware

As conventional fluorescence microscopy and confocal laser scanning microscopy generally produce images with blurring at the upper and lower planes along the z-axis due to non-focal plane image information, the observation of biological images requires “deconvolution.” Therefore, a microscope system’s individual blur function (point spread function) is determined theoretically or by actual measurement of microbeads and processed mathematically to reduce noise and eliminate blurring as much as possible. Here the author describes the use of open-source software and open hardware design to build a deconvolution microscope at low cost, using readily available software and hardware. The advantage of this method is its cost-effectiveness and ability to construct a microscope system using commercially available optical components and open-source software. Although this system does not utilize expensive equipment, such as confocal and total internal reflection fluorescence microscopes, decent images can be obtained even without previous experience in electronics and optics.

scholarly journals Computational generation of an annotated gigalibrary of synthesizable, composite peptidic macrocycles

2020 ◽  
Vol 117 (40) ◽  
pp. 24679-24690
Author(s):  
Ishika Saha ◽  
Eric K. Dang ◽  
Dennis Svatunek ◽  
Kendall N. Houk ◽  
Patrick G. Harran
Keyword(s):  
Virtual Screening ◽  
Open Source ◽  
Open Source Software ◽  
Large Scale ◽  
Three Dimensional ◽  
Pharmacological Properties ◽  
Robust Methods ◽  
Small Peptide ◽  
Multistep Reaction ◽  
Condensed Heterocycles

Peptidomimetic macrocycles have the potential to regulate challenging therapeutic targets. Structures of this type having precise shapes and drug-like character are particularly coveted, but are relatively difficult to synthesize. Our laboratory has developed robust methods that integrate small-peptide units into designed scaffolds. These methods create macrocycles and embed condensed heterocycles to diversify outcomes and improve pharmacological properties. The hypothetical scope of the methodology is vast and far outpaces the capacity of our experimental format. We now describe a computational rendering of our methodology that creates an in silico three-dimensional library of composite peptidic macrocycles. Our open-source platform, CPMG (Composite Peptide Macrocycle Generator), has algorithmically generated a library of 2,020,794,198 macrocycles that can result from the multistep reaction sequences we have developed. Structures are generated based on predicted site reactivity and filtered on the basis of physical and three-dimensional properties to identify maximally diverse compounds for prioritization. For conformational analyses, we also introduce ConfBuster++, an RDKit port of the open-source software ConfBuster, which allows facile integration with CPMG and ready parallelization for better scalability. Our approach deeply probes ligand space accessible via our synthetic methodology and provides a resource for large-scale virtual screening.

scholarly journals Methodology for creating 3D paper unfolded models with complex geometry using open-source software and resources with free personal and commercial license

2018 ◽  
Vol 2 (1) ◽  
pp. 39-46
Author(s):  
Kremena Tsankova Markova ◽  
Tihomir Atanassov Dovramadjiev ◽  
Ginka Velikova Jecheva
Keyword(s):  
Exact Sequence ◽  
Open Source ◽  
Design Process ◽  
Open Source Software ◽  
Complex Geometry ◽  
Three Dimensional ◽  
Functional Capabilities ◽  
The Creation ◽  
Technological Means ◽  
Three Dimensional Models

The creation of 3D paper unfolded models with complex geometry requires precision in the design process. Achieving this is through the use of accessible resources and modern technological means which possess the necessary technical and functional capabilities. The successful realization of the models is through the use of a structured methodology containing design stages that are defined in the exact sequence. The present study aims to create the unfoldings of complex three-dimensional models by covering the stages of providing accessible resurses with a personal and commercial license that are transformed in sequence until the ready-made variants.

Demonstration of an Aerodynamic Design Process for Turbomachines Using Open Source Software Tools

2010 ◽  
Author(s):  
Oliver Borm ◽  
Balint Balassa ◽  
Sebastian Barthmes ◽  
Julius Fellerhoff ◽  
Andreas Ku¨hrmann ◽  
...  
Keyword(s):  
Open Source ◽  
Design Process ◽  
Open Source Software ◽  
Compressible Flows ◽  
Three Dimensional ◽  
Axial Compressor ◽  
Software Tools ◽  
Two Dimensional ◽  
Aerodynamic Design ◽  
Student Projects

This paper demonstrates an aerodynamic design process for turbomachines for compressible flows, using exclusively open source software tools. Some relevant software already existed and few additional components were required, which have been developed mainly by students and are available at ftp.lfa.mw.tum.de. The geometry of turbomachine blades is described with a newly developed NURBS based blade designer. One-dimensional preliminary analysis is done with OpenOffice.org Calc and an extended mean line program, where loss models are already included. For two-dimensional through-flow computations a compressible streamline curvature method was implemented. Two-dimensional blade-to-blade and three-dimensional simulations are performed with the CFD toolbox OpenFOAM. The two- and three-dimensional results are visualized and analyzed using the open source postprocessing tool ParaView. The presented tools are regularly used in student projects. A generic one stage axial compressor was created with the workflow as a showcase in order to demonstrate the capabilities of the open source software tools.

PTCLab: free and open-source software for calculating phase transformation crystallography

2016 ◽  
Vol 49 (3) ◽  
pp. 1099-1106 ◽  
Author(s):  
X.-F. Gu ◽  
T. Furuhara ◽  
W.-Z. Zhang
Keyword(s):  
Phase Transformation ◽  
Open Source ◽  
Open Source Software ◽  
Stereographic Projection ◽  
Three Dimensional ◽  
Phenomenological Theory ◽  
Interfacial Structure ◽  
Invariant Line ◽  
Line Model ◽  
Edge Matching

PTCLab(Phase Transformation Crystallography Lab) is free and open-source software to calculate the crystallographic features formed during a phase transformation, such as orientation relationship, interface orientation, interfacial structureetc. This program covers the crystallographic theories for both martensitic and diffusional transformation and allows users to represent the results in stereographic projection. The crystallographic models treated inPTCLabinclude the classical phenomenological theory of martensite crystallography (PTMC), the double shear version of PTMC, the invariant line model, O-lattice theory, the O-line model, the recently developed three-dimensional near coincidence site method, the edge-to-edge matching model and variant selection analysis. In addition, a number of basic crystallographic calculations for single or multiple crystal structures can be performed with the calculation pad. High-quality composite stereographic projection and electron diffraction patterns can be also obtained by the present application.PTCLabis written in Python, runnable cross platform, and is distributed at https://sourceforge.net/projects/tclab/.

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