Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
Employs colocalization across different microscopy platforms. frcoloc can recognize representative spectra for one cellular compartment in fact reads. It is based on a random forest classifier and tested with conventional k-fold cross validation and leave-one-out cross-validation methods. This tool can predict a crisp segmentation, which makes the result accessible to cross-validation.
Extracts quantitative and biologically relevant information from single molecule localization microscopy (SMLM) data sets. ClusDoC combines two analysis techniques of cluster detection and colocalization. The software provides outputs at the level of molecules (e.g., distribution of DoC scores), of clusters (e.g., size, density, morphology), and of cells (e.g., comparisons across different conditions). It can also generate maps for visualization of the data. ClusDoC can be applied to address a variety of biological questions in different fields.
Allows spatial point pattern and interaction analysis. MosaicIA provides standardized ways to (1) correct for the influence of the distribution of points within one set onto the distance distribution to another set; (2) infer parameters of the interaction potential, such as the strength and length scale of the interaction; (3) perform statistical hypothesis tests for the presence of an interaction. It has been tested on both synthetic and real-world data.
Provides a method for determining true and random colocalization for experimental scenarios. CDA calculates modified Manders coefficients, M1ROI and M2ROI and detects colocalization in cellular and subcellular compartments thanks to standard confocal microscopy and computational image correlation techniques. The module can be used through the ImageJ software and can be applied to various fields including fluorescent wide field or confocal microscopy.
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