Find and compare the best bioinformatics software tools for quantifying and analysing fluorescence signal on conventional fluorescence microscopy images. Tools are ranked by the biomedical research community.
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.
A tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images. CellX decodes the information across the cell membrane and guarantees optimal detection of the cell boundaries on a per-cell basis. Graph cuts account for the information of the cell boundaries through directional cross-correlations, and they automatically incorporate spatial constraints. The method accurately segments images of various cell types grown in dense cultures that are acquired with different microscopy techniques.
Performs 2D immunofluorescence images to pinpoint and number synaptic protein puncta. SynPAnal provides an application that intends to partially automate processing tasks of files generated by confocal laser scanning microscopy. The application focuses on the quantification of puncta attributes but can also be applied for basic fluorescent intensity measuring as well as for basic morphometric analysis of neurons.
Deduces multi-feature phenotypic crosstalk from perturbation assays. PHOCOS takes into consideration the potential interactions among different attributes of biomarkers. It can retrieve core, direct-effect motifs from missing links, noise and indirect effects. This tool can produce ‘high-resolution’ views of which phenotypic attributes support interaction among biomarkers. It is useful for microscopy images and others biological datasets.
Segments packed cells while quantifying protein clusters by using a single fluorescent marker. SegmentMe is a click and-drag software dedicated to the processing of protein clusters dynamics. The application exists as a 2D projection version as well as in 3D. The application is divided into a processing and an analysis panel and includes features for three-frame time or spatial averaging.
Allows determination of the number of foci in a single cell, a focus intensity per cell, as well as a cell intensity. FociCounter was tested by analysing gamma-H2AX foci in CHO and MO59K cells irradiated in vitro with X-rays. It was validated by comparing the results obtained with the outcome of automated image analysis and flow cytometry. The software was developed for research laboratories possessing a fluorescent microscope in combination with a digital camera. FociCounter was designed for the most common image formats that are two-dimensional.
Provides macros for ImageJ to automatically analyze the size and intensity of objects/regions in microscope images. imagej-interactive-thresholding is useful for the quantification of image data in cell biology and other areas of research. It can measure the fluorescence intensity within the segmented regions in a different image channel. This tool allows users to modify the automatically detected regions prior.
An advanced EEM parameterization tool, to analyse the level of fluorescence which is related to the concentrations of a fluorophores (like fulvic/humic-like compounds, tryptophan and tyrosine). The method can detect low concentrations of these compounds in environmental samples.
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.
0 - 0 of 0