GIANI: open-source software for automated analysis of 3D microscopy images

AbstractThe study of cellular and developmental processes in physiologically relevant three-dimensional (3D) systems facilitates an understanding of mechanisms underlying cell fate, disease and injury. While cutting-edge microscopy technologies permit the routine acquisition of 3D datasets, there is currently a lack of user-friendly, open-source software to analyse such images. Here we describe GIANI (djpbarry.github.io/Giani), new software for the analysis of 3D images, implemented as a plugin for the popular FIJI platform. The design primarily facilitates segmentation of nuclei and cells, followed by quantification of morphology and protein expression. GIANI enables routine and reproducible batch-processing of large numbers of images and also comes with scripting and command line tools, such that users can incorporate its functionality into their own scripts and easily run GIANI on a high-performance computing cluster. We demonstrate the utility of GIANI by quantifying cell morphology and protein expression in mouse early embryos. More generally, we anticipate that GIANI will be a useful tool for researchers in a variety of biomedical fields.

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PhytoSFDM version 1.0.0: Phytoplankton Size and Functional Diversity Model

Geoscientific Model Development ◽

10.5194/gmd-9-4071-2016 ◽

2016 ◽

Vol 9 (11) ◽

pp. 4071-4085 ◽

Cited By ~ 6

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.

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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

Frontiers in Oncology ◽

10.3389/fonc.2021.731336 ◽

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.

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

Protocol Exchange ◽

10.1038/protex.2013.026 ◽

2013 ◽

Cited By ~ 17

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

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Key Concepts and Definitions of Open Source Communities

Encyclopedia of Networked and Virtual Organizations ◽

10.4018/978-1-59904-885-7.ch099 ◽

2010 ◽

pp. 753-760

Author(s):

Ruben van Wendel de Joode ◽

Sebastian Spaeth

Keyword(s):

Software Development ◽

Open Source ◽

Open Source Software ◽

Online Communities ◽

Source Code ◽

Professional Organizations ◽

Large Numbers ◽

Key Concepts ◽

Open Source Communities ◽

Do So

Most open source software is developed in online communities. These communities are typically referred to as “open source software communities” or “OSS communities.” In OSS communities, the source code, which is the human-readable part of software, is treated as something that is open and that should be downloadable and modifiable to anyone who wishes to do so. The availability of the source code has enabled a practice of decentralized software development in which large numbers of people contribute time and effort. Communities like Linux and Apache, for instance, have been able to connect thousands of individual programmers and professional organizations (although most project communities remain relatively small). These people and organizations are not confined to certain geographical places; on the contrary, they come from literally all continents and they interact and collaborate virtually.

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

Journal of Imaging ◽

10.3390/jimaging5120088 ◽

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.

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Open source software for quantification of cell migration, protrusions, and fluorescence intensities

The Journal of Cell Biology ◽

10.1083/jcb.201501081 ◽

2015 ◽

Vol 209 (1) ◽

pp. 163-180 ◽

Cited By ~ 82

Author(s):

David J. Barry ◽

Charlotte H. Durkin ◽

Jasmine V. Abella ◽

Michael Way

Keyword(s):

Cell Migration ◽

Open Source ◽

Imaging Techniques ◽

Automated Analysis ◽

Spatial And Temporal Scales ◽

Migration Rates ◽

Automated Quantification ◽

Membrane Protrusions ◽

Automated Tools ◽

User Friendly

Cell migration is frequently accompanied by changes in cell morphology (morphodynamics) on a range of spatial and temporal scales. Despite recent advances in imaging techniques, the application of unbiased computational image analysis methods for morphodynamic quantification is rare. For example, manual analysis using kymographs is still commonplace, often caused by lack of access to user-friendly, automated tools. We now describe software designed for the automated quantification of cell migration and morphodynamics. Implemented as a plug-in for the open-source platform, ImageJ, ADAPT is capable of rapid, automated analysis of migration and membrane protrusions, together with associated fluorescently labeled proteins, across multiple cells. We demonstrate the ability of the software by quantifying variations in cell population migration rates on different extracellular matrices. We also show that ADAPT can detect and morphologically profile filopodia. Finally, we have used ADAPT to compile an unbiased description of a “typical” bleb formed at the plasma membrane and quantify the effect of Arp2/3 complex inhibition on bleb retraction.

