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An open source application for the visualization and analysis of 4D biological datasets. Developed by researchers, it is primarily used for the analysis and quantification of 4D live-imaged confocal data. The software's modular design makes it easy to include existing libraries, or to implement new algorithms. Cell geometries extracted with MorphoGraphX can be exported and used as templates for simulation models, providing a powerful platform to investigate the interactions between shape, genes and growth.
Rayburst sampling
An algorithm for automated three-dimensional shape analysis from laser scanning microscopy images. The Rayburst algorithm provides a primitive for the development of higher level algorithms that solve specific shape analysis problems. Examples are provided of applications to 3D neuronal morphometry: (i) estimation of diameters in tubular neuronal dendritic branching structures, and (ii) measurement of volumes and surface areas for dendritic spines and spatially complex histopathologic structures.
MiCASA / Multitaper Circularly Averaged Spectral Analysis
Detects statistically robust phenotypic differences. MiCASA is an unbiased, user-independent method for identifying the phenotypic differences between conditions. It focuses attention on those aspects of the phenotype that have statistical relevance. This package may be used to provide a useful summary of the distribution and interactions between well-known cell types in the thymus. However, MiCASA can be used with any pair of markers.
Proposes a large collection of generic tools based on mathematical morphology to process binary and grey-level 2D and 3D images, integrated into user-friendly plugins. The library provides different categories of functions, corresponding to standard image processing workflows: (i) image processing and filtering; (ii) segmentation; (iii) post-processing; (iv) quantitative analysis; (v) library re-usability. The cell-resolved data provided by MorphoLibJ will be useful for the analysis of cell lineage, and the modelling of plant growth and morphogenesis in 3D.
A simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholding a contrast measure over the resulting regions. As output, NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects and their position within the nucleus.
A wavelet-based image-analysis software providing a fast automatic detection scheme for circular patterns (spots), combined with the precise estimation of their size. SpotCaliper is able to automatically find spots of varying size, and gives a precise measurement on their radius. The detections are collected in a table, displaying the following parameters: unique identifier (ID) of the spot, its location (x and y coordinates), radius, confidence, contrast, SNR and type. It is implemented as an ImageJ plugin with a friendly user interface. The user is allowed to edit the results by modifying the measurements (in a semi-automated way), extract data for further analysis. The fine tuning of the detections includes the possibility of adjusting or removing the original detections, as well as adding further spots. The main advantage of the software is its ability to capture the size of spots in a fast and accurate way.
Quantifies local boundary characteristics of a closed geometric shape. LobeFinder is a highly useful convex hull-based program that identifies key features such as pavement cell lobes. This method operates on cell perimeter coordinates extracted from images of pavement cells and returns an array of useful cell shape data. It also includes a value for lobe number and a map of their positions. It creates a coordinate system to quantify local growth behaviors at the interface of two cells.
Calculates the fractal dimensionality of a 3D structure. calcFD is designed to work with intermediate files from FreeSurfer analysis pipeline, but can also use other volumes. The toolbox includes options to use different masking files and is implemented to use either the box-counting or dilation algorithms and to use either the filled volume or just the surface of the structure. The toolbox can easily be run on all of the participants in a FreeSurfer subject folder, or just on specified subject folders. The Matlab toolbox also includes several functions designed to improve functionality, such as the automatic ‘cropping’ of the volume space to the smallest bounding box necessary to contain the volume, improving computation time drastically. Example files are also provided to aid in using the toolbox for the user‘s needs.
iRoCS Toolbox
An interactive Qt4 analysis tool for attaching the intrinsic root coordinate system to 3-D confocal recordings of the Arabidopsis root apical meristem. This allows quantitative comparative studies of root populations in a sound and intuitive context. iRoCS Toolbox consists of the data browser labelling and a set of command line tools for batch processing. Main features are: (i) 3-D Visualization of the volume in an orthographic view; (ii) manual annotation of anatomical reference structures (QC, nuclei); (iii) automatic detection and annotation of cells and/or nuclei with several meaningful properties, like position, radius, tissue, cell file, cell cycle state, volume; (iv) full control. Any step can be manually corrected and re-fed into the modeling; (v) retrieval and localization of key events like cell divisions.
