Fluorescent microscope imaging technologies have developed at a rapid pace in recent years. High-throughput 2D fluorescent imaging platforms are now in wide use and are being applied on a proteome wide scale. Multiple fluorophore 3D imaging of live cells is being used to give detailed localization and subcellular structure information. Further, 2D and 3D video microscopy are giving important insights into the dynamics of protein localization and transport. In parallel with these developments, significant research has gone into developing new methodologies for quantifying and extracting meaning from the imaging data.
Quantifies nuclear foci. FoCo permits users to perform foci counting on images, either RGB or grayscale ones, that contain nuclei and foci. It enables to verify the reliability of automatic foci quantifications by comparing automatic and manual quantification results. This program also can be used for producing foci quantifications for low signal/noise ratios and densely distributed foci.
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.
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.
Facilitates common analysis tasks related to fluorescence imaging. Functionality SIMA includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. A graphical user interface (GUI) has also been developed for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages.
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.
Aims to reduce labour and to decrease subjectivity in counting individual neighbouring cells. Cell-o-Tape can automatically determine the location of a feature point traditionally estimated visually. It permits users to specify exactly where on the image it operates. This tool allows users to improve the quality of the output using their expert knowledge, whilst performing the main labour-intensive processing in an automated, objective way.
Offers a platform for high content image analysis. CellVigene is an application made for the quantitation signal intensity and area in multiple channel or level. It includes features for automating the detection of micronuclei and nuclei, for quantifying pathologies as well as to perform mitotic spindle localization. This software can also be used for tissue microarray analysis and includes a module for 3D visualization of a composite image.