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The CCP13FibreFixprogram suite: semi-automated analysis of diffraction patterns from non-crystalline materials

Journal of Applied Crystallography ◽

10.1107/s0021889806048643 ◽

2007 ◽

Vol 40 (1) ◽

pp. 178-184 ◽

Cited By ~ 21

Author(s):

Ganeshalingam Rajkumar ◽

Hind A. AL-Khayat ◽

Felicity Eakins ◽

Carlo Knupp ◽

John M. Squire

Keyword(s):

Structural Information ◽

Protein Crystallography ◽

Three Dimensional ◽

Automated Analysis ◽

Crystalline Materials ◽

Space Groups ◽

Naturally Occurring ◽

Single User ◽

Diffraction Patterns ◽

User Friendly

The extraction of useful information from recorded diffraction patterns from non-crystalline materials is non-trivial and is not a well defined operation. Unlike protein crystallography where one expects to see well behaved diffraction spots in predictable positions defined by standard space groups, the diffraction patterns from non-crystalline materials are very diverse. They can range from uniaxially oriented fibre patterns which are completely sampled as Bragg peaks, but rotationally averaged around the fibre axis, to fibre patterns that are completely unsampled, to either kind of pattern with considerable axial misalignment (disorientation), to liquid-like order and even to mixtures of these various structure types. In the case of protein crystallography, the specimen is generated artificially and only used if the degree of order is sufficient to yield a three-dimensional density map of high enough resolution to be interpreted sensibly. However, with non-crystalline diffraction, many of the specimens of interest are naturally occurring (e.g.cellulose, rubber, collagen, muscle, hair, silk) and to elucidate their structure it is necessary to extract structural information from the materials as they actually are and to whatever resolution is available. Even when synthetic fibres are generated from purified components (e.g.nylon, polyethylene, DNA, polysaccharides, amyloidsetc.) and diffraction occurs to high resolution, it is rarely possible to obtain perfect uniaxial alignment. The CCP13 project was established in the 1990s to generate software which will be generally useful for analysis of non-crystalline diffraction patterns. Various individual programs were written which allowed separate steps in the analysis procedure to be carried out. Many of these programs have now been integrated into a single user-friendly package known asFibreFix, which is freely downloadable from http://www.ccp13.ac.uk. Here the main features ofFibreFixare outlined and some of its applications are illustrated.

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

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2007304117 ◽

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.

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Integrated open-source software for multiscale electrophysiology

Scientific Data ◽

10.1038/s41597-019-0242-z ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 2

Author(s):

Konstantinos Nasiotis ◽

Martin Cousineau ◽

François Tadel ◽

Adrien Peyrache ◽

Richard M. Leahy ◽

...

Keyword(s):

Data Analysis ◽

Open Source ◽

Open Source Software ◽

Analysis Data ◽

Open Science ◽

Dense Array ◽

Unrestricted Access ◽

Research Transparency ◽

Programming Skills ◽

User Friendly

Abstract The methods for electrophysiology in neuroscience have evolved tremendously over the recent years with a growing emphasis on dense-array signal recordings. Such increased complexity and augmented wealth in the volume of data recorded, have not been accompanied by efforts to streamline and facilitate access to processing methods, which too are susceptible to grow in sophistication. Moreover, unsuccessful attempts to reproduce peer-reviewed publications indicate a problem of transparency in science. This growing problem could be tackled by unrestricted access to methods that promote research transparency and data sharing, ensuring the reproducibility of published results. Here, we provide a free, extensive, open-source software that provides data-analysis, data-management and multi-modality integration solutions for invasive neurophysiology. Users can perform their entire analysis through a user-friendly environment without the need of programming skills, in a tractable (logged) way. This work contributes to open-science, analysis standardization, transparency and reproducibility in invasive neurophysiology.

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