VPV / Volume Phenotype Viewer
Enables rapid identification of phenotypically abnormal structures. Data are easily loaded by drag and drop, with support for most commonly used file formats. On loading the registration results, embryos may be overlaid with the t-statistic heatmaps to reveal regions of dysmorphology. We have adopted a hot red/blue colour scheme to be consistent with previously reported results. The heatmap data can be filtered by t statistic value to emphasize regions of different statistical significances. Vector field data can also be loaded into VPV and filtered by magnitude to identify where the most significant deformations have taken place during registration.
A plugin for bone image analysis in ImageJ. BoneJ provides free, open source tools for trabecular geometry and whole bone shape analysis. It calculates several trabecular, cross-sectional and particulate parameters in a convenient format. Java technology allows BoneJ to run on commodity computers, independent of scanner devices, fully utilising hardware resources. ImageJ’s plugin infrastructure provides a flexible working environment that can be tailored to diverse experimental setups. BoneJ is a working program and a starting point for further development, which will be directed by users’ requests and the emergence of new techniques.
DRACO-STEM / Dual Reconstruction by Adjacency Complex- SAM Tissue Enhanced Mesh
Computes a 3D triangular mesh of the tissue. DRACO-STEM is based on the dualization of a simplicial complex of adjacency, and the triangulation and optimization of the resulting polyhedral geometry to proceed. This tool follows three steps for the processing: delaunay complex creation, adjacency complex optimization and dual reconstruction. It was applied to triangular tissue meshes generated from a dataset of segmented tissue images.
3D Tissue Organization Toolbox
Provides all the necessary methods for nuclei segmentation, cell identification and analysis of cell interaction in 3D. 3D Tissue Organization Toolbox is an ImageJ plugin that covers different aspects of spatial analysis of tissues in 3D, ranging from nuclei segmentation to analysis of different aspects of cellular interaction and network mapping. It was used to investigate current and novel aspects of the unique architecture of the pancreatic islet of Langerhans.
FMAj / Fly Muscle Analysis in Java
Performs quantitative characterization of muscle phenotypes in time-series images. FMAj is composed of three modules: (i) the first one captures experimental metadata derived from the images or via manual annotation by the user; (ii) the second performs segmentation of muscle cells and nuclei in a semi-automated fashion.; (iii) the third module achieves comparative phenotypic analysis, such as comparing the cell morphology between control and genetically perturbed cells.
A metrology toolbox for SFM, specifically aimed at biomolecules like DNA and proteins, which features (a) semi-automatic high-throughput analysis of individual molecules; (b) ease of use working within MATLAB environment or as a stand-alone application; (c) compatibility with MultiMode (Bruker), NanoWizard (JPK instruments), Asylum (Asylum research), ASCII, and TIFF files, that can be adjusted with minor modifications to other formats. Assembled in a single user interface, SFMetrics serves as a semi-automatic analysis tool capable of measuring several geometrical properties (length, volume and angles) from DNA and protein complexes, but is also applicable to other samples with irregular shapes.
BCOMS / Biologically Constrained Optimization based cell Membrane Segmentation
Automates cell shape extraction in C. elegans embryos. BCOMS provides a user-friendly framework that computerizes not only the segmentation process but also the evaluation process. The performance of BCOMS was validated by comparisons with the ground truth and by comparing the results in two adjacent time points. This method is also applicable to other model organisms by customizing the biological constraints.
An easy to use software application that will greatly speed and standardize quantification of neuron organization. IPLaminator rapidly analyzes neurite stratification patterns in the retina and other neural tissues. A range of user options allows researchers to bin inner plexiform layer (IPL) stratification based on fixed points, such as the neurites of cholinergic amacrine cells, or to define a number of bins into which the IPL will be divided. Options to analyze tissues such as cortex were also added. Statistical analysis of the output then allows a quantitative value to be assigned to differences in laminar patterning observed in different models, genotypes or across developmental time.
A MATLAB based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. CellSegm has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classification of cell candidates. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in MATLAB, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.
Automating Morphological Profiling with Generic Deep Convolutional Networks
Uses deep feature transfer for generating morphological profiles without human interaction. Automating Morphological Profiling with Generic Deep Convolutional Networks achieves higher accuracies than previous classical methods, needs less time and expertise to extract profiles and allows for true automated high content screening by taking the human out of the loop. Furthermore, it enables fully automated processing of microscopy images without need for single cell identification.
Amira 3D Software for Life Sciences
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